1
|
Geretz A, Ehrenberg PK, Clifford RJ, Laliberté A, Prelli Bozzo C, Eiser D, Kundu G, Yum LK, Apps R, Creegan M, Gunady M, Shangguan S, Sanders-Buell E, Sacdalan C, Phanuphak N, Tovanabutra S, Russell RM, Bibollet-Ruche F, Robb ML, Michael NL, Ake JA, Vasan S, Hsu DC, Hahn BH, Kirchhoff F, Thomas R. Single-cell transcriptomics identifies prothymosin α restriction of HIV-1 in vivo. Sci Transl Med 2023; 15:eadg0873. [PMID: 37531416 DOI: 10.1126/scitranslmed.adg0873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 12/01/2022] [Accepted: 06/21/2023] [Indexed: 08/04/2023]
Abstract
Host restriction factors play key roles in innate antiviral defense, but it remains poorly understood which of them restricts HIV-1 in vivo. Here, we used single-cell transcriptomic analysis to identify host factors associated with HIV-1 control during acute infection by correlating host gene expression with viral RNA abundance within individual cells. Wide sequencing of cells from one participant with the highest plasma viral load revealed that intracellular viral RNA transcription correlates inversely with expression of the gene PTMA, which encodes prothymosin α. This association was genome-wide significant (Padjusted < 0.05) and was validated in 28 additional participants from Thailand and the Americas with HIV-1 CRF01_AE and subtype B infections, respectively. Overexpression of prothymosin α in vitro confirmed that this cellular factor inhibits HIV-1 transcription and infectious virus production. Our results identify prothymosin α as a host factor that restricts HIV-1 infection in vivo, which has implications for viral transmission and cure strategies.
Collapse
Affiliation(s)
- Aviva Geretz
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Robert J Clifford
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Alexandre Laliberté
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Daina Eiser
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Gautam Kundu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Lauren K Yum
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Richard Apps
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Creegan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Mohamed Gunady
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Shida Shangguan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Carlo Sacdalan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Nittaya Phanuphak
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Ronnie M Russell
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frederic Bibollet-Ruche
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Nelson L Michael
- Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Julie A Ake
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Sandhya Vasan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Denise C Hsu
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD 20817, USA
| | - Beatrice H Hahn
- Departments of Medicine and Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| |
Collapse
|
2
|
Leslie JL, Weddle E, Yum LK, Lin Y, Jenior ML, Lee B, Ma JZ, Kirkpatrick BD, Nayak U, Platts-Mills JA, Agaisse HF, Haque R, Petri WA. Lewis Blood-group Antigens Are Associated With Altered Susceptibility to Shigellosis. Clin Infect Dis 2021; 72:e868-e871. [PMID: 32940644 PMCID: PMC8315233 DOI: 10.1093/cid/ciaa1409] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Indexed: 12/02/2022] Open
Abstract
In a cohort of infants, we found that lack of the Lewis histo-blood group antigen was associated with increased susceptibility to shigellosis. Broadly inhibiting fucosylation in epithelial cells in vitro decreased invasion by Shigella flexneri. These results support a role for fucosylated glycans in susceptibility to shigellosis.
Collapse
Affiliation(s)
- Jhansi L Leslie
- Department of Medicine, Division of International Health and Infectious Diseases, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Erin Weddle
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Lauren K Yum
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Ye Lin
- Department of Statistics, University of Virginia, Charlottesville, Virginia, USA
| | - Matthew L Jenior
- Department of Biomedical Engineering, University of Virginia School of Medicine and School of Engineering, Charlottesville, Virginia, USA
| | - Benjamin Lee
- Vaccine Testing Center and Department of Pediatrics, The University of Vermont College of Medicine, Burlington, Vermont, USA
| | - Jennie Z Ma
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Beth D Kirkpatrick
- Department of Medicine and Vaccine Testing Center, The University of Vermont College of Medicine, Burlington, Vermont, USA
| | - Uma Nayak
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - James A Platts-Mills
- Department of Medicine, Division of International Health and Infectious Diseases, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Herve F Agaisse
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - William A Petri
- Department of Medicine, Division of International Health and Infectious Diseases, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| |
Collapse
|
3
|
Abstract
The bacterial pathogen Shigella flexneri causes more than 250 million cases of bacillary dysentery (blood in stool) every year across the world. This human-specific disease is characterized by profuse bloody diarrhea, dramatic ulceration of the colonic epithelium and immune cell infiltration of the colonic tissue. A major challenge in understanding the mechanisms supporting bacillary dysentery is the reliance on animal models that do not fully recapitulate the symptoms observed in humans, including bloody diarrhea. Here we outline advances provided by a recently developed infant rabbit model of bacillary dysentery. The infant rabbit model defines bacillary dysentery as a critical combination of massive vascular lesions and dramatic epithelial fenestration due to intracellular infection and cell-to-cell spread, respectively. The infant rabbit model provides an unprecedented framework for understanding how the cell biology of Shigella flexneri infection relates to pathogenesis.
Collapse
Affiliation(s)
- Lauren K. Yum
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Hervé Agaisse
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA, USA,CONTACT Hervé Agaisse Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia22908, USA
| |
Collapse
|
4
|
Michard C, Yum LK, Agaisse H. WIPF2 promotesShigella flexneriactin‐based motility and cell‐to‐cell spread. Cell Microbiol 2019; