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Mehedi M, Ricklefs S, Takada A, Sturdevant D, Porcella SF, Marzi A, Feldmann H. RNA Editing as a General Trait of Ebolaviruses. J Infect Dis 2023; 228:S498-S507. [PMID: 37348869 PMCID: PMC10651210 DOI: 10.1093/infdis/jiad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/20/2023] [Indexed: 06/24/2023] Open
Abstract
RNA editing has been discovered as an essential mechanism for the transcription of the glycoprotein (GP) gene of Ebola virus but not Marburg virus. We developed a rapid transcript quantification assay (RTQA) to analyze RNA transcripts generated through RNA editing and used immunoblotting with a pan-ebolavirus monoclonal antibody to confirm different GP gene-derived products. RTQA successfully quantified GP gene transcripts during infection with representative members of 5 ebolavirus species. Immunoblotting verified expression of the soluble GP and the transmembrane GP. Our results defined RNA editing as a general trait of ebolaviruses. The degree of editing, however, varies among ebolaviruses with Reston virus showing the lowest and Bundibugyo virus the highest degree of editing.
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Affiliation(s)
| | - Stacy Ricklefs
- Genomics Unit, Research Technology Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Dan Sturdevant
- Genomics Unit, Research Technology Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Stephen F Porcella
- Genomics Unit, Research Technology Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
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2
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Easton A, Gao S, Lawton SP, Bennuru S, Khan A, Dahlstrom E, Oliveira RG, Kepha S, Porcella SF, Webster J, Anderson R, Grigg ME, Davis RE, Wang J, Nutman TB. Molecular evidence of hybridization between pig and human Ascaris indicates an interbred species complex infecting humans. eLife 2020; 9:e61562. [PMID: 33155980 PMCID: PMC7647404 DOI: 10.7554/elife.61562] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
Human ascariasis is a major neglected tropical disease caused by the nematode Ascaris lumbricoides. We report a 296 megabase (Mb) reference-quality genome comprised of 17,902 protein-coding genes derived from a single, representative Ascaris worm. An additional 68 worms were collected from 60 human hosts in Kenyan villages where pig husbandry is rare. Notably, the majority of these worms (63/68) possessed mitochondrial genomes that clustered closer to the pig parasite Ascaris suum than to A. lumbricoides. Comparative phylogenomic analyses identified over 11 million nuclear-encoded SNPs but just two distinct genetic types that had recombined across the genomes analyzed. The nuclear genomes had extensive heterozygosity, and all samples existed as genetic mosaics with either A. suum-like or A. lumbricoides-like inheritance patterns supporting a highly interbred Ascaris species genetic complex. As no barriers appear to exist for anthroponotic transmission of these 'hybrid' worms, a one-health approach to control the spread of human ascariasis will be necessary.
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Affiliation(s)
- Alice Easton
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
- Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Shenghan Gao
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
- Beijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
| | - Scott P Lawton
- Epidemiology Research Unit (ERU) Department of Veterinary and Animal Sciences, Northern Faculty, Scotland’s Rural College (SRUC)InvernessUnited Kingdom
| | - Sasisekhar Bennuru
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
| | - Asis Khan
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
| | - Eric Dahlstrom
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Rita G Oliveira
- Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Stella Kepha
- London School of Tropical Medicine and HygieneLondonUnited Kingdom
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUnited States
| | - Joanne Webster
- Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
- Royal Veterinary College, University of London, Department of Pathobiology and Population SciencesHertfordshireUnited Kingdom
| | - Roy Anderson
- Department of Infectious Disease Epidemiology, Imperial College LondonLondonUnited Kingdom
| | - Michael E Grigg
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
| | - Jianbin Wang
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of MedicineAuroraUnited States
- Department of Biochemistry and Cellular and Molecular Biology, University of TennesseeKnoxvilleUnited States
| | - Thomas B Nutman
- Helminth Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Disease, National Institutes of HealthBethesdaUnited States
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3
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Rose R, Hall M, Redd AD, Lamers S, Barbier AE, Porcella SF, Hudelson SE, Piwowar-Manning E, McCauley M, Gamble T, Wilson EA, Kumwenda J, Hosseinipour MC, Hakim JG, Kumarasamy N, Chariyalertsak S, Pilotto JH, Grinsztejn B, Mills LA, Makhema J, Santos BR, Chen YQ, Quinn TC, Fraser C, Cohen MS, Eshleman SH, Laeyendecker O. Phylogenetic Methods Inconsistently Predict the Direction of HIV Transmission Among Heterosexual Pairs in the HPTN 052 Cohort. J Infect Dis 2019; 220:1406-1413. [PMID: 30590741 PMCID: PMC6761953 DOI: 10.1093/infdis/jiy734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND We evaluated use of phylogenetic methods to predict the direction of human immunodeficiency virus (HIV) transmission. METHODS For 33 pairs of HIV-infected patients (hereafter, "index patients") and their partners who acquired genetically linked HIV infection during the study, samples were collected from partners and index patients close to the time when the partner seroconverted (hereafter, "SC samples"); for 31 pairs, samples collected from the index patient at an earlier time point (hereafter, "early index samples") were also available. Phylogenies were inferred using env next-generation sequences (1 tree per pair/subtype). The direction of transmission (DoT) predicted from each tree was classified as correct or incorrect on the basis of which sequences (those from the index patient or the partner) were closest to the root. DoT was also assessed using maximum parsimony to infer ancestral node states for 100 bootstrap trees. RESULTS DoT was predicted correctly for both single-pair and subtype-specific trees in 22 pairs (67%) by using SC samples and in 23 pairs (74%) by using early index samples. DoT was predicted incorrectly for 4 pairs (15%) by using SC or early index samples. In the bootstrap analysis, DoT was predicted correctly for 18 pairs (55%) by using SC samples and for 24 pairs (73%) by using early index samples. DoT was predicted incorrectly for 7 pairs (21%) by using SC samples and for 4 pairs (13%) by using early index samples. CONCLUSIONS Phylogenetic methods based solely on the tree topology of HIV env sequences, particularly without consideration of phylogenetic uncertainty, may be insufficient for determining DoT.
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Affiliation(s)
| | - Matthew Hall
- Big Data Institute, University of Oxford, United Kingdom
| | - Andrew D Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Baltimore, Maryland
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | - Stephen F Porcella
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH, Hamilton, Montana
| | - Sarah E Hudelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Marybeth McCauley
- Science Facilitation Department, Durham, Chapel Hill, North Carolina
| | - Theresa Gamble
- Science Facilitation Department, Durham, Chapel Hill, North Carolina
| | - Ethan A Wilson
- Vaccine and Infectious Disease Science Division, Fred Hutchinson Cancer Research Institute, Seattle, Washington
| | | | - Mina C Hosseinipour
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | | | | | - Jose H Pilotto
- Hospital Geral de Nova Iguaçu, Rio de Janeiro, Brazil
- Laboratorio de AIDS e Imunologia Molecular (IOC/Fiocruz), Rio de Janeiro, Brazil
| | - Beatriz Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas-INI-Fiocruz, Rio de Janeiro, Brazil
| | - Lisa A Mills
- Centers for Disease Control and Prevention (CDC) Division of HIV/AIDS Prevention/KEMRI–CDC Research and Public Health Collaboration HIV Research Branch, Kisumu, Kenya
| | | | - Breno R Santos
- Servico de Infectologia, Hospital Nossa Senhora da Conceicao/GHC, Porto Alegre, Brazil
| | - Ying Q Chen
- Vaccine and Infectious Disease Science Division, Fred Hutchinson Cancer Research Institute, Seattle, Washington
| | - Thomas C Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Baltimore, Maryland
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Myron S Cohen
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Susan H Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Oliver Laeyendecker
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Baltimore, Maryland
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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4
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Ssemwanga D, Doria-Rose NA, Redd AD, Shiakolas AR, Longosz AF, Nsubuga RN, Mayanja BN, Asiki G, Seeley J, Kamali A, Ransier A, Darko S, Walker MP, Bruno D, Martens C, Douek D, Porcella SF, Quinn TC, Mascola JR, Kaleebu P. Characterization of the Neutralizing Antibody Response in a Case of Genetically Linked HIV Superinfection. J Infect Dis 2019; 217:1530-1534. [PMID: 29579256 DOI: 10.1093/infdis/jiy071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/31/2018] [Indexed: 01/08/2023] Open
Abstract
This report describes the identification of a genetically confirmed linked heterosexual human immunodeficiency virus (HIV) superinfection (HIV-SI) in a woman with chronic HIV infection who acquired a second strain of the virus from her husband. Serum neutralizing antibody (NAb) responses against their homologous and heterologous viruses, including the superinfecting strain, in the woman and her husband were examined before and after onset of HIV-SI. The woman displayed a moderately potent and broad anti-HIV NAb response prior to superinfection but did not possess NAb activity against the superinfecting strain. This case highlights the unique potential of linked HIV-SI studies to examine natural protection from HIV infection.
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Affiliation(s)
- Deogratius Ssemwanga
- Uganda Research Unit on AIDS, Medical Research Council/Uganda Virus Research Institute, Entebbe
| | | | - Andrew D Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Andrew F Longosz
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda
| | - Rebecca N Nsubuga
- Uganda Research Unit on AIDS, Medical Research Council/Uganda Virus Research Institute, Entebbe
| | - Billy N Mayanja
- Uganda Research Unit on AIDS, Medical Research Council/Uganda Virus Research Institute, Entebbe
| | - Gershim Asiki
- Uganda Research Unit on AIDS, Medical Research Council/Uganda Virus Research Institute, Entebbe
| | - Janet Seeley
- Uganda Research Unit on AIDS, Medical Research Council/Uganda Virus Research Institute, Entebbe.,Department of Clinical Research, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Anatoli Kamali
- Uganda Research Unit on AIDS, Medical Research Council/Uganda Virus Research Institute, Entebbe
| | | | | | - Michael P Walker
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH, Hamilton, Montana
| | - Daniel Bruno
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH, Hamilton, Montana
| | - Craig Martens
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH, Hamilton, Montana
| | | | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH, Hamilton, Montana
| | - Thomas C Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Pontiano Kaleebu
- Uganda Research Unit on AIDS, Medical Research Council/Uganda Virus Research Institute, Entebbe.,Department of Clinical Research, London School of Hygiene and Tropical Medicine, United Kingdom
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5
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Rose R, Redd AD, Lamers S, Porcella SF, Hudelson SE, Piwowar-Manning E, McCauley M, Gamble T, Wilson EA, Kumwenda J, Hosseinipour MC, Hakim JG, Kumarasamy N, Chariyalertsak S, Pilotto JH, Grinsztejn B, Mills LA, Makhema J, Santos BR, Chen YQ, Quinn TC, Cohen MS, Eshleman SH, Laeyendecker O. A11 Evaluation of phylogenetic inference methods to determine direction of HIV transmission. Virus Evol 2019. [PMCID: PMC6736083 DOI: 10.1093/ve/vez002.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
It has been postulated that the direction of HIV transmission between two individuals can be determined by phylogenetic analysis of HIV sequences. This approach may be problematic, since HIV sequences from newly infected individuals are often more similar to index sequences from samples collected years before transmission, compared to those from samples collected at the time of transmission. We evaluated the accuracy of phylogenetic methods for determining the direction of HIV transmission by analyzing next-generation sequencing (NGS) data from index–partner pairs enrolled in the HIV Prevention Trials Network (HPTN) 052 trial. HIV-infected index and HIV-uninfected partner participants were enrolled as serodiscordant couples; samples were analyzed from couples with index-to-partner HIV transmission that was confirmed by genetic linkage studies. NGS for HIV gp41 (HXB2 coordinates: 7691–8374) was performed using plasma samples from thirty-nine index–partner pairs (seventy-eight samples collected within 3 months of partner seroconversion). Maximum likelihood trees were generated using the entire dataset using FastTree v.2. Topological patterns of HIV from each index–partner pair were analyzed. The analysis included 9,368 consensus sequences and 521,145 total sequence reads for the seventy-eight samples analyzed. In 10 per cent (four out of thirty-nine) of couples, the phylogeny was inconsistent with the known direction of transmission. In 26 per cent (ten out of thirty-nine) of couples, the phylogeny results could not discern directionality. In 64 per cent (twenty-five out of thirty-nine) of couples, the results correctly indicated index-to-partner transmission; in two of these twenty-five cases, only one index sequence was closest to the most recent common ancestor. Phylogenetic analysis of NGS data obtained from samples collected within 3 months of transmission correctly determined the direction of transmission in 64 per cent of the cases analyzed. In 36 per cent of the cases, the phylogenetic topology did not support the known direction of infection, and in one-third of these cases the observed topology was opposite to the known direction of transmission. This demonstrates that phylogenetic topology alone may not be sufficient to accurately determine the direction of HIV transmission.
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Affiliation(s)
- R Rose
- BioInfoExperts, LLC, Thibodaux, LA, USA
| | | | - S Lamers
- BioInfoExperts, LLC, Thibodaux, LA, USA
| | | | - S E Hudelson
- Department of Medicience, Johns Hopkins University, Baltimore, MD, USA
| | - E Piwowar-Manning
- Department of Medicience, Johns Hopkins University, Baltimore, MD, USA
| | | | | | - E A Wilson
- Vaccine and Infectious Disease Science Division, Fred Hutchinson Cancer Research Institute, Seattle, WA, USA
| | - J Kumwenda
- College of Medicine-Johns Hopkins Project, Blantyre, Malawi
| | - M C Hosseinipour
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J G Hakim
- University of Zimbabwe, Harare, Zimbabwe
| | | | - S Chariyalertsak
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai, Thailand
| | - J H Pilotto
- Hospital Geral de Nova Iguaçu and Laboratorio de AIDS e Imunologia Molecular, Rio de Janeiro, Brazil
| | - B Grinsztejn
- Instituto Nacional de Infectologia Evandro Chagas-INI-Fiocruz, Rio de Janeiro, Brazil
| | - L A Mills
- CDC Division of HIV/AIDS Prevention/KEMRI-CDC Research and Public Health Collaboration HIV Research Branch, Kisumu, Kenya
| | - J Makhema
- Botswana Harvard Aids Institute, Gabarone, Botswana
| | - B R Santos
- Servico de Infectologia, Hospital Nossa Senhora da Conceicao/GHC, Porto Alegro, Brazil
| | - Y Q Chen
- Vaccine and Infectious Disease Science Division, Fred Hutchinson Cancer Research Institute, Seattle, WA, USA
| | | | - M S Cohen
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - S H Eshleman
- Department of Medicience, Johns Hopkins University, Baltimore, MD, USA
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6
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Tuen M, Bimela JS, Banin AN, Ding S, Harkins GW, Weiss S, Itri V, Durham AR, Porcella SF, Soni S, Mayr L, Meli J, Torimiro JN, Tongo M, Wang X, Kong XP, Nádas A, Kaufmann DE, Brumme ZL, Nanfack AJ, Quinn TC, Zolla-Pazner S, Redd AD, Finzi A, Gorny MK, Nyambi PN, Duerr R. Immune Correlates of Disease Progression in Linked HIV-1 Infection. Front Immunol 2019; 10:1062. [PMID: 31139189 PMCID: PMC6527802 DOI: 10.3389/fimmu.2019.01062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/25/2019] [Indexed: 01/01/2023] Open
Abstract
Genetic and immunologic analyses of epidemiologically-linked HIV transmission enable insights into the impact of immune responses on clinical outcomes. Human vaccine trials and animal studies of HIV-1 infection have suggested immune correlates of protection; however, their role in natural infection in terms of protection from disease progression is mostly unknown. Four HIV-1+ Cameroonian individuals, three of them epidemiologically-linked in a polygamous heterosexual relationship and one incidence-matched case, were studied over 15 years for heterologous and cross-neutralizing antibody responses, antibody binding, IgA/IgG levels, antibody-dependent cellular cytotoxicity (ADCC) against cells expressing wild-type or CD4-bound Env, viral evolution, Env epitopes, and host factors including HLA-I alleles. Despite viral infection with related strains, the members of the transmission cluster experienced contrasting clinical outcomes including cases of rapid progression and long-term non-progression in the absence of strongly protective HLA-I or CCR5Δ32 alleles. Slower progression and higher CD4/CD8 ratios were associated with enhanced IgG antibody binding to native Env and stronger V1V2 antibody binding responses in the presence of viruses with residue K169 in V2. ADCC against cells expressing Env in the CD4-bound conformation in combination with low Env-specific IgA/IgG ratios correlated with better clinical outcome. This data set highlights for the first time that V1V2-directed antibody responses and ADCC against cells expressing open, CD4-exposed Env, in the presence of low plasma IgA/IgG ratios, can correlate with clinical outcome in natural infection. These parameters are comparable to the major correlates of protection, identified post-hoc in the RV144 vaccine trial; thus, they may also modulate the rate of clinical progression once infected. The findings illustrate the potential of immune correlate analysis in natural infection to guide vaccine development.
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Affiliation(s)
- Michael Tuen
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Jude S Bimela
- Department of Pathology, New York University School of Medicine, New York, NY, United States.,Department of Biochemistry, University of Yaoundé 1, Yaoundé, Cameroon
| | - Andrew N Banin
- Department of Pathology, New York University School of Medicine, New York, NY, United States.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Shilei Ding
- Centre de Recherche du CHUM, Montréal, QC, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Gordon W Harkins
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Svenja Weiss
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vincenza Itri
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Allison R Durham
- Division of Intramural Research, National Institutes of Health-National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, Division of Intramural Research, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, United States
| | - Sonal Soni
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Luzia Mayr
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Josephine Meli
- Medical Diagnostic Center, Yaoundé, Cameroon.,Yaoundé General Hospital, Yaoundé, Cameroon
| | - Judith N Torimiro
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon.,"Chantal Biya" International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Marcel Tongo
- Center of Research for Emerging and Re-Emerging Diseases, Institute of Medical Research and Study of Medicinal Plants, Yaoundé, Cameroon.,School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, KwaZulu-Natal Research Innovation and Sequencing Platform, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Xiaohong Wang
- Veterans Affairs New York Harbor Healthcare Systems, New York, NY, United States
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States
| | - Arthur Nádas
- New York University School of Medicine, Institute of Environmental Medicine, New York, NY, United States
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Montréal, QC, Canada.,Department of Medicine, Université de Montréal, Montréal, QC, Canada.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada.,British Columbia Centre for Excellence in HIV/AIDS, St. Paul's Hospital, Vancouver, BC, Canada
| | - Aubin J Nanfack
- Department of Pathology, New York University School of Medicine, New York, NY, United States.,Medical Diagnostic Center, Yaoundé, Cameroon.,"Chantal Biya" International Reference Centre for Research on HIV/AIDS Prevention and Management, Yaoundé, Cameroon
| | - Thomas C Quinn
- Division of Intramural Research, National Institutes of Health-National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States.,Department of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Susan Zolla-Pazner
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Andrew D Redd
- Division of Intramural Research, National Institutes of Health-National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States.,Department of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, QC, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Miroslaw K Gorny
- Department of Pathology, New York University School of Medicine, New York, NY, United States
| | - Phillipe N Nyambi
- Department of Pathology, New York University School of Medicine, New York, NY, United States.,Veterans Affairs New York Harbor Healthcare Systems, New York, NY, United States
| | - Ralf Duerr
- Department of Pathology, New York University School of Medicine, New York, NY, United States
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7
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Redd AD, Helleberg M, Sievers M, Schmidt SD, Doria-Rose NA, Bruno D, Traeger S, Martens C, Fonager J, Kronborg G, Packman Z, Mascola JR, Porcella SF, Gerstoft J, Quinn TC. Limited anti-HIV neutralizing antibody breadth and potency before and after HIV superinfection in Danish men who have sex with men. Infect Dis (Lond) 2018; 51:56-61. [PMID: 30317905 DOI: 10.1080/23744235.2018.1500708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
BACKGROUND The role of the anti-HIV neutralizing antibody response in protecting against HIV superinfection, and changes in neutralizing antibody potency and breadth after HIV superinfection have not been fully elucidated. This study examined the rate of HIV superinfection in men who have sex with men (MSM) also diagnosed with syphilis in Denmark, and the anti-HIV neutralizing antibody response in men who became superinfected. MATERIALS AND METHODS MSM enrolled in the Danish HIV cohort who acquired syphilis were examined longitudinally for HIV superinfection using a validated next-generation sequencing assay. HIV superinfection cases were matched 3:1 to controls, and neutralizing antibody responses before (cases/controls) and after (cases) HIV superinfection were determined using a 20-pseudovirus panel. RESULTS Four cases of HIV superinfection were identified from 95 MSM screened for a rate of HIV superinfection of 1.56/100 pys (95% CI = 0.43-4.01). Prior to HIV superinfection neutralizing antibody responses were low in breadth and potency, and did not differ between cases and controls (p = 1.0). In cases, neutralizing antibody responses increased modestly after HIV superinfection. CONCLUSIONS These data support the theory that the natural neutralizing antibody response to HIV infection may not be the controlling factor in protecting against a subsequent HIV challenge.
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Affiliation(s)
- Andrew D Redd
- a Laboratory of Immunoregulation, Division of Intramural Research, NIAID, NIH , Bethesda , USA.,b Department of Medicine , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - Marie Helleberg
- c Department of Infectious Diseases , Copenhagen University Hospital , Rigshospitalet , Denmark
| | - Matthew Sievers
- b Department of Medicine , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | | | | | - Daniel Bruno
- e Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH , Hamilton , MT , USA
| | - Shelby Traeger
- e Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH , Hamilton , MT , USA
| | - Craig Martens
- e Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH , Hamilton , MT , USA
| | - Jannik Fonager
- f Section for Virus Surveillance and Research, Department of Virus & Microbiological Special Diagnostics, Infectious Disease Preparedness , Statens Serum Institut , Copenhagen , Denmark
| | - Gitte Kronborg
- g Department of Infectious Diseases , Copenhagen University Hospital , Hvidovre , Denmark
| | - Zoe Packman
- h Department of Pathology , Johns Hopkins University School of Medicine , Baltimore , MD , USA
| | - John R Mascola
- d Vaccine Research Center, NIAID, NIH , Bethesda , MD , USA
| | - Stephen F Porcella
- e Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH , Hamilton , MT , USA
| | - Jan Gerstoft
- c Department of Infectious Diseases , Copenhagen University Hospital , Rigshospitalet , Denmark
| | - Thomas C Quinn
- a Laboratory of Immunoregulation, Division of Intramural Research, NIAID, NIH , Bethesda , USA.,b Department of Medicine , Johns Hopkins University School of Medicine , Baltimore , MD , USA
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8
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Poon AFY, Prodger JL, Lynch BA, Lai J, Reynolds SJ, Kasule J, Capoferri AA, Lamers SL, Rodriguez CW, Bruno D, Porcella SF, Martens C, Quinn TC, Redd AD. Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays. Retrovirology 2018; 15:47. [PMID: 29976219 PMCID: PMC6034329 DOI: 10.1186/s12977-018-0426-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/14/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The ability of HIV-1 to integrate into the genomes of quiescent host immune cells, establishing a long-lived latent viral reservoir (LVR), is the primary obstacle to curing these infections. Quantitative viral outgrowth assays (QVOAs) are the gold standard for estimating the size of the replication-competent HIV-1 LVR, measured by the number of infectious units per million (IUPM) cells. QVOAs are time-consuming because they rely on culturing replicate wells to amplify the production of virus antigen or nucleic acid to reproducibly detectable levels. Sequence analysis can reduce the required number of culture wells because the virus genetic diversity within the LVR provides an internal replication and dilution series. Here we develop a Bayesian method to jointly estimate the IUPM and variant frequencies (a measure of clonality) from the sequence diversity of QVOAs. RESULTS Using simulation experiments, we find our Bayesian approach confers significantly greater accuracy over current methods to estimate the IUPM, particularly for reduced numbers of QVOA replicates and/or increasing actual IUPM. Furthermore, we determine that the improvement in accuracy is greater with increasing genetic diversity in the sample population. We contrast results of these different methods applied to new HIV-1 sequence data derived from QVOAs from two individuals with suppressed viral loads from the Rakai Health Sciences Program in Uganda. CONCLUSIONS Utilizing sequence variation has the additional benefit of providing information on the contribution of clonality of the LVR, where high clonality (the predominance of a single genetic variant) suggests a role for cell division in the long-term persistence of the reservoir. In addition, our Bayesian approach can be adapted to other limiting dilution assays where positive outcomes can be partitioned by their genetic heterogeneity, such as immune cell populations and other viruses.
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Affiliation(s)
- Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Western University, London, ON, Canada.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Briana A Lynch
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Steven J Reynolds
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Adam A Capoferri
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | | | - Daniel Bruno
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Craig Martens
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Thomas C Quinn
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew D Redd
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
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9
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Raghwani J, Redd AD, Longosz AF, Wu CH, Serwadda D, Martens C, Kagaayi J, Sewankambo N, Porcella SF, Grabowski MK, Quinn TC, Eller MA, Eller LA, Wabwire-Mangen F, Robb ML, Fraser C, Lythgoe KA. Evolution of HIV-1 within untreated individuals and at the population scale in Uganda. PLoS Pathog 2018; 14:e1007167. [PMID: 30052678 PMCID: PMC6082572 DOI: 10.1371/journal.ppat.1007167] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 08/08/2018] [Accepted: 06/20/2018] [Indexed: 12/15/2022] Open
Abstract
HIV-1 undergoes multiple rounds of error-prone replication between transmission events, resulting in diverse viral populations within and among individuals. In addition, the virus experiences different selective pressures at multiple levels: during the course of infection, at transmission, and among individuals. Disentangling how these evolutionary forces shape the evolution of the virus at the population scale is important for understanding pathogenesis, how drug- and immune-escape variants are likely to spread in populations, and the development of preventive vaccines. To address this, we deep-sequenced two regions of the HIV-1 genome (p24 and gp41) from 34 longitudinally-sampled untreated individuals from Rakai District in Uganda, infected with subtypes A, D, and inter-subtype recombinants. This dataset substantially increases the availability of HIV-1 sequence data that spans multiple years of untreated infection, in particular for different geographical regions and viral subtypes. In line with previous studies, we estimated an approximately five-fold faster rate of evolution at the within-host compared to the population scale for both synonymous and nonsynonymous substitutions, and for all subtypes. We determined the extent to which this mismatch in evolutionary rates can be explained by the evolution of the virus towards population-level consensus, or the transmission of viruses similar to those that establish infection within individuals. Our findings indicate that both processes are likely to be important.
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Affiliation(s)
- Jayna Raghwani
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, United Kingdom
| | - Andrew D. Redd
- Laboratory of Immunoregulation, Division of Intramural Research, NIAID, NIH, Baltimore MD, United States of America
- Department of Medicine, Johns Hopkins Medical Institute, Johns Hopkins University, Baltimore MD, United States of America
| | - Andrew F. Longosz
- Laboratory of Immunoregulation, Division of Intramural Research, NIAID, NIH, Baltimore MD, United States of America
| | - Chieh-Hsi Wu
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - David Serwadda
- Rakai Health Sciences Program, Kalisizo, Uganda
- School of Public Health, Makerere University, Kampala, Uganda
| | - Craig Martens
- Genomics Unit, RTS, RTB, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH, Hamilton MT, United States of America
| | | | - Nelson Sewankambo
- Rakai Health Sciences Program, Kalisizo, Uganda
- School of Medicine, Makerere University, Kampala, Uganda
| | - Stephen F. Porcella
- Genomics Unit, RTS, RTB, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH, Hamilton MT, United States of America
| | - Mary K. Grabowski
- Department of Pathology, Johns Hopkins Medical Institute, Johns Hopkins University, Baltimore, MD, United States of America
| | - Thomas C. Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, NIAID, NIH, Baltimore MD, United States of America
- Department of Medicine, Johns Hopkins Medical Institute, Johns Hopkins University, Baltimore MD, United States of America
| | - Michael A. Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Fred Wabwire-Mangen
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Merlin L. Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Katrina A. Lythgoe
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, United Kingdom
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10
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Levenson EA, Martens C, Kanakabandi K, Turner CV, Virtaneva K, Paneru M, Ricklefs S, Sosnovtsev SV, Johnson JA, Porcella SF, Green KY. Comparative Transcriptomic Response of Primary and Immortalized Macrophages to Murine Norovirus Infection. J Immunol 2018; 200:4157-4169. [PMID: 29735480 DOI: 10.4049/jimmunol.1700384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/16/2018] [Indexed: 01/10/2023]
Abstract
Murine norovirus (NoV) is genetically similar to human NoV and offers both an efficient in vitro cell culture system and an animal model by which to investigate the molecular basis of replication. In this study, we present a detailed global view of host alterations to cellular pathways that occur during the progression of a NoV infection. This was accomplished for both Mus musculus BALB/c-derived RAW264.7 (RAW) cells, an immortalized cell line widely used in in vitro replication studies, and primary bone marrow-derived macrophages (BMDM), representing a permissive in vivo target cell in the host. Murine NoV replicated in both cell types, although detected genome copies were approximately one log lower in BMDM compared with RAW cells. RAW and BMDM cells shared an IRF3/7-based IFN response that occurred early in infection. In RAW cells, transcriptional upregulation and INF-β expression were not coupled in that a significant delay in the detection of secreted INF-β was observed. In contrast, primary BMDM showed an early upregulation of transcripts and immediate release of INF-β that might account for lower virus yield. Differences in the transcriptional pathway responses included a marked decrease in expression of key genes in the cell cycle and lipid pathways in RAW cells compared with that of BMDM. Our comparative analysis indicates the existence of varying host responses to virus infection in populations of permissive cells. Awareness of these differences at the gene level will be important in the application of a given permissive culture system to the study of NoV immunity, pathogenesis, and drug development.
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Affiliation(s)
- Eric A Levenson
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Craig Martens
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Kishore Kanakabandi
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Charles V Turner
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Kimmo Virtaneva
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Monica Paneru
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Stacy Ricklefs
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Stanislav V Sosnovtsev
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Jordan A Johnson
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
| | - Stephen F Porcella
- Rocky Mountain Laboratories Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Kim Y Green
- Caliciviruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892; and
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11
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Gangaplara A, Martens C, Dahlstrom E, Metidji A, Gokhale AS, Glass DD, Lopez-Ocasio M, Baur R, Kanakabandi K, Porcella SF, Shevach EM. Type I interferon signaling attenuates regulatory T cell function in viral infection and in the tumor microenvironment. PLoS Pathog 2018; 14:e1006985. [PMID: 29672594 PMCID: PMC5929570 DOI: 10.1371/journal.ppat.1006985] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 05/01/2018] [Accepted: 03/21/2018] [Indexed: 12/11/2022] Open
Abstract
Regulatory T cells (Tregs) play a cardinal role in the immune system by suppressing detrimental autoimmune responses, but their role in acute, chronic infectious diseases and tumor microenvironment remains unclear. We recently demonstrated that IFN-α/β receptor (IFNAR) signaling promotes Treg function in autoimmunity. Here we dissected the functional role of IFNAR-signaling in Tregs using Treg-specific IFNAR deficient (IFNARfl/flxFoxp3YFP-Cre) mice in acute LCMV Armstrong, chronic Clone-13 viral infection, and in tumor models. In both viral infection and tumor models, IFNARfl/flxFoxp3YFP-Cre mice Tregs expressed enhanced Treg associated activation antigens. LCMV-specific CD8+ T cells and tumor infiltrating lymphocytes from IFNARfl/flxFoxp3YFP-Cre mice produced less antiviral and antitumor IFN-γ and TNF-α. In chronic viral model, the numbers of antiviral effector and memory CD8+ T cells were decreased in IFNARfl/flxFoxp3YFP-Cre mice and the effector CD4+ and CD8+ T cells exhibited a phenotype compatible with enhanced exhaustion. IFNARfl/flxFoxp3YFP-Cre mice cleared Armstrong infection normally, but had higher viral titers in sera, kidneys and lungs during chronic infection, and higher tumor burden than the WT controls. The enhanced activated phenotype was evident through transcriptome analysis of IFNARfl/flxFoxp3YFP-Cre mice Tregs during infection demonstrated differential expression of a unique gene signature characterized by elevated levels of genes involved in suppression and decreased levels of genes mediating apoptosis. Thus, IFN signaling in Tregs is beneficial to host resulting in a more effective antiviral response and augmented antitumor immunity. Type I interferons (IFNs) play a predominant role in the immune response to infectious pathogens. The cellular targets of IFNs have been difficult to dissect because of the ubiquitous expression of the type I interferon receptor (IFNAR). The immune response of mice to lymphocytic choriomeningitis virus (LCMV) is one of the major models for analyzing the action of IFNs. Regulatory T cells (Tregs) have been implicated in the control of LCMV and it has been proposed that IFN may influence their function. The major goal of this study was to define the contribution of IFN signaling on Treg function during different stages LCMV infection. Tregs from mice with selective deletion of IFNAR manifested enhanced suppressive activity during acute/chronic LCMV infection resulting in increased CD8 T cell anergy, defective generation of memory T cells and persistence of virus. Similar effects of IFNAR signaling in Tregs were seen in a tumor model. We identified a unique set of genes in Tregs modulated by IFN signaling that may contribute to the enhanced suppressive function of IFNAR deficient Tregs. IFNs play a beneficial role during acute/chronic viral infections not only by contributing to viral clearance but also by attenuating the function of Tregs.
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MESH Headings
- Animals
- Antiviral Agents/pharmacology
- Arenaviridae Infections/drug therapy
- Arenaviridae Infections/immunology
- Arenaviridae Infections/metabolism
- Arenaviridae Infections/virology
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cells, Cultured
- Colonic Neoplasms/drug therapy
- Colonic Neoplasms/immunology
- Colonic Neoplasms/metabolism
- Colonic Neoplasms/virology
- Immunity, Innate/drug effects
- Immunity, Innate/immunology
- Interferon Type I/pharmacology
- Interferon-gamma/metabolism
- Lymphocytic Choriomeningitis/drug therapy
- Lymphocytic Choriomeningitis/immunology
- Lymphocytic Choriomeningitis/metabolism
- Lymphocytic Choriomeningitis/virology
- Lymphocytic choriomeningitis virus/drug effects
- Melanoma, Experimental/drug therapy
- Melanoma, Experimental/immunology
- Melanoma, Experimental/metabolism
- Melanoma, Experimental/virology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Receptor, Interferon alpha-beta/physiology
- Signal Transduction/drug effects
- T-Lymphocytes, Regulatory/drug effects
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- T-Lymphocytes, Regulatory/virology
- Tumor Microenvironment/drug effects
- Tumor Microenvironment/immunology
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Affiliation(s)
- Arunakumar Gangaplara
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Craig Martens
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Eric Dahlstrom
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Amina Metidji
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
- The Francis Crick Institute, London, United Kingdom
| | - Ameya S. Gokhale
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Deborah D. Glass
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Maria Lopez-Ocasio
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Rachel Baur
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Kishore Kanakabandi
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Stephen F. Porcella
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Ethan M. Shevach
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
- * E-mail:
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12
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Portugal S, Tran TM, Ongoiba A, Bathily A, Li S, Doumbo S, Skinner J, Doumtabe D, Kone Y, Sangala J, Jain A, Davies DH, Hung C, Liang L, Ricklefs S, Homann MV, Felgner PL, Porcella SF, Färnert A, Doumbo OK, Kayentao K, Greenwood BM, Traore B, Crompton PD. Treatment of Chronic Asymptomatic Plasmodium falciparum Infection Does Not Increase the Risk of Clinical Malaria Upon Reinfection. Clin Infect Dis 2017; 64:645-653. [PMID: 28362910 DOI: 10.1093/cid/ciw849] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/13/2016] [Indexed: 11/14/2022] Open
Abstract
Background Chronic asymptomatic Plasmodium falciparum infections are common in endemic areas and are thought to contribute to the maintenance of malaria immunity. Whether treatment of these infections increases the subsequent risk of clinical episodes of malaria is unclear. Methods In a 3-year study in Mali, asymptomatic individuals with or without P. falciparum infection at the end of the 6-month dry season were identified by polymerase chain reaction (PCR), and clinical malaria risk was compared during the ensuing 6-month malaria transmission season. At the end of the second dry season, 3 groups of asymptomatic children were identified: (1) children infected with P. falciparum as detected by rapid diagnostic testing (RDT) who were treated with antimalarials (n = 104), (2) RDT-negative children whose untreated P. falciparum infections were detected retrospectively by PCR (n = 55), and (3) uninfected children (RDT/PCR negative) (n = 434). Clinical malaria risk during 2 subsequent malaria seasons was compared. Plasmodium falciparum-specific antibody kinetics during the dry season were compared in children who did or did not harbor asymptomatic P. falciparum infections. Results Chronic asymptomatic P. falciparum infection predicted decreased clinical malaria risk during the subsequent malaria season(s); treatment of these infections did not alter this reduced risk. Plasmodium falciparum-specific antibodies declined similarly in children who did or did not harbor chronic asymptomatic P. falciparum infection during the dry season. Conclusions These findings challenge the notion that chronic asymptomatic P. falciparum infection maintains malaria immunity and suggest that mass drug administration during the dry season should not increase the subsequent risk of clinical malaria.
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Affiliation(s)
- Silvia Portugal
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Tuan M Tran
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA.,Division of Infectious Diseases, Department of Medicine, Indianapolis University School of Medicine, Indiana
| | - Aissata Ongoiba
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Mali
| | - Aboudramane Bathily
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Mali
| | - Shanping Li
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Safiatou Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Mali
| | - Jeff Skinner
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Didier Doumtabe
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Mali
| | - Younoussou Kone
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Mali
| | - Jules Sangala
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Mali
| | - Aarti Jain
- University of California, Irvine, California, USA
| | - D Huw Davies
- University of California, Irvine, California, USA
| | | | - Li Liang
- University of California, Irvine, California, USA
| | - Stacy Ricklefs
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Manijeh Vafa Homann
- Department of Infectious Diseases, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | | | - Stephen F Porcella
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Anna Färnert
- Department of Infectious Diseases, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Ogobara K Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Mali
| | - Kassoum Kayentao
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Mali
| | - Brian M Greenwood
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, UK
| | - Boubacar Traore
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Mali
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
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13
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Kumar K, Srinivasan P, Nold MJ, Moch JK, Reiter K, Sturdevant D, Otto TD, Squires RB, Herrera R, Nagarajan V, Rayner JC, Porcella SF, Geromanos SJ, Haynes JD, Narum DL. Profiling invasive Plasmodium falciparum merozoites using an integrated omics approach. Sci Rep 2017; 7:17146. [PMID: 29215067 PMCID: PMC5719419 DOI: 10.1038/s41598-017-17505-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 11/22/2017] [Indexed: 02/06/2023] Open
Abstract
The symptoms of malaria are brought about by blood-stage parasites, which are established when merozoites invade human erythrocytes. Our understanding of the molecular events that underpin erythrocyte invasion remains hampered by the short-period of time that merozoites are invasive. To address this challenge, a Plasmodium falciparum gamma-irradiated long-lived merozoite (LLM) line was developed and investigated. Purified LLMs invaded erythrocytes by an increase of 10–300 fold compared to wild-type (WT) merozoites. Using an integrated omics approach, we investigated the basis for the phenotypic difference. Only a few single nucleotide polymorphisms within the P. falciparum genome were identified and only marginal differences were observed in the merozoite transcriptomes. By contrast, using label-free quantitative mass-spectrometry, a significant change in protein abundance was noted, of which 200 were proteins of unknown function. We determined the relative molar abundance of over 1100 proteins in LLMs and further characterized the major merozoite surface protein complex. A unique processed MSP1 intermediate was identified in LLM but not observed in WT suggesting that delayed processing may be important for the observed phenotype. This integrated approach has demonstrated the significant role of the merozoite proteome during erythrocyte invasion, while identifying numerous unknown proteins likely to be involved in invasion.
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Affiliation(s)
- Krishan Kumar
- Laboratory of Malaria Immunology and Vaccinology, NIAID, NIH, Rockville, MD, USA
| | - Prakash Srinivasan
- Laboratory of Malaria and Vector Research, NIAID, NIH, Rockville, MD, USA. .,Johns Hopkins Malaria Research Institute, Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | | | - J Kathleen Moch
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Karine Reiter
- Laboratory of Malaria Immunology and Vaccinology, NIAID, NIH, Rockville, MD, USA
| | - Dan Sturdevant
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, USA
| | - Thomas D Otto
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - R Burke Squires
- Computational Biology Section, Bioinformatics and Computational Biosciences Branch, NIAID, NIH, Bethesda, MD, USA
| | - Raul Herrera
- Laboratory of Malaria Immunology and Vaccinology, NIAID, NIH, Rockville, MD, USA
| | - Vijayaraj Nagarajan
- Computational Biology Section, Bioinformatics and Computational Biosciences Branch, NIAID, NIH, Bethesda, MD, USA
| | - Julian C Rayner
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT, USA
| | | | - J David Haynes
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - David L Narum
- Laboratory of Malaria Immunology and Vaccinology, NIAID, NIH, Rockville, MD, USA.
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Prodger JL, Lai J, Reynolds SJ, Keruly JC, Moore RD, Kasule J, Kityamuweesi T, Buule P, Serwadda D, Nason M, Capoferri AA, Porcella SF, Siliciano RF, Redd AD, Siliciano JD, Quinn TC. Reduced Frequency of Cells Latently Infected With Replication-Competent Human Immunodeficiency Virus-1 in Virally Suppressed Individuals Living in Rakai, Uganda. Clin Infect Dis 2017; 65:1308-1315. [PMID: 28535179 PMCID: PMC5850010 DOI: 10.1093/cid/cix478] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/19/2017] [Indexed: 01/17/2023] Open
Abstract
Background Human immunodeficiency virus type 1 (HIV-1) persists in latently infected resting CD4+ T cells (rCD4 cells), posing a major barrier to curing HIV-1 infection. Previous studies have quantified this pool of latently infected cells in Americans; however, no study has quantified this reservoir in sub-Saharan Africans, who make up the largest population of HIV-1-infected individuals globally. Methods Peripheral blood was collected from 70 virally suppressed HIV-1-infected individuals from Rakai District, Uganda, who had initiated antiretroviral therapy (ART) during chronic infection. The quantitative viral outgrowth assay was used to determine frequency of latently infected rCD4 cells containing replication-competent virus. Multivariate regression was used to identify correlates of reservoir size and to compare reservoir size between this Ugandan cohort and a previously studied cohort of individuals from Baltimore, Maryland. Results The median frequency of latently infected rCD4 cells in this Ugandan cohort was 0.36 infectious units per million cells (IUPM; 95% confidence interval, 0.26-0.55 IUPM), 3-fold lower than the frequency observed in the Baltimore cohort (1.08 IUPM; .72-1.49 IUPM; P < .001). Reservoir size in Ugandans was correlated positively with set-point viral load and negatively with duration of viral suppression. Conclusions Virally suppressed Ugandans had a 3-fold lower frequency of rCD4 cells latently infected with replication-competent HIV-1, compared with previous observations in a cohort of American patients, also treated with ART during chronic infection. The biological mechanism driving the observed smaller reservoir in Ugandans is of interest and may be of significance to HIV-1 eradication efforts.
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Affiliation(s)
- Jessica L Prodger
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health and
| | - Jun Lai
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
| | - Steven J Reynolds
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
- Rakai Health Sciences Program, Kalisizo,Uganda
| | - Jeanne C Keruly
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
| | - Richard D Moore
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo,Uganda
| | - David Serwadda
- Rakai Health Sciences Program, Kalisizo,Uganda
- Makerere University, Kampala, Uganda
| | - Martha Nason
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Adam A Capoferri
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana; and
| | - Robert F Siliciano
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
- Howard Hughes Medical Institute, Baltimore, Maryland
| | - Andrew D Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
| | - Janet D Siliciano
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Thomas C Quinn
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, and
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health and
- Division of Infectious Diseases, Johns Hopkins University School of Medicine,Baltimore, Maryland
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15
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Gangaplara A, Martens C, Metidji A, Schmidt R, Kanakabandi K, Glass D, Gokhale AS, Lopez-Ocasio M, Porcella SF, Shevach EM. Type I interferon signaling attenuates Regulatory T cells function in LCMV infection. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.78.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Regulatory T cells (Tregs) play a cardinal role in the immune system by suppressing detrimental autoimmune responses, but their role in acute and chronic infectious diseases remains unclear. We recently demonstrated that IFN-α/β receptor (IFNAR) signaling promotes Treg function in autoimmunity. To dissect the functional role of IFNAR-signaling in Tregs during acute and chronic viral infection, we infected Treg-specific IFNAR deficient (IFNARfl/flxFoxp3YFP-Cre) mice with LCMV Armstrong and Clone-13. In both models, IFNARfl/flxFoxp3YFP-Cre mice Tregs expressed enhanced expression of Treg associated activation antigens. The enhanced activated phenotype was also seen when we compared the transcriptomes of IFNARfl/flxFoxp3YFP-Cre and wild type (WT) Tregs by RNA-Seq on day 25-post Clone-13 infection. LCMV-specific CD8+ T cells from IFNARfl/flxFoxp3YFP-Cre mice produced less antiviral IFNγ and TNFα in both acute and chronic LCMV. In the chronic model, the numbers of anti-viral effector and memory CD8+ T cells were decreased in IFNARfl/flxFoxp3YFP-Cre mice and the effector CD4+ and CD8+ T cells exhibited a phenotype compatible with enhanced exhaustion. IFNARfl/flxFoxp3YFP-Cre mice cleared Armstrong infection normally, but had higher viral titers in sera, kidneys and lungs than WT mice during chronic infection. Thus, type I IFN signaling in Tregs is context-dependent, resulting in enhanced suppressor function in some models of autoimmunity, but decreased suppressor function in acute and chronic viral infection.
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16
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Meissner EG, McLaughlin M, Matthews L, Gharib AM, Wood BJ, Levy E, Sinkus R, Virtaneva K, Sturdevant D, Martens C, Porcella SF, Goodman ZD, Kanwar B, Myers R, Subramanian M, Hadigan C, Masur H, Kleiner DE, Heller T, Kottilil S, Kovacs JA, Morse CG. Simtuzumab treatment of advanced liver fibrosis in HIV and HCV-infected adults: results of a 6-month open-label safety trial. Liver Int 2016; 36:1783-1792. [PMID: 27232579 PMCID: PMC5116256 DOI: 10.1111/liv.13177] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/25/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND Chronic liver injury can result in fibrosis that may progress over years to end-stage liver disease. The most effective anti-fibrotic therapy is treatment of the underlying disease, however when not possible, interventions to reverse or slow fibrosis progression are needed. AIM The aim of this study was to study the safety and tolerability of simtuzumab, a monoclonal antibody directed against lysyl oxidase-like 2 (LOXL2) enzyme, in subjects with hepatitis C virus (HCV), human immunodeficiency virus (HIV), or HCV-HIV co-infection and advanced liver disease. METHODS Eighteen subjects with advanced liver fibrosis received simtuzumab 700 mg intravenously every 2 weeks for 22 weeks. Transjugular liver biopsies were performed during screening and at the end of treatment to measure hepatic venous pressure gradient (HVPG) and to stage fibrosis. RESULTS Treatment was well-tolerated with no discontinuations due to adverse events. No significant changes were seen in HVPG or liver biopsy fibrosis score after treatment. Exploratory transcriptional and protein profiling using paired pre- and post-treatment liver biopsy and serum samples suggested up-regulation of TGF-β3 and IL-10 pathways with treatment. CONCLUSION In this open-label, pilot clinical trial, simtuzumab treatment was well-tolerated in HCV- and HIV-infected subjects with advanced liver disease. Putative modulation of TGF-β3 and IL-10 pathways during simtuzumab treatment merits investigation in future trials.
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Affiliation(s)
- Eric G. Meissner
- National Institute of Allergy and Infectious Diseases, Laboratory of Immunoregulation, Bethesda, MD,Medical University of South Carolina, Division of Infectious Diseases, Department of Microbiology and Immunology, Charleston, SC,NIH Clinical Center, Critical Care Medicine Department, AIDS Section, Bethesda, MD
| | - Mary McLaughlin
- National Institute of Allergy and Infectious Diseases, Laboratory of Immunoregulation, Bethesda, MD
| | - Lindsay Matthews
- NIH Clinical Center, Critical Care Medicine Department, AIDS Section, Bethesda, MD
| | - Ahmed M. Gharib
- National Institute of Diabetes and Digestive and Kidney Diseases, Biomedical and Metabolic Imaging Branch, Bethesda, MD
| | | | - Elliot Levy
- NIH Clinical Center, Radiology and Imaging Sciences
| | - Ralph Sinkus
- Kings College, Biomedical Engineering, Imaging Sciences and Biomedical Engineering Division, London
| | - Kimmo Virtaneva
- National Institute of Allergy and Infectious Diseases, Genomics Unit, Research Technology Section, Rocky Mountain Laboratories, Hamilton, Montana
| | - Dan Sturdevant
- National Institute of Allergy and Infectious Diseases, Genomics Unit, Research Technology Section, Rocky Mountain Laboratories, Hamilton, Montana
| | - Craig Martens
- National Institute of Allergy and Infectious Diseases, Genomics Unit, Research Technology Section, Rocky Mountain Laboratories, Hamilton, Montana
| | - Stephen F. Porcella
- National Institute of Allergy and Infectious Diseases, Genomics Unit, Research Technology Section, Rocky Mountain Laboratories, Hamilton, Montana
| | | | | | | | | | - Colleen Hadigan
- National Institute of Allergy and Infectious Diseases, Laboratory of Immunoregulation, Bethesda, MD
| | - Henry Masur
- NIH Clinical Center, Critical Care Medicine Department, AIDS Section, Bethesda, MD
| | | | - Theo Heller
- National Institute of Diabetes and Digestive and Kidney Diseases, Liver Diseases Branch, Bethesda, MD
| | - Shyam Kottilil
- National Institute of Allergy and Infectious Diseases, Laboratory of Immunoregulation, Bethesda, MD
| | - Joseph A. Kovacs
- NIH Clinical Center, Critical Care Medicine Department, AIDS Section, Bethesda, MD
| | - Caryn G. Morse
- NIH Clinical Center, Critical Care Medicine Department, AIDS Section, Bethesda, MD
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17
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Mlera L, Melik W, Offerdahl DK, Dahlstrom E, Porcella SF, Bloom ME. Analysis of the Langat Virus Genome in Persistent Infection of an Ixodes scapularis Cell Line. Viruses 2016; 8:v8090252. [PMID: 27626437 PMCID: PMC5035966 DOI: 10.3390/v8090252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/30/2016] [Accepted: 09/07/2016] [Indexed: 12/30/2022] Open
Abstract
Tick-borne flaviviruses (TBFVs) cause a broad spectrum of disease manifestations ranging from asymptomatic to mild febrile illness and life threatening encephalitis. These single-stranded positive-sense (ss(+)) RNA viruses are naturally maintained in a persistent infection of ixodid ticks and small-medium sized mammals. The development of cell lines from the ixodid ticks has provided a valuable surrogate system for studying the biology of TBFVs in vitro. When we infected ISE6 cells, an Ixodes scapularis embryonic cell line, with Langat virus (LGTV) we observed that the infection proceeded directly into persistence without any cytopathic effect. Analysis of the viral genome at selected time points showed that no defective genomes were generated during LGTV persistence by 10 weeks of cell passage. This was in contrast to LGTV persistence in 293T cells in which defective viral genomes are detectable by five weeks of serial cell passage. We identified two synonymous nucleotide changes i.e., 1893A→C (29% of 5978 reads at 12 h post infection (hpi)) and 2284T→A (34% of 4191 reads at 12 hpi) in the region encoding for the viral protein E. These results suggested that the mechanisms supporting LGTV persistence are different between tick and mammalian cells.
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Affiliation(s)
- Luwanika Mlera
- Biology of Vector-Borne Viruses Section, Laboratory of Virology, National Institutes of Health, Hamilton, MT 59840, USA.
| | - Wessam Melik
- Biology of Vector-Borne Viruses Section, Laboratory of Virology, National Institutes of Health, Hamilton, MT 59840, USA.
| | - Danielle K Offerdahl
- Biology of Vector-Borne Viruses Section, Laboratory of Virology, National Institutes of Health, Hamilton, MT 59840, USA.
| | - Eric Dahlstrom
- Genomics Unit, Research Technologies Branch, Hamilton, MT 59840, USA.
| | | | - Marshall E Bloom
- Biology of Vector-Borne Viruses Section, Laboratory of Virology, National Institutes of Health, Hamilton, MT 59840, USA.
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18
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Wilder HK, Raffel SJ, Barbour AG, Porcella SF, Sturdevant DE, Vaisvil B, Kapatral V, Schmitt DP, Schwan TG, Lopez JE. Transcriptional Profiling the 150 kb Linear Megaplasmid of Borrelia turicatae Suggests a Role in Vector Colonization and Initiating Mammalian Infection. PLoS One 2016; 11:e0147707. [PMID: 26845332 PMCID: PMC4741519 DOI: 10.1371/journal.pone.0147707] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/07/2016] [Indexed: 11/28/2022] Open
Abstract
Adaptation is key for survival as vector-borne pathogens transmit between the arthropod and vertebrate, and temperature change is an environmental signal inducing alterations in gene expression of tick-borne spirochetes. While plasmids are often associated with adaptation, complex genomes of relapsing fever spirochetes have hindered progress in understanding the mechanisms of vector colonization and transmission. We utilized recent advances in genome sequencing to generate the most complete version of the Borrelia turicatae 150 kb linear megaplasmid (lp150). Additionally, a transcriptional analysis of open reading frames (ORFs) in lp150 was conducted and identified regions that were up-regulated during in vitro cultivation at tick-like growth temperatures (22°C), relative to bacteria grown at 35°C and infected murine blood. Evaluation of the 3’ end of lp150 identified a cluster of ORFs that code for putative surface lipoproteins. With a microbe’s surface proteome serving important roles in pathogenesis, we confirmed the ORFs expression in vitro and in the tick compared to spirochetes infecting murine blood. Transcriptional evaluation of lp150 indicates the plasmid likely has essential roles in vector colonization and/or initiating mammalian infection. These results also provide a much needed transcriptional framework to delineate the molecular mechanisms utilized by relapsing fever spirochetes during their enzootic cycle.
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Affiliation(s)
- Hannah K. Wilder
- Department of Pediatrics, Section of Tropical Medicine, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, United States of America
| | - Sandra J. Raffel
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Alan G. Barbour
- Departments of Microbiology & Molecular Genetics, Medicine, and Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Stephen F. Porcella
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Daniel E. Sturdevant
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | | | | | | | - Tom G. Schwan
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Job E. Lopez
- Department of Pediatrics, Section of Tropical Medicine, Baylor College of Medicine and Texas Children’s Hospital, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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19
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Jindra PT, Conway SE, Ricklefs SM, Porcella SF, Anzick SL, Haagenson M, Wang T, Spellman S, Milford E, Kraft P, McDermott DH, Abdi R. Analysis of a Genetic Polymorphism in the Costimulatory Molecule TNFSF4 with Hematopoietic Stem Cell Transplant Outcomes. Biol Blood Marrow Transplant 2015; 22:27-36. [PMID: 26348892 DOI: 10.1016/j.bbmt.2015.08.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 08/31/2015] [Indexed: 10/23/2022]
Abstract
Despite stringent procedures to secure the best HLA matching between donors and recipients, life-threatening complications continue to occur after hematopoietic stem cell transplantation (HSCT). Studying single nucleotide polymorphism (SNP) in genes encoding costimulatory molecules could help identify patients at risk for post-HSCT complications. In a stepwise approach we selected SNPs in key costimulatory molecules including CD274, CD40, CD154, CD28, and TNFSF4 and systematically analyzed their association with post-HSCT outcomes. Our discovery cohort analysis of 1157 HLA-A, -B, -C, -DRB1, and -DQB1 matched cases found that patients with donors homozygous for the C variant of rs10912564 in TNFSF4 (48%) had better disease-free survival (P = .029) and overall survival (P = .009) with less treatment-related mortality (P = .006). Our data demonstrate the TNFSF4C variant had a higher affinity for the nuclear transcription factor Myb and increased percentage of TNFSF4-positive B cells after stimulation compared with CT or TT genotypes. However, these associations were not validated in a more recent cohort, potentially because of changes in standard of practice or absence of a true association. Given the discovery cohort, functional data, and importance of TNFSF4 in infection clearance, TNFSF4C may associate with outcomes and warrants future studies.
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Affiliation(s)
- Peter T Jindra
- Transplant Research Center, Renal Division, Brigham and Women's Hospital and Children's Hospital, Boston, Massachusetts
| | - Susan E Conway
- Transplant Research Center, Renal Division, Brigham and Women's Hospital and Children's Hospital, Boston, Massachusetts
| | - Stacy M Ricklefs
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Sarah L Anzick
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Mike Haagenson
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Tao Wang
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Stephen Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota
| | - Edgar Milford
- Transplant Research Center, Renal Division, Brigham and Women's Hospital and Children's Hospital, Boston, Massachusetts
| | - Peter Kraft
- Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - David H McDermott
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Reza Abdi
- Transplant Research Center, Renal Division, Brigham and Women's Hospital and Children's Hospital, Boston, Massachusetts.
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20
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Percopo CM, Rice TA, Brenner TA, Dyer KD, Luo JL, Kanakabandi K, Sturdevant DE, Porcella SF, Domachowske JB, Keicher JD, Rosenberg HF. Immunobiotic Lactobacillus administered post-exposure averts the lethal sequelae of respiratory virus infection. Antiviral Res 2015; 121:109-19. [PMID: 26145728 PMCID: PMC4536168 DOI: 10.1016/j.antiviral.2015.07.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/28/2015] [Accepted: 07/01/2015] [Indexed: 01/08/2023]
Abstract
We reported previously that priming of the respiratory tract with immunobiotic Lactobacillus prior to virus challenge protects mice against subsequent lethal infection with pneumonia virus of mice (PVM). We present here the results of gene microarray which document differential expression of proinflammatory mediators in response to PVM infection alone and those suppressed in response to Lactobacillus plantarum. We also demonstrate for the first time that intranasal inoculation with live or heat-inactivated L. plantarum or Lactobacillus reuteri promotes full survival from PVM infection when administered within 24h after virus challenge. Survival in response to L. plantarum administered after virus challenge is associated with suppression of proinflammatory cytokines, limited virus recovery, and diminished neutrophil recruitment to lung tissue and airways. Utilizing this post-virus challenge protocol, we found that protective responses elicited by L. plantarum at the respiratory tract were distinct from those at the gastrointestinal mucosa, as mice devoid of the anti-inflammatory cytokine, interleukin (IL)-10, exhibit survival and inflammatory responses that are indistinguishable from those of their wild-type counterparts. Finally, although L. plantarum interacts specifically with pattern recognition receptors TLR2 and NOD2, the respective gene-deleted mice were fully protected against lethal PVM infection by L. plantarum, as are mice devoid of type I interferon receptors. Taken together, L. plantarum is a versatile and flexible agent that is capable of averting the lethal sequelae of severe respiratory infection both prior to and post-virus challenge via complex and potentially redundant mechanisms.
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Affiliation(s)
- Caroline M Percopo
- Inflammation Immunobiology Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tyler A Rice
- Inflammation Immunobiology Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Todd A Brenner
- Inflammation Immunobiology Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kimberly D Dyer
- Inflammation Immunobiology Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Janice L Luo
- Inflammation Immunobiology Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kishore Kanakabandi
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Daniel E Sturdevant
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Joseph B Domachowske
- Department of Pediatrics, Upstate Medical University, State University of New York Upstate Medical University, Syracuse, NY, USA
| | - Jesse D Keicher
- Infectious Disease, Drug Discovery, Glaxo Smith Kline, Inc., Research Triangle Park, NC, USA
| | - Helene F Rosenberg
- Inflammation Immunobiology Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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Redd AD, Wendel SK, Longosz AF, Fogel JM, Dadabhai S, Kumwenda N, Sun J, Walker MP, Bruno D, Martens C, Eshleman SH, Porcella SF, Quinn TC, Taha TE. Evaluation of postpartum HIV superinfection and mother-to-child transmission. AIDS 2015; 29:1567-73. [PMID: 26244396 PMCID: PMC4609898 DOI: 10.1097/qad.0000000000000740] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE This study examined HIV superinfection in HIV-infected women postpartum, and its association with mother-to-child transmission (MTCT). DESIGN Plasma samples were obtained from HIV-infected women who transmitted HIV to their infants after 6 weeks of age (transmitters, n = 91) and HIV-infected women who did not transmit HIV to their infants (nontransmitters, n = 91). These women were originally enrolled in a randomized trial for prevention of MTCT of HIV in Malawi (Post-Exposure Prophylaxis of Infants trial in Malawi). METHODS Two HIV genomic regions (p24 and gp41) were analyzed by next-generation sequencing for HIV superinfection. HIV superinfection was established if the follow-up sample contained a new, phylogenetically distinct viral population. HIV superinfection and transmission risk were examined by multiple logistic regression, adjusted for Post-Exposure Prophylaxis of Infants study arm, baseline viral load, baseline CD4 cell count, time to resumption of sex, and breastfeeding duration. RESULTS Transmitters had lower baseline CD4 cell counts (P = 0.001) and higher viral loads (P < 0.0001) compared with nontransmitters. There were five cases of superinfection among transmitters (rate of superinfection = 4.7/100 person-years) compared with five cases among the nontransmitters (rate of superinfection = 4.4/100 person-years; P = 0.78). HIV superinfection was not associated with increased risk of postnatal MTCT of HIV after controlling for maternal age, baseline viral load, and CD4 cell count (adjusted odds ratio = 2.32, P = 0.30). Longer breastfeeding duration was independently associated with a lower risk of HIV superinfection after controlling for study arm and baseline viral load (P = 0.05). CONCLUSION There was a significant level of HIV superinfection in women postpartum, but this was not associated with an increased risk of MTCT via breastfeeding.
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Affiliation(s)
- Andrew D. Redd
- Laboratory of Immunoregulation, NIAID, NIH
- Johns Hopkins School of Medicine, Johns Hopkins University
| | | | | | | | - Sufia Dadabhai
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University
| | - Newton Kumwenda
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University
| | - Jin Sun
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University
| | - Michael P. Walker
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH
| | - Daniel Bruno
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH
| | - Craig Martens
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH
| | | | - Stephen F. Porcella
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, NIAID, NIH
| | - Thomas C. Quinn
- Laboratory of Immunoregulation, NIAID, NIH
- Johns Hopkins School of Medicine, Johns Hopkins University
| | - Taha E. Taha
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University
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22
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Bryke CR, McDermott DH, Gao JL, Liu Q, Siwicki M, Martens C, Jacobs P, Velez D, Yim E, Hsu N, Dai Z, Marquesen MM, Stregevsky E, Kwatemaa N, Theobald N, Long Priel DA, Pittaluga S, Raffeld MA, Calvo KR, Maric I, Desmond R, Holmes KL, Kuhns DB, Balabanian K, Bachelerie F, Porcella SF, Malech HL, Murphy PM. WHIM Syndrome Cured by Chromothripsis. Cancer Genet 2015. [DOI: 10.1016/j.cancergen.2015.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Portugal S, Tipton CM, Sohn H, Kone Y, Wang J, Li S, Skinner J, Virtaneva K, Sturdevant DE, Porcella SF, Doumbo OK, Doumbo S, Kayentao K, Ongoiba A, Traore B, Sanz I, Pierce SK, Crompton PD. Malaria-associated atypical memory B cells exhibit markedly reduced B cell receptor signaling and effector function. eLife 2015; 4. [PMID: 25955968 PMCID: PMC4444601 DOI: 10.7554/elife.07218] [Citation(s) in RCA: 200] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/06/2015] [Indexed: 01/06/2023] Open
Abstract
Protective antibodies in Plasmodium falciparum malaria are only acquired after years of repeated infections. Chronic malaria exposure is associated with a large increase in atypical memory B cells (MBCs) that resemble B cells expanded in a variety of persistent viral infections. Understanding the function of atypical MBCs and their relationship to classical MBCs will be critical to developing effective vaccines for malaria and other chronic infections. We show that VH gene repertoires and somatic hypermutation rates of atypical and classical MBCs are indistinguishable indicating a common developmental history. Atypical MBCs express an array of inhibitory receptors and B cell receptor (BCR) signaling is stunted in atypical MBCs resulting in impaired B cell responses including proliferation, cytokine production and antibody secretion. Thus, in response to chronic malaria exposure, atypical MBCs appear to differentiate from classical MBCs becoming refractory to BCR-mediated activation and potentially interfering with the acquisition of malaria immunity. DOI:http://dx.doi.org/10.7554/eLife.07218.001 The human immune system works to protect individuals from harmful microbes, such as the parasites that cause malaria. One line of defense is to produce a large array of proteins called antibodies that specifically bind to microbes to mark them for destruction by the immune system. The immune system also produces long-lived memory B cells that are able to mount a quicker and more effective antibody response if the microbe enters the body again. This means that most people only become ill with a particular disease the first time they encounter the microbe that causes it. However, malaria is unusual in that it can take many years of exposure to the parasite that causes it before an individual produces enough antibodies and memory B cells to be protected from the disease. There is also no vaccine that provides effective and long-lasting protection against malaria. Vaccinations rely on stimulating the body's natural defenses, and so understanding more about antibodies and memory B cells in relation to malaria may aid future efforts to develop a vaccine. Researchers have discovered that many of the memory B cells that accumulate in people who have been exposed to the malaria parasite over long-periods of time are different from the normal memory B cells. But it was not clear what role these ‘atypical’ cells play in immunity to malaria. To address this question, Portugal et al. studied the genetics and activity of B cells collected from children and adults living in Mali who—by living in a region where malaria is common—had been repeatedly exposed to the parasite. The experiments indicate that atypical and normal memory B cells both develop from the same precursor cells. However, the genes that are active in each cell type are different, resulting in the atypical cells being less able to respond to the parasite than the normal memory B cells. Portugal et al.'s findings suggest that the atypical cells develop from normal memory B cells during long-term exposure to malaria, which may delay the development of immunity to this disease. Future challenges include understanding what drives the formation of the atypical memory B cells in malaria, and finding out why they are less active than the normal cells. This could aid the development of vaccines and/or therapies that restore their activity in patients. DOI:http://dx.doi.org/10.7554/eLife.07218.002
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Affiliation(s)
- Silvia Portugal
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Christopher M Tipton
- Departments of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, United States
| | - Haewon Sohn
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Younoussou Kone
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Jing Wang
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Shanping Li
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Jeff Skinner
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Kimmo Virtaneva
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, United States
| | - Daniel E Sturdevant
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, United States
| | - Stephen F Porcella
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, United States
| | - Ogobara K Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Safiatou Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Kassoum Kayentao
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Aissata Ongoiba
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Boubacar Traore
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Inaki Sanz
- Departments of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, United States
| | - Susan K Pierce
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
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Tsuda Y, Hoenen T, Banadyga L, Weisend C, Ricklefs SM, Porcella SF, Ebihara H. An Improved Reverse Genetics System to Overcome Cell-Type-Dependent Ebola Virus Genome Plasticity. J Infect Dis 2015; 212 Suppl 2:S129-37. [PMID: 25810440 DOI: 10.1093/infdis/jiu681] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Reverse genetics systems represent a key technique for studying replication and pathogenesis of viruses, including Ebola virus (EBOV). During the rescue of recombinant EBOV from Vero cells, a high frequency of mutations was observed throughout the genomes of rescued viruses, including at the RNA editing site of the glycoprotein gene. The influence that such genomic instability could have on downstream uses of rescued virus may be detrimental, and we therefore sought to improve the rescue system. Here we report an improved EBOV rescue system with higher efficiency and genome stability, using a modified full-length EBOV clone in Huh7 cells. Moreover, by evaluating a variety of cells lines, we revealed that EBOV genome instability is cell-type dependent, a fact that has significant implications for the preparation of standard virus stocks. Thus, our improved rescue system will have an impact on both basic and translational research in the filovirus field.
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Affiliation(s)
- Yoshimi Tsuda
- Molecular Virology and Host-Pathogen Interaction Unit Department of Microbiology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Thomas Hoenen
- Disease Modeling and Transmission Section, Laboratory of Virology
| | | | - Carla Weisend
- Molecular Virology and Host-Pathogen Interaction Unit
| | - Stacy M Ricklefs
- Genomics Unit, Research Technology Section, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Stephen F Porcella
- Genomics Unit, Research Technology Section, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
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25
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McDermott DH, Gao JL, Liu Q, Siwicki M, Martens C, Jacobs P, Velez D, Yim E, Bryke CR, Hsu N, Dai Z, Marquesen MM, Stregevsky E, Kwatemaa N, Theobald N, Long Priel DA, Pittaluga S, Raffeld MA, Calvo KR, Maric I, Desmond R, Holmes KL, Kuhns DB, Balabanian K, Bachelerie F, Porcella SF, Malech HL, Murphy PM. Chromothriptic cure of WHIM syndrome. Cell 2015; 160:686-699. [PMID: 25662009 DOI: 10.1016/j.cell.2015.01.014] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/03/2014] [Accepted: 01/05/2015] [Indexed: 12/18/2022]
Abstract
Chromothripsis is a catastrophic cellular event recently described in cancer in which chromosomes undergo massive deletion and rearrangement. Here, we report a case in which chromothripsis spontaneously cured a patient with WHIM syndrome, an autosomal dominant combined immunodeficiency disease caused by gain-of-function mutation of the chemokine receptor CXCR4. In this patient, deletion of the disease allele, CXCR4(R334X), as well as 163 other genes from one copy of chromosome 2 occurred in a hematopoietic stem cell (HSC) that repopulated the myeloid but not the lymphoid lineage. In competitive mouse bone marrow (BM) transplantation experiments, Cxcr4 haploinsufficiency was sufficient to confer a strong long-term engraftment advantage of donor BM over BM from either wild-type or WHIM syndrome model mice, suggesting a potential mechanism for the patient's cure. Our findings suggest that partial inactivation of CXCR4 may have general utility as a strategy to promote HSC engraftment in transplantation.
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Affiliation(s)
- David H McDermott
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ji-Liang Gao
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qian Liu
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marie Siwicki
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Craig Martens
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Paejonette Jacobs
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel Velez
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erin Yim
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christine R Bryke
- Quest Diagnostics, Chantilly, VA 20151, USA; Department of Cytogenetics, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Nancy Hsu
- Quest Diagnostics, Chantilly, VA 20151, USA; Department of Cytogenetics, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Zunyan Dai
- Quest Diagnostics, Chantilly, VA 20151, USA; Department of Human Genetics, Emory University School of Medicine, Decatur, GA 30030, USA
| | - Martha M Marquesen
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elina Stregevsky
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nana Kwatemaa
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Narda Theobald
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Debra A Long Priel
- Clinical Services Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark A Raffeld
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine R Calvo
- Division of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Irina Maric
- Division of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronan Desmond
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Haematology, Tallaght Hospital, Dublin 24, Ireland
| | - Kevin L Holmes
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Douglas B Kuhns
- Clinical Services Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Karl Balabanian
- INSERM UMR- S996, Laboratory of Excellence in Research on Medication and Innovative Therapeutics, Université Paris-Sud, 92140 Clamart, France
| | - Françoise Bachelerie
- INSERM UMR- S996, Laboratory of Excellence in Research on Medication and Innovative Therapeutics, Université Paris-Sud, 92140 Clamart, France
| | - Stephen F Porcella
- Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Harry L Malech
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Philip M Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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26
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Dewas C, Chen X, Honda T, Junttila I, Linton J, Udey MC, Porcella SF, Sturdevant DE, Feigenbaum L, Koo L, Williams J, Paul WE. TSLP expression: analysis with a ZsGreen TSLP reporter mouse. J Immunol 2014; 194:1372-80. [PMID: 25539812 DOI: 10.4049/jimmunol.1400519] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Thymic stromal lymphopoietin (TSLP) is a type I cytokine that plays a central role in induction of allergic inflammatory responses. Its principal targets have been reported to be dendritic cells and/or CD4 T cells; epithelial cells are a principal source. We report in this study the development of a reporter mouse (TSLP-ZsG) in which a ZsGreen (ZsG)-encoding construct has been inserted by recombineering into a bacterial artificial chromosome immediately at the translation initiating ATG of TSLP. The expression of ZsG by mice transgenic for the recombinant BAC appears to be a faithful surrogate for TSLP expression, particularly in keratinocytes and medullary thymic epithelial cells. Limited ZsG and TSLP mRNA was observed in bone marrow-derived mast cells, basophils, and dendritic cells. Using the TSLP-ZsG reporter mouse, we show that TNF-α and IL-4/IL-13 are potent inducers of TSLP expression by keratinocytes and that local activation of Th2 and Th1 cells induces keratinocyte TSLP expression. We suggest that the capacity of TSLP to both induce Th2 differentiation and to be induced by activated Th2 cells raises the possibility that TSLP may be involved in a positive feedback loop to enhance allergic inflammatory conditions.
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Affiliation(s)
- Cedric Dewas
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Xi Chen
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Tetsuya Honda
- Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Ilkka Junttila
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jay Linton
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Mark C Udey
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Stephen F Porcella
- Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Daniel E Sturdevant
- Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Lionel Feigenbaum
- Laboratory Animal Science Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; and
| | - Lily Koo
- Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Joy Williams
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - William E Paul
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892;
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27
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Tchitchek N, Safronetz D, Rasmussen AL, Martens C, Virtaneva K, Porcella SF, Feldmann H, Ebihara H, Katze MG. Sequencing, annotation and analysis of the Syrian hamster (Mesocricetus auratus) transcriptome. PLoS One 2014; 9:e112617. [PMID: 25398096 PMCID: PMC4232415 DOI: 10.1371/journal.pone.0112617] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 10/06/2014] [Indexed: 11/18/2022] Open
Abstract
Background The Syrian hamster (golden hamster, Mesocricetus auratus) is gaining importance as a new experimental animal model for multiple pathogens, including emerging zoonotic diseases such as Ebola. Nevertheless there are currently no publicly available transcriptome reference sequences or genome for this species. Results A cDNA library derived from mRNA and snRNA isolated and pooled from the brains, lungs, spleens, kidneys, livers, and hearts of three adult female Syrian hamsters was sequenced. Sequence reads were assembled into 62,482 contigs and 111,796 reads remained unassembled (singletons). This combined contig/singleton dataset, designated as the Syrian hamster transcriptome, represents a total of 60,117,204 nucleotides. Our Mesocricetus auratus Syrian hamster transcriptome mapped to 11,648 mouse transcripts representing 9,562 distinct genes, and mapped to a similar number of transcripts and genes in the rat. We identified 214 quasi-complete transcripts based on mouse annotations. Canonical pathways involved in a broad spectrum of fundamental biological processes were significantly represented in the library. The Syrian hamster transcriptome was aligned to the current release of the Chinese hamster ovary (CHO) cell transcriptome and genome to improve the genomic annotation of this species. Finally, our Syrian hamster transcriptome was aligned against 14 other rodents, primate and laurasiatheria species to gain insights about the genetic relatedness and placement of this species. Conclusions This Syrian hamster transcriptome dataset significantly improves our knowledge of the Syrian hamster's transcriptome, especially towards its future use in infectious disease research. Moreover, this library is an important resource for the wider scientific community to help improve genome annotation of the Syrian hamster and other closely related species. Furthermore, these data provide the basis for development of expression microarrays that can be used in functional genomics studies.
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Affiliation(s)
- Nicolas Tchitchek
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - David Safronetz
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Angela L Rasmussen
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Craig Martens
- Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Kimmo Virtaneva
- Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Heinz Feldmann
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Hideki Ebihara
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Michael G Katze
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America; Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
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28
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Xie Z, Nagarajan V, Sturdevant DE, Iwaki S, Chan E, Wisch L, Young M, Nelson CM, Porcella SF, Druey KM. Genome-wide SNP analysis of the Systemic Capillary Leak Syndrome (Clarkson disease). Rare Dis 2014; 1. [PMID: 24808988 PMCID: PMC4009617 DOI: 10.4161/rdis.27445] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The Systemic Capillary Leak Syndrome (SCLS) is an extremely rare, orphan disease that resembles, and is frequently erroneously diagnosed as, systemic anaphylaxis. The disorder is characterized by repeated, transient, and seemingly unprovoked episodes of hypotensive shock and peripheral edema due to transient endothelial hyperpermeability. SCLS is often accompanied by a monoclonal gammopathy of unknown significance (MGUS). Using Affymetrix Single Nucleotide Polymorphism (SNP) microarrays, we performed the first genome-wide SNP analysis of SCLS in a cohort of 12 disease subjects and 18 controls. Exome capture sequencing was performed on genomic DNA from nine of these patients as validation for the SNP-chip discoveries and de novo data generation. We identified candidate susceptibility loci for SCLS, which included a region flanking CAV3 (3p25.3) as well as SNP clusters in PON1 (7q21.3), PSORS1C1 (6p21.3), and CHCHD3 (7q33). Among the most highly ranked discoveries were gene-associated SNPs in the uncharacterized LOC100130480 gene (rs6417039, rs2004296). Top case-associated SNPs were observed in BTRC (rs12355803, 3rs4436485), ARHGEF18 (rs11668246), CDH13 (rs4782779), and EDG2 (rs12552348), which encode proteins with known or suspected roles in B cell function and/or vascular integrity. 61 SNPs that were significantly associated with SCLS by microarray analysis were also detected and validated by exome deep sequencing. Functional annotation of highly ranked SNPs revealed enrichment of cell projections, cell junctions and adhesion, and molecules containing pleckstrin homology, Ras/Rho regulatory, and immunoglobulin Ig-like C2/fibronectin type III domains, all of which involve mechanistic functions that correlate with the SCLS phenotype. These results highlight SNPs with potential relevance to SCLS.
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Affiliation(s)
- Zhihui Xie
- Molecular Signal Transduction Section; NIAID/NIH; Bethesda, MD USA
| | - Vijayaraj Nagarajan
- Computational Biology Section; Bioinformatics and Computational Biosciences Branch; OCICB; NIAID/NIH; Bethesda, MD USA
| | - Daniel E Sturdevant
- Genomics Unit, Research Technologies Section; Rocky Mountain Laboratories; NIAID/NIH, Hamilton, MT USA
| | - Shoko Iwaki
- Molecular Signal Transduction Section; NIAID/NIH; Bethesda, MD USA
| | - Eunice Chan
- Molecular Signal Transduction Section; NIAID/NIH; Bethesda, MD USA
| | - Laura Wisch
- Molecular Signal Transduction Section; NIAID/NIH; Bethesda, MD USA
| | - Michael Young
- Clinical Research Directorate/CMRP; SAIC-Frederick, Inc; Frederick National Laboratory for Clinical Research; Frederick, MD USA
| | - Celeste M Nelson
- Molecular Signal Transduction Section; NIAID/NIH; Bethesda, MD USA
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Section; Rocky Mountain Laboratories; NIAID/NIH, Hamilton, MT USA
| | - Kirk M Druey
- Molecular Signal Transduction Section; NIAID/NIH; Bethesda, MD USA
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29
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Groseth A, Mampilli V, Weisend C, Dahlstrom E, Porcella SF, Russell BJ, Tesh RB, Ebihara H. Molecular characterization of human pathogenic bunyaviruses of the Nyando and Bwamba/Pongola virus groups leads to the genetic identification of Mojuí dos Campos and Kaeng Khoi virus. PLoS Negl Trop Dis 2014; 8:e3147. [PMID: 25188437 PMCID: PMC4154671 DOI: 10.1371/journal.pntd.0003147] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 07/23/2014] [Indexed: 11/19/2022] Open
Abstract
Background Human infection with Bwamba virus (BWAV) and the closely related Pongola virus (PGAV), as well as Nyando virus (NDV), are important causes of febrile illness in Africa. However, despite seroprevalence studies that indicate high rates of infection in many countries, these viruses remain relatively unknown and unstudied. In addition, a number of unclassified bunyaviruses have been isolated over the years often with uncertain relationships to human disease. Methodology/Principal Findings In order to better understand the genetic and evolutionary relationships among orthobunyaviruses associated with human disease, we have sequenced the complete genomes for all 3 segments of multiple strains of BWAV (n = 2), PGAV (n = 2) and NDV (n = 4), as well as the previously unclassified Mojuí dos Campos (MDCV) and Kaeng Khoi viruses (KKV). Based on phylogenetic analysis, we show that these viruses populate 2 distinct branches, one made up of BWAV and PGAV and the other composed of NDV, MDCV and KKV. Interestingly, the NDV strains analyzed form two distinct clades which differed by >10% on the amino acid level across all protein products. In addition, the assignment of two bat-associated bunyaviruses into the NDV group, which is clearly associated with mosquito-borne infection, led us to analyze the ability of these different viruses to grow in bat (RE05 and Tb 1 Lu) and mosquito (C6/36) cell lines, and indeed all the viruses tested were capable of efficient growth in these cell types. Conclusions/Significance On the basis of our analyses, it is proposed to reclassify the NDV strains ERET147 and YM176-66 as a new virus species. Further, our analysis definitively identifies the previously unclassified bunyaviruses MDCV and KKV as distinct species within the NDV group and suggests that these viruses may have a broader host range than is currently appreciated. Bunyavirus infections cause febrile illnesses of varying severity worldwide; however, despite their public health importance most remain relatively unstudied. In order to clarify the genetic relationships among African orthobunyaviruses associated with human infection, we have sequenced multiple strains of Bwamba (BWAV), Pongola (PGAV) and Nyando virus (NDV). Based on genetic analysis we showed that, while different BWAV and PGAV virus strains are closely related, NDV strains were highly variable and warrant classification as two distinct virus species. In addition, sequencing of the previously unclassified Mojuí dos Campos (MDCV) and Kaeng Khoi (KKV) viruses showed that both are closely related to NDV. This was unexpected considering that these viruses were isolated in South America and Southeast Asia, respectively, and are mainly associated with bats. Further, our experiments also indicated that BWAV and PGAV, as well as NDV, MDCV and KKV, are able to infect both bat and mosquito cell lines, suggesting that ecological studies focusing on these potential host and vector species are warranted. In the future, the availability of complete genetic information for these viruses, together with an understanding of their genetic relationships, will aid in better defining the distribution and public health impact of these viruses.
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Affiliation(s)
- Allison Groseth
- Molecular Virology and Host-Pathogen Interaction Unit, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Veena Mampilli
- Molecular Virology and Host-Pathogen Interaction Unit, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Carla Weisend
- Molecular Virology and Host-Pathogen Interaction Unit, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Eric Dahlstrom
- RML Genomics Unit, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Stephen F. Porcella
- RML Genomics Unit, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Brandy J. Russell
- Division of Vector-Borne Infectious Diseases, Centers for Disease Control & Prevention, Fort Collins, Colorado, United States of America
| | - Robert B. Tesh
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Hideki Ebihara
- Molecular Virology and Host-Pathogen Interaction Unit, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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Adam RD, Dahlstrom EW, Martens CA, Bruno DP, Barbian KD, Ricklefs SM, Hernandez MM, Narla NP, Patel RB, Porcella SF, Nash TE. Genome sequencing of Giardia lamblia genotypes A2 and B isolates (DH and GS) and comparative analysis with the genomes of genotypes A1 and E (WB and Pig). Genome Biol Evol 2014; 5:2498-511. [PMID: 24307482 PMCID: PMC3879983 DOI: 10.1093/gbe/evt197] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Giardia lamblia (syn G. intestinalis, G. duodenalis) is the most common pathogenic intestinal parasite of humans worldwide and is a frequent cause of endemic and epidemic diarrhea. G. lamblia is divided into eight genotypes (A-H) which infect a wide range of mammals and humans, but human infections are caused by Genotypes A and B. To unambiguously determine the relationship among genotypes, we sequenced GS and DH (Genotypes B and A2) to high depth coverage and compared the assemblies with the nearly completed WB genome and draft sequencing surveys of Genotypes E (P15; pig isolate) and B (GS; human isolate). Our results identified DH as the smallest Giardia genome sequenced to date, while GS is the largest. Our open reading frame analyses and phylogenetic analyses showed that GS was more distant from the other three genomes than any of the other three were from each other. Whole-genome comparisons of DH_A2 and GS_B with the optically mapped WB_A1 demonstrated substantial synteny across all five chromosomes but also included a number of rearrangements, inversions, and chromosomal translocations that were more common toward the chromosome ends. However, the WB_A1/GS_B alignment demonstrated only about 70% sequence identity across the syntenic regions. Our findings add to information presented in previous reports suggesting that GS is a different species of Giardia as supported by the degree of genomic diversity, coding capacity, heterozygosity, phylogenetic distance, and known biological differences from WB_A1 and other G. lamblia genotypes.
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Affiliation(s)
- Rodney D. Adam
- Departments of Medicine and Immunobiology, University of Arizona College of Medicine
- *Corresponding author: E-mail:
| | - Eric W. Dahlstrom
- Research Technologies Section, Genomics Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, Hamilton, MT
| | - Craig A. Martens
- Research Technologies Section, Genomics Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, Hamilton, MT
| | - Daniel P. Bruno
- Research Technologies Section, Genomics Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, Hamilton, MT
| | - Kent D. Barbian
- Research Technologies Section, Genomics Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, Hamilton, MT
| | - Stacy M. Ricklefs
- Research Technologies Section, Genomics Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, Hamilton, MT
| | - Matthew M. Hernandez
- Research Technologies Section, Genomics Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, Hamilton, MT
| | - Nirmala P. Narla
- Departments of Medicine and Immunobiology, University of Arizona College of Medicine
| | - Rima B. Patel
- Departments of Medicine and Immunobiology, University of Arizona College of Medicine
| | - Stephen F. Porcella
- Research Technologies Section, Genomics Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, Hamilton, MT
| | - Theodore E. Nash
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Diseases, NIH, Bethesda, MD
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Sacktor N, Nakasujja N, Redd AD, Manucci J, Laeyendecker O, Wendel SK, Porcella SF, Martens C, Bruno D, Skolasky RL, Okonkwo OC, Robertson K, Musisi S, Katabira E, Quinn TC. HIV subtype is not associated with dementia among individuals with moderate and advanced immunosuppression in Kampala, Uganda. Metab Brain Dis 2014; 29:261-8. [PMID: 24515303 PMCID: PMC4024330 DOI: 10.1007/s11011-014-9498-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 01/28/2014] [Indexed: 10/25/2022]
Abstract
HIV-associated neurocognitive disorders (HAND) are a common neurological manifestation of HIV infection. A previous study suggested that HIV dementia may be more common among patients with subtype D virus than among those with subtype A virus among HIV+ individuals with advanced immunosuppression. We conducted a study to evaluate the frequency of HIV dementia, and the association of HIV dementia with HIV subtype and compartmentalization among HIV+ individuals with moderate and advanced immunosuppression (CD4 lymphocyte count >150 cells/μL and <250 cells/μL). The study enrolled 117 antiretroviral naïve HIV+ individuals in Kampala, Uganda. HIV+ individuals received neurological, neuropsychological testing, and functional assessments, and gag and gp41 regions were subtyped. Subjects were considered infected with a specific subtype if both regions analyzed were from the same subtype. 41% of the HIV+ individuals had HIV dementia (mean CD4 lymphocyte count = 233 cells/μL). 67 individuals had subtype A, 25 individuals had subtype D, 24 individuals were classified as A/D recombinants, and one individual had subtype C. There was no difference in the frequency of HIV dementia when stratified by HIV subtype A and D and no association with compartmentalization between the cerebrospinal fluid and peripheral blood. These results suggest that HIV dementia is common in HIV+ individuals in Uganda. There was no association between HIV subtype and dementia among HIV+ individuals with moderate and advanced immunosuppression. Future studies should be performed to confirm these results.
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Affiliation(s)
- Ned Sacktor
- Department of Neurology, Johns Hopkins Bayview Medical Center, 301 Building, Suite 2100, 4940 Eastern Ave., Baltimore, MD, 21224, USA,
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Metenou S, Coulibaly YI, Sturdevant D, Dolo H, Diallo AA, Soumaoro L, Coulibaly ME, Kanakabandi K, Porcella SF, Klion AD, Nutman TB. Highly heterogeneous, activated, and short-lived regulatory T cells during chronic filarial infection. Eur J Immunol 2014; 44:2036-47. [PMID: 24737144 DOI: 10.1002/eji.201444452] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/21/2014] [Accepted: 04/10/2014] [Indexed: 12/14/2022]
Abstract
The mechanisms underlying the increase in the numbers of regulatory T (Treg) cells in chronic infection settings remain unclear. Here we have delineated the phenotype and transcriptional profiles of Treg cells from 18 filarial-infected (Fil(+) ) and 19 filarial-uninfected (Fil(-) ) subjects. We found that the frequencies of Foxp3(+) Treg cells expressing CTLA-4, GITR, LAG-3, and IL-10 were significantly higher in Fil(+) subjects compared with that in Fil(-) subjects. Foxp3-expressing Treg-cell populations in Fil(+) subjects were also more heterogeneous and had higher expression of IL-10, CCL-4, IL-29, CTLA-4, and TGF-β than Fil(-) subjects, each of these cytokines having been implicated in immune suppression. Moreover, Foxp3-expressing Treg cells from Fil(+) subjects had markedly upregulated expression of activation-induced apoptotic genes with concomitant downregulation of those involved in cell survival. To determine whether the expression of apoptotic genes was due to Treg-cell activation, we found that the expression of CTLA-4, CDk8, RAD50, TNFRSF1A, FOXO3, and RHOA were significantly upregulated in stimulated cells compared with unstimulated cells. Taken together, our results suggest that in patent filarial infection, the expanded Treg-cell populations are heterogeneous, short-lived, activated, and express higher levels of molecules known to modulate immune responsiveness, suggesting that filarial infection is associated with high Treg-cell turnover.
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Affiliation(s)
- Simon Metenou
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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McKenzie AT, Pomerantsev AP, Sastalla I, Martens C, Ricklefs SM, Virtaneva K, Anzick S, Porcella SF, Leppla SH. Transcriptome analysis identifies Bacillus anthracis genes that respond to CO2 through an AtxA-dependent mechanism. BMC Genomics 2014; 15:229. [PMID: 24661624 PMCID: PMC3987803 DOI: 10.1186/1471-2164-15-229] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 03/12/2014] [Indexed: 11/30/2022] Open
Abstract
Background Upon infection of a mammalian host, Bacillus anthracis responds to host cues, and particularly to elevated temperature (37°C) and bicarbonate/CO2 concentrations, with increased expression of virulence factors that include the anthrax toxins and extracellular capsular layer. This response requires the presence of the pXO1 virulence plasmid-encoded pleiotropic regulator AtxA. To better understand the genetic basis of this response, we utilized a controlled in vitro system and Next Generation sequencing to determine and compare RNA expression profiles of the parental strain and an isogenic AtxA-deficient strain in a 2 × 2 factorial design with growth environments containing or lacking carbon dioxide. Results We found 15 pXO1-encoded genes and 3 chromosomal genes that were strongly regulated by the separate or synergistic actions of AtxA and carbon dioxide. The majority of the regulated genes responded to both AtxA and carbon dioxide rather than to just one of these factors. Interestingly, we identified two previously unrecognized small RNAs that are highly expressed under physiological carbon dioxide concentrations in an AtxA-dependent manner. Expression levels of the two small RNAs were found to be higher than that of any other gene differentially expressed in response to these conditions. Secondary structure and small RNA-mRNA binding predictions for the two small RNAs suggest that they may perform important functions in regulating B. anthracis virulence. Conclusions A majority of genes on the virulence plasmid pXO1 that are regulated by the presence of either CO2 or AtxA separately are also regulated synergistically in the presence of both. These results also elucidate novel pXO1-encoded small RNAs that are associated with virulence conditions.
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Affiliation(s)
| | - Andrei P Pomerantsev
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892, USA.
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Safronetz D, Sogoba N, Lopez JE, Maiga O, Dahlstrom E, Zivcec M, Feldmann F, Haddock E, Fischer RJ, Anderson JM, Munster VJ, Branco L, Garry R, Porcella SF, Schwan TG, Feldmann H. Geographic distribution and genetic characterization of Lassa virus in sub-Saharan Mali. PLoS Negl Trop Dis 2013; 7:e2582. [PMID: 24340119 PMCID: PMC3855028 DOI: 10.1371/journal.pntd.0002582] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/28/2013] [Indexed: 01/13/2023] Open
Abstract
Background Lassa fever is an acute viral illness characterized by multi-organ failure and hemorrhagic manifestations. Lassa fever is most frequently diagnosed in Nigeria, Sierra Leone, Liberia, and Guinea, although sporadic cases have been recorded in other West African countries, including Mali. The etiological agent of Lassa fever is Lassa virus (LASV), an Arenavirus which is maintained in nature and frequently transmitted to humans by Mastomys natalensis. The purpose of this study was to better define the geographic distribution of LASV-infected rodents in sub-Saharan Mali. Methodologies/Principal Findings Small mammals were live-trapped at various locations across Mali for the purpose of identifying potential zoonotic pathogens. Serological and molecular assays were employed and determined LASV infected rodents were exclusively found in the southern Mali near the border of Côte d'Ivoire. Overall, 19.4% of Mastomys natalensis sampled in this region had evidence of LASV infection, with prevalence rates for individual villages ranging from 0 to 52%. Full-length genomic sequences were determined using high throughput sequencing methodologies for LASV isolates generated from tissue samples of rodents collected in four villages and confirmed the phylogenetic clustering of Malian LASV with strain AV. Conclusions/Significance The risk of human infections with LASV is greatest in villages in southern Mali. Lassa fever should be considered in the differential diagnosis for febrile individuals and appropriate diagnostic techniques need to be established to determine the incidence of infection and disease in these regions. Lassa fever is an acute infection associated with hemorrhagic manifestations and multi-organ failure in West Africa. The etiological agent of Lassa fever is Lassa virus (LASV), a rodent-borne arenavirus, which is maintained in nature and transmitted to humans by the multimammate rat, Mastomys natalensis. Despite the ubiquitous nature of the rodent reservoir, LASV-infected animals are most commonly documented in Nigeria, Sierra Leone, Guinea and Liberia. These four countries represent the historic endemic region for Lassa fever, although there is increasing evidence of sporadic cases occurring in other West African nations including Mali. To better define the geographic distribution of LASV-infected rodents in Mali, we tested samples from small animals collected at 27 sites across the country. Although M. natalensis was the predominant rodent species in the majority of villages, evidence of LASV infection was exclusively found in southern Mali, where overall nearly 20% of rodents were positive. The full genomic sequence was determined for five isolates and confirmed LASV in Mali is closely related to strain AV. We conclude that there is a risk of human exposure to LASV in villages in southern Mali and Lassa fever should be considered in the differential diagnosis for acutely ill, febrile patients.
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Affiliation(s)
- David Safronetz
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail: (DS); (HF)
| | - Nafomon Sogoba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Job E. Lopez
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Ousmane Maiga
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Eric Dahlstrom
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Marko Zivcec
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Friederike Feldmann
- Rocky Mountain Veterinary Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Elaine Haddock
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Robert J. Fischer
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Jennifer M. Anderson
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Vincent J. Munster
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Luis Branco
- Department of Microbiology and Immunology, Tulane School of Medicine, New Orleans, Louisiana, United States of America
- Autoimmune Technologies LLC, New Orleans, Louisiana, United States of America
| | - Robert Garry
- Department of Microbiology and Immunology, Tulane School of Medicine, New Orleans, Louisiana, United States of America
| | - Stephen F. Porcella
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Tom G. Schwan
- Laboratory of Zoonotic Pathogens, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Heinz Feldmann
- Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail: (DS); (HF)
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Song L, Carlson JH, Zhou B, Virtaneva K, Whitmire WM, Sturdevant GL, Porcella SF, McClarty G, Caldwell HD. Plasmid-mediated transformation tropism of chlamydial biovars. Pathog Dis 2013; 70:189-93. [PMID: 24214488 DOI: 10.1111/2049-632x.12104] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/04/2013] [Indexed: 11/28/2022] Open
Abstract
Chlamydia trachomatis and C. muridarum are human and mouse pathogens, respectively, which show high conservation of gene order and content. Both species contain a common 7.5-kb plasmid that is an important virulence factor. Recently described transformation systems have been used to characterize C. trachomatis L2 plasmid gene functions; however, similar studies have not been reported for C. trachomatis ocular tropic serovar A or the mouse strain, C. muridarum. Here, we have conducted genetic experiments with C. trachomatis serovar A and C. muridarum and report the following: (1) successful transformation of C. muridarum and C. trachomatis serovar A is restricted to a shuttle vector with a C. muridarum or C. trachomatis serovar A plasmid backbone, respectively; (2) transformation of plasmid-deficient C. muridarum with the C. muridarum-based shuttle vector complement glycogen accumulation and inclusion morphology; and (3) C. muridarum plasmid-encoded Pgp4 is a regulator of chromosomal (glgA) and plasmid (pgp3) virulence genes. In summary, our findings show a previously unrecognized and unexpected role for the chlamydial plasmid in its transformation tropism and confirm the plasmids regulatory role of virulence genes in C. muridarum.
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Affiliation(s)
- Lihua Song
- Laboratory of Intracellular Parasites, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA; State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China
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36
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Mehedi M, Hoenen T, Robertson S, Ricklefs S, Dolan MA, Taylor T, Falzarano D, Ebihara H, Porcella SF, Feldmann H. Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure. PLoS Pathog 2013; 9:e1003677. [PMID: 24146620 PMCID: PMC3798607 DOI: 10.1371/journal.ppat.1003677] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 08/17/2013] [Indexed: 11/18/2022] Open
Abstract
Ebolavirus (EBOV), the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. In this study, we report for the first time that minigenomes containing the glycoprotein gene editing site can undergo RNA editing, thereby eliminating the requirement for a biosafety level 4 laboratory to study EBOV RNA editing. Using a newly developed dual-reporter minigenome, we have characterized the mechanism of EBOV RNA editing, and have identified cis-acting sequences that are required for editing, located between 9 nt upstream and 9 nt downstream of the editing site. Moreover, we show that a secondary structure in the upstream cis-acting sequence plays an important role in RNA editing. EBOV RNA editing is glycoprotein gene-specific, as a stretch encoding for 7 adenosine residues located in the viral polymerase gene did not serve as an editing site, most likely due to an absence of the necessary cis-acting sequences. Finally, the EBOV protein VP30 was identified as a trans-acting factor for RNA editing, constituting a novel function for this protein. Overall, our results provide novel insights into the RNA editing mechanism of EBOV, further understanding of which might result in novel intervention strategies against this viral pathogen.
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Affiliation(s)
- Masfique Mehedi
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Thomas Hoenen
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Shelly Robertson
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Stacy Ricklefs
- Research Technology Branch, Genomics Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Michael A. Dolan
- Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Travis Taylor
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Darryl Falzarano
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Hideki Ebihara
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Stephen F. Porcella
- Research Technology Branch, Genomics Unit, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Heinz Feldmann
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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Guyard C, Raffel SJ, Schrumpf ME, Dahlstrom E, Sturdevant D, Ricklefs SM, Martens C, Hayes SF, Fischer ER, Hansen BT, Porcella SF, Schwan TG. Periplasmic flagellar export apparatus protein, FliH, is involved in post-transcriptional regulation of FlaB, motility and virulence of the relapsing fever spirochete Borrelia hermsii. PLoS One 2013; 8:e72550. [PMID: 24009690 PMCID: PMC3757020 DOI: 10.1371/journal.pone.0072550] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 07/10/2013] [Indexed: 01/07/2023] Open
Abstract
Spirochetes are bacteria characterized in part by rotating periplasmic flagella that impart their helical or flat-wave morphology and motility. While most other bacteria rely on a transcriptional cascade to regulate the expression of motility genes, spirochetes employ post-transcriptional mechanism(s) that are only partially known. In the present study, we characterize a spontaneous non-motile mutant of the relapsing fever spirochete Borrelia hermsii that was straight, non-motile and deficient in periplasmic flagella. We used next generation DNA sequencing of the mutant's genome, which when compared to the wild-type genome identified a 142 bp deletion in the chromosomal gene encoding the flagellar export apparatus protein FliH. Immunoblot and transcription analyses showed that the mutant phenotype was linked to the posttranscriptional deficiency in the synthesis of the major periplasmic flagellar filament core protein FlaB. Despite the lack of FlaB, the amount of FlaA produced by the fliH mutant was similar to the wild-type level. The turnover of the residual pool of FlaB produced by the fliH mutant was comparable to the wild-type spirochete. The non-motile mutant was not infectious in mice and its inoculation did not induce an antibody response. Trans-complementation of the mutant with an intact fliH gene restored the synthesis of FlaB, a normal morphology, motility and infectivity in mice. Therefore, we propose that the flagellar export apparatus protein regulates motility of B. hermsii at the post-transcriptional level by influencing the synthesis of FlaB.
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Affiliation(s)
- Cyril Guyard
- Public Health Ontario, Toronto, Ontario, Canada ; University of Toronto, Toronto, Ontario, Canada.
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Myeni S, Child R, Ng TW, Kupko JJ, Wehrly TD, Porcella SF, Knodler LA, Celli J. Brucella modulates secretory trafficking via multiple type IV secretion effector proteins. PLoS Pathog 2013; 9:e1003556. [PMID: 23950720 PMCID: PMC3738490 DOI: 10.1371/journal.ppat.1003556] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/27/2013] [Indexed: 01/18/2023] Open
Abstract
The intracellular pathogenic bacterium Brucella generates a replicative vacuole (rBCV) derived from the endoplasmic reticulum via subversion of the host cell secretory pathway. rBCV biogenesis requires the expression of the Type IV secretion system (T4SS) VirB, which is thought to translocate effector proteins that modulate membrane trafficking along the endocytic and secretory pathways. To date, only a few T4SS substrates have been identified, whose molecular functions remain unknown. Here, we used an in silico screen to identify putative T4SS effector candidate proteins using criteria such as limited homology in other bacterial genera, the presence of features similar to known VirB T4SS effectors, GC content and presence of eukaryotic-like motifs. Using β-lactamase and CyaA adenylate cyclase reporter assays, we identified eleven proteins translocated into host cells by Brucella, five in a VirB T4SS-dependent manner, namely BAB1_0678 (BspA), BAB1_0712 (BspB), BAB1_0847 (BspC), BAB1_1671 (BspE) and BAB1_1948 (BspF). A subset of the translocated proteins targeted secretory pathway compartments when ectopically expressed in HeLa cells, and the VirB effectors BspA, BspB and BspF inhibited protein secretion. Brucella infection also impaired host protein secretion in a process requiring BspA, BspB and BspF. Single or combined deletions of bspA, bspB and bspF affected Brucella ability to replicate in macrophages and persist in the liver of infected mice. Taken together, these findings demonstrate that Brucella modulates secretory trafficking via multiple T4SS effector proteins that likely act coordinately to promote Brucella pathogenesis. Many intracellular parasites ensure their survival and proliferation within host cells by secreting an array of effector molecules that modulate various cellular functions. Among these, Brucella abortus, the causative agent of the worldwide zoonosis brucellosis, controls the intracellular trafficking of its vacuole, the Brucella-containing vacuole (BCV), towards compartments of the secretory pathway via the expression of a Type IV secretion system (T4SS), VirB, which is thought to translocate effector proteins. Here, we have used bioinformatic algorithms and protein translocation reporter assays to identify novel Brucella proteins translocated into host cells, some of which are VirB T4SS substrates and targeted secretory pathway compartments when ectopically expressed in mammalian cells. Three VirB effectors, BspA, BspB and BspF, inhibited protein secretion and contributed to varying degrees to bacterial inhibition of host protein secretion, pathogen intracellular growth and persistence in the liver of infected mice. These findings demonstrate that Brucella modulates secretory trafficking via multiple T4SS effector proteins to promote Brucella pathogenesis.
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Affiliation(s)
- Sebenzile Myeni
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Robert Child
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Tony W. Ng
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - John J. Kupko
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Tara D. Wehrly
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Stephen F. Porcella
- Genomics Unit, Research Technologies Section, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Leigh A. Knodler
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University, Pullman, Washington, United States of America
| | - Jean Celli
- Laboratory of Intracellular Parasites, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
- * E-mail:
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Kelada S, Sethupathy P, Okoye IS, Kistasis E, Czieso S, White SD, Chou D, Martens C, Ricklefs SM, Virtaneva K, Sturdevant DE, Porcella SF, Belkaid Y, Wynn TA, Wilson MS. miR-182 and miR-10a are key regulators of Treg specialisation and stability during Schistosome and Leishmania-associated inflammation. PLoS Pathog 2013; 9:e1003451. [PMID: 23825948 PMCID: PMC3695057 DOI: 10.1371/journal.ppat.1003451] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 05/07/2013] [Indexed: 12/22/2022] Open
Abstract
A diverse suite of effector immune responses provide protection against various pathogens. However, the array of effector responses must be immunologically regulated to limit pathogen- and immune-associated damage. CD4+Foxp3+ regulatory T cells (Treg) calibrate immune responses; however, how Treg cells adapt to control different effector responses is unclear. To investigate the molecular mechanism of Treg diversity we used whole genome expression profiling and next generation small RNA sequencing of Treg cells isolated from type-1 or type-2 inflamed tissue following Leishmania major or Schistosoma mansoni infection, respectively. In-silico analyses identified two miRNA “regulatory hubs” miR-10a and miR-182 as critical miRNAs in Th1- or Th2-associated Treg cells, respectively. Functionally and mechanistically, in-vitro and in-vivo systems identified that an IL-12/IFNγ axis regulated miR-10a and its putative transcription factor, Creb. Importantly, reduced miR-10a in Th1-associated Treg cells was critical for Treg function and controlled a suite of genes preventing IFNγ production. In contrast, IL-4 regulated miR-182 and cMaf in Th2-associed Treg cells, which mitigated IL-2 secretion, in part through repression of IL2-promoting genes. Together, this study indicates that CD4+Foxp3+ cells can be shaped by local environmental factors, which orchestrate distinct miRNA pathways preserving Treg stability and suppressor function. The diversity of pathogens that the immune system encounters are controlled by a diverse suite of immunological effector responses. Preserving a well-controlled protective immune response is essential. Too vigorous an effector response can be as damaging as too little. Regulatory T cells (Treg) calibrate immune responses; however, how Treg cells adapt to control the diverse suite of effector responses is unclear. In this study we investigated the molecular identity of regulatory T cells that control distinct effector immune responses against two discrete pathogens, an intracellular parasitic protozoa, Leishmania major, and an extracellular helminth parasite, Schitsosoma mansoni. The two Treg populations studied were phenotypically and functionally different. We identified molecular pathways that influence this diversity and more specifically, we identified that two miRNAs (miR-182 and miR-10a) act as “regulatory hubs” critically controlling distinct properties within each Treg population. This is the first study identifying the upstream molecular pathways controlling Treg cell specialization and provides a new platform of Treg cell manipulation to fine-tune their function.
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Affiliation(s)
- Samir Kelada
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Isobel S. Okoye
- Division of Molecular Immunology, MRC, National Institute for Medical Research, London, United Kingdom
| | - Eleni Kistasis
- Division of Molecular Immunology, MRC, National Institute for Medical Research, London, United Kingdom
| | - Stephanie Czieso
- Division of Molecular Immunology, MRC, National Institute for Medical Research, London, United Kingdom
| | - Sandra D. White
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, Bethesda, Maryland, United States of America
| | - David Chou
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, Bethesda, Maryland, United States of America
| | - Craig Martens
- Research Technologies Section, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Stacy M. Ricklefs
- Research Technologies Section, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Kimmo Virtaneva
- Research Technologies Section, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Dan E. Sturdevant
- Research Technologies Section, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Stephen F. Porcella
- Research Technologies Section, Rocky Mountain Laboratories, Hamilton, Montana, United States of America
| | - Yasmine Belkaid
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, Bethesda, Maryland, United States of America
| | - Thomas A. Wynn
- Laboratory of Parasitic Diseases, National Institutes of Allergy and Infectious Disease, Bethesda, Maryland, United States of America
| | - Mark S. Wilson
- Division of Molecular Immunology, MRC, National Institute for Medical Research, London, United Kingdom
- * E-mail:
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Uhlemann AC, Kennedy AD, Martens C, Porcella SF, Deleo FR, Lowy FD. Toward an understanding of the evolution of Staphylococcus aureus strain USA300 during colonization in community households. Genome Biol Evol 2013; 4:1275-85. [PMID: 23104992 PMCID: PMC3542572 DOI: 10.1093/gbe/evs094] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus aureus is a frequent cause of serious infections and also a human commensal. The emergence of community-associated methicillin-resistant S. aureus led to a dramatic increase in skin and soft tissue infections worldwide. This epidemic has been driven by a limited number of clones, such as USA300 in the United States. To better understand the extent of USA300 evolution and diversification within communities, we performed comparative whole-genome sequencing of three clinical and five colonizing USA300 isolates collected longitudinally from three unrelated households over a 15-month period. Phylogenetic analysis that incorporated additional geographically diverse USA300 isolates indicated that all but one likely arose from a common recent ancestor. Although limited genetic adaptation occurred over the study period, the greatest genetic heterogeneity occurred between isolates from different households and within one heavily colonized household. This diversity allowed for a more accurate tracking of interpersonal USA300 transmission. Sequencing of persisting USA300 isolates revealed mutations in genes involved in major aspects of S. aureus function: adhesion, cell wall biosynthesis, virulence, and carbohydrate metabolism. Genetic variations also included accumulation of multiple polymorphisms within select genes of two multigene operons, suggestive of small genome rearrangements rather than de novo single point mutations. Such rearrangements have been underappreciated in S. aureus and may represent novel means of strain variation. Subtle genetic changes may contribute to USA300 fitness and persistence. Elucidation of small genome rearrangements reveals a potentially new and intriguing mechanism of directed S. aureus genome diversification in environmental niches and during pathogen-host interactions.
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Affiliation(s)
- Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University, College of Physicians & Surgeons, New York, NY, USA.
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Redd AD, Collinson-Streng AN, Chatziandreou N, Mullis CE, Laeyendecker O, Martens C, Ricklefs S, Kiwanuka N, Nyein PH, Lutalo T, Grabowski MK, Kong X, Manucci J, Sewankambo N, Wawer MJ, Gray RH, Porcella SF, Fauci AS, Sagar M, Serwadda D, Quinn TC. Previously transmitted HIV-1 strains are preferentially selected during subsequent sexual transmissions. J Infect Dis 2012; 206:1433-42. [PMID: 22997233 DOI: 10.1093/infdis/jis503] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A genetic bottleneck is known to exist for human immunodeficiency virus (HIV) at the point of sexual transmission. However, the nature of this bottleneck and its effect on viral diversity over time is unclear. METHODS Interhost and intrahost HIV diversity was analyzed in a stable population in Rakai, Uganda, from 1994 to 2002. HIV-1 envelope sequences from both individuals in initially HIV-discordant relationships in which transmission occurred later were examined using Sanger sequencing of bulk polymerase chain reaction (PCR) products (for 22 couples), clonal analysis (for 3), and next-generation deep sequencing (for 9). RESULTS Intrahost viral diversity was significantly higher than changes in interhost diversity (P < .01). The majority of HIV-1-discordant couples examined via bulk PCR (16 of 22 couples), clonal analysis (3 of 3), and next-generation deep sequencing (6 of 9) demonstrated that the viral populations present in the newly infected recipient were more closely related to the donor partner's HIV-1 variants found earlier during infection as compared to those circulating near the estimated time of transmission (P = .03). CONCLUSIONS These findings suggest that sexual transmission constrains viral diversity at the population level, partially because of the preferential transmission of ancestral as opposed to contemporary strains circulating in the transmitting partner. Future successful vaccine strategies may need to target these transmitted ancestral strains.
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Affiliation(s)
- Andrew D Redd
- Laboratory of Immunoregulation, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
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Abstract
Poxviruses are large DNA viruses that replicate within the cytoplasm and encode a complete transcription system, including a multisubunit RNA polymerase, stage-specific transcription factors, capping and methylating enzymes, and a poly(A) polymerase. Expression of the more than 200 open reading frames by vaccinia virus, the prototype poxvirus, is temporally regulated: early mRNAs are synthesized immediately after infection, whereas intermediate and late mRNAs are synthesized following genome replication. The postreplicative transcripts are heterogeneous in length and overlap the entire genome, which pose obstacles for high resolution mapping. We used tag-based methods in conjunction with high throughput cDNA sequencing to determine the precise 5'-capped and 3'-polyadenylated ends of postreplicative RNAs. Polymerase slippage during initiation of intermediate and late RNA synthesis results in a 5'-poly(A) leader that allowed the unambiguous identification of true transcription start sites. Ninety RNA start sites were located just upstream of intermediate and late open reading frames, but many more appeared anomalous, occurring within coding and non-coding regions, indicating pervasive transcription initiation. We confirmed the presence of functional promoter sequences upstream of representative anomalous start sites and demonstrated that alternative start sites within open reading frames could generate truncated isoforms of proteins. In an analogous manner, poly(A) sequences allowed accurate mapping of the numerous 3'-ends of postreplicative RNAs, which were preceded by a pyrimidine-rich sequence in the DNA coding strand. The distribution of postreplicative promoter sequences throughout the genome provides enormous transcriptional complexity, and the large number of previously unmapped RNAs may have novel functions.
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Affiliation(s)
- Zhilong Yang
- Laboratory of Viral Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892-3210, USA
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43
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Redd AD, Mullis CE, Serwadda D, Kong X, Martens C, Ricklefs SM, Tobian AAR, Xiao C, Grabowski MK, Nalugoda F, Kigozi G, Laeyendecker O, Kagaayi J, Sewankambo N, Gray RH, Porcella SF, Wawer MJ, Quinn TC. The rates of HIV superinfection and primary HIV incidence in a general population in Rakai, Uganda. J Infect Dis 2012; 206:267-74. [PMID: 22675216 DOI: 10.1093/infdis/jis325] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus (HIV) superinfection has been documented in high-risk individuals; however, the rate of superinfection among HIV-infected individuals within a general population remains unknown. METHODS A novel next-generation ultra-deep sequencing technique was utilized to determine the rate of HIV superinfection in a heterosexual population by examining two regions of the viral genome in longitudinal samples from recent HIV seroconverters (n=149) in Rakai District, Uganda. RESULTS The rate of superinfection was 1.44 per 100 person years (PYs) (95% confidence interval [CI], .4-2.5) and consisted of both inter- and intrasubtype superinfections. This was compared to primary HIV incidence in 20 220 initially HIV-negative individuals in the general population in Rakai (1.15 per 100 PYs; 95% CI, 1.1-1.2; P= .26). Propensity score matching (PS) was used to control for differences in sociodemographic and behavioral characteristics between the HIV-positive individuals at risk for superinfection and the HIV-negative population at baseline and follow-up. After PS matching, the estimated rate of primary incidence was 3.28 per 100 PYs (95% CI, 2.0-5.3; P = .07) controlling for baseline differences and 2.51 per 100 PYs (95% CI, 1.5-4.3; P = .24) controlling for follow-up differences. CONCLUSIONS This suggests that the rate of HIV superinfection in a general population is substantial, which could have a significant impact on future public health and HIV vaccine strategies.
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Affiliation(s)
- Andrew D Redd
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD 21205, USA.
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Eshleman SH, Hudelson SE, Redd AD, Wang L, Debes R, Chen YQ, Martens CA, Ricklefs SM, Selig EJ, Porcella SF, Munshaw S, Ray SC, Piwowar-Manning E, McCauley M, Hosseinipour MC, Kumwenda J, Hakim JG, Chariyalertsak S, de Bruyn G, Grinsztejn B, Kumarasamy N, Makhema J, Mayer KH, Pilotto J, Santos BR, Quinn TC, Cohen MS, Hughes JP. Analysis of genetic linkage of HIV from couples enrolled in the HIV Prevention Trials Network 052 trial. J Infect Dis 2011; 204:1918-26. [PMID: 21990420 DOI: 10.1093/infdis/jir651] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The HIV Prevention Trials Network (HPTN) 052 trial demonstrated that early initiation of antiretroviral therapy (ART) reduces human immunodeficiency virus (HIV) transmission from HIV-infected adults (index participants) to their HIV-uninfected sexual partners. We analyzed HIV from 38 index-partner pairs and 80 unrelated index participants (controls) to assess the linkage of seroconversion events. METHODS Linkage was assessed using phylogenetic analysis of HIV pol sequences and Bayesian analysis of genetic distances between pol sequences from index-partner pairs and controls. Selected samples were also analyzed using next-generation sequencing (env region). RESULTS In 29 of the 38 (76.3%) cases analyzed, the index was the likely source of the partner's HIV infection (linked). In 7 cases (18.4%), the partner was most likely infected from a source other than the index participant (unlinked). In 2 cases (5.3%), linkage status could not be definitively established. CONCLUSIONS Nearly one-fifth of the seroconversion events in HPTN 052 were unlinked. The association of early ART and reduced HIV transmission was stronger when the analysis included only linked events. This underscores the importance of assessing the genetic linkage of HIV seroconversion events in HIV prevention studies involving serodiscordant couples.
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Affiliation(s)
- Susan H Eshleman
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21205, USA.
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Duggal P, Guo X, Haque R, Peterson KM, Ricklefs S, Mondal D, Alam F, Noor Z, Verkerke HP, Marie C, Leduc CA, Chua SC, Myers MG, Leibel RL, Houpt E, Gilchrist CA, Sher A, Porcella SF, Petri WA. A mutation in the leptin receptor is associated with Entamoeba histolytica infection in children. J Clin Invest 2011; 121:1191-8. [PMID: 21393862 DOI: 10.1172/jci45294] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 12/22/2010] [Indexed: 11/17/2022] Open
Abstract
Malnutrition substantially increases susceptibility to Entamoeba histolytica in children. Leptin is a hormone produced by adipocytes that inhibits food intake, influences the immune system, and is suppressed in malnourished children. Therefore we hypothesized that diminished leptin function may increase susceptibility to E. histolytica infection. We prospectively observed a cohort of children, beginning at preschool age, for infection by the parasite E. histolytica every other day over 9 years and evaluated them for genetic variants in leptin (LEP) and the leptin receptor (LEPR). We found increased susceptibility to intestinal infection by this parasite associated with an amino acid substitution in the cytokine receptor homology domain 1 of LEPR. Children carrying the allele for arginine (223R) were nearly 4 times more likely to have an infection compared with those homozygous for the ancestral glutamine allele (223Q). An association of this allele with amebic liver abscess was also determined in an independent cohort of adult patients. In addition, mice carrying at least 1 copy of the R allele of Lepr were more susceptible to infection and exhibited greater levels of mucosal destruction and intestinal epithelial apoptosis after amebic infection. These findings suggest that leptin signaling is important in mucosal defense against amebiasis and that polymorphisms in the leptin receptor explain differences in susceptibility of children in the Bangladesh cohort to amebiasis.
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Affiliation(s)
- Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
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Rockx B, Feldmann F, Brining D, Gardner D, LaCasse R, Kercher L, Long D, Rosenke R, Virtaneva K, Sturdevant DE, Porcella SF, Mattoon J, Parnell M, Baric RS, Feldmann H. Comparative pathogenesis of three human and zoonotic SARS-CoV strains in cynomolgus macaques. PLoS One 2011; 6:e18558. [PMID: 21533129 PMCID: PMC3080360 DOI: 10.1371/journal.pone.0018558] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 03/04/2011] [Indexed: 01/13/2023] Open
Abstract
The severe acute respiratory syndrome (SARS) epidemic was characterized by increased pathogenicity in the elderly due to an early exacerbated innate host response. SARS-CoV is a zoonotic pathogen that entered the human population through an intermediate host like the palm civet. To prevent future introductions of zoonotic SARS-CoV strains and subsequent transmission into the human population, heterologous disease models are needed to test the efficacy of vaccines and therapeutics against both late human and zoonotic isolates. Here we show that both human and zoonotic SARS-CoV strains can infect cynomolgus macaques and resulted in radiological as well as histopathological changes similar to those seen in mild human cases. Viral replication was higher in animals infected with a late human phase isolate compared to a zoonotic isolate. While there were significant differences in the number of host genes differentially regulated during the host responses between the three SARS-CoV strains, the top pathways and functions were similar and only apparent early during infection with the majority of genes associated with interferon signaling pathways. This study characterizes critical disease models in the evaluation and licensure of therapeutic strategies against SARS-CoV for human use.
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Affiliation(s)
- Barry Rockx
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America.
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Sønder SU, Saret S, Tang W, Sturdevant DE, Porcella SF, Siebenlist U. IL-17-induced NF-kappaB activation via CIKS/Act1: physiologic significance and signaling mechanisms. J Biol Chem 2011; 286:12881-90. [PMID: 21335551 DOI: 10.1074/jbc.m110.199547] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Interleukin-17 (IL-17) is essential in host defense against extracellular bacteria and fungi, especially at mucosal sites, but it also contributes significantly to inflammatory and autoimmune disease pathologies. Binding of IL-17 to its receptor leads to recruitment of adaptor protein CIKS/Act1 via heterotypic association of their respective SEFIR domains and activation of transcription factor NF-κB; it is not known whether CIKS and/or NF-κB are required for all gene induction events. Here we report that CIKS is essential for all IL-17-induced immediate-early genes in primary mouse embryo fibroblasts, whereas NF-κB is profoundly involved. We also identify a novel subdomain in the N terminus of CIKS that is essential for IL-17-mediated NF-κB activation. This domain is both necessary and sufficient for interaction between CIKS and TRAF6, an adaptor required for NF-κB activation. The ability of decoy peptides to block this interaction may provide a new therapeutic strategy for intervention in IL-17-driven autoimmune and inflammatory diseases.
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Affiliation(s)
- Søren Ulrik Sønder
- Laboratory of Immunoregulation, NIAID, National Institutes of Health, Bethesda, Maryland 20852, USA
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Greenberg DE, Shoffner AR, Zelazny AM, Fenster ME, Zarember KA, Stock F, Ding L, Marshall-Batty KR, Wasserman RL, Welch DF, Kanakabandi K, Sturdevant DE, Virtaneva K, Porcella SF, Murray PR, Malech HL, Holland SM. Recurrent Granulibacter bethesdensis infections and chronic granulomatous disease. Emerg Infect Dis 2010; 16:1341-8. [PMID: 20735916 PMCID: PMC3294967 DOI: 10.3201/eid1609.091800] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- David E Greenberg
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1684, USA.
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Adam RD, Nigam A, Seshadri V, Martens CA, Farneth GA, Morrison HG, Nash TE, Porcella SF, Patel R. The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution. BMC Genomics 2010; 11:424. [PMID: 20618957 PMCID: PMC2996952 DOI: 10.1186/1471-2164-11-424] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 07/09/2010] [Indexed: 11/10/2022] Open
Abstract
Background Giardia lamblia trophozoites colonize the intestines of susceptible mammals and cause diarrhea, which can be prolonged despite an intestinal immune response. The variable expression of the variant-specific surface protein (VSP) genes may contribute to this prolonged infection. Only one is expressed at a time, and switching expression from one gene to another occurs by an epigenetic mechanism. Results The WB Giardia isolate has been sequenced at 10× coverage and assembled into 306 contigs as large as 870 kb in size. We have used this assembly to evaluate the genomic organization and evolution of the vsp repertoire. We have identified 228 complete and 75 partial vsp gene sequences for an estimated repertoire of 270 to 303, making up about 4% of the genome. The vsp gene diversity includes 30 genes containing tandem repeats, and 14 vsp pairs of identical genes present in either head to head or tail to tail configurations (designated as inverted pairs), where the two genes are separated by 2 to 4 kb of non-coding DNA. Interestingly, over half the total vsp repertoire is present in the form of linear gene arrays that can contain up to 10 vsp gene members. Lastly, evidence for recombination within and across minor clades of vsp genes is provided. Conclusions The data we present here is the first comprehensive analysis of the vsp gene family from the Genotype A1 WB isolate with an emphasis on vsp characterization, function, evolution and contributions to pathogenesis of this important pathogen.
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Affiliation(s)
- Rodney D Adam
- Departments of Medicine and Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA.
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Sturdevant DE, Virtaneva K, Martens C, Bozinov D, Ogundare O, Castro N, Kanakabandi K, Beare PA, Omsland A, Ohmsland A, Carlson JH, Kennedy AD, Heinzen RA, Celli J, Greenberg DE, DeLeo FR, Porcella SF. Host-microbe interaction systems biology: lifecycle transcriptomics and comparative genomics. Future Microbiol 2010; 5:205-19. [PMID: 20143945 DOI: 10.2217/fmb.09.125] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The use of microarray and comparative genomic technologies for the analysis of host-pathogen interactions has led to a greater understanding of the biological systems involved in infectious disease processes. Transcriptome analysis of intracellular pathogens at single or multiple time points during infection offers insight into the pathogen intracellular lifecycle. Host-pathogen transcriptome analysis in vivo, over time, enables characterization of both the pathogen and the host during the dynamic, multicellular host response. Comparative genomics using hybridization microarray-based comparative whole-genome resequencing or de novo whole-genome sequencing can identify the genetic factors responsible for pathogen evolutionary divergence, emergence, reemergence or the genetic basis for different pathogenic phenotypes. Together, microarray and comparative genomic technologies will continue to advance our understanding of pathogen evolution and assist in combating human infectious disease.
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Affiliation(s)
- Daniel E Sturdevant
- Genomics Unit, Research Technologies Section, Research Technologies Branch, Rocky Mountain Laboratories, NIH, 904 South 4th Street, Hamilton, MT 59840, USA.
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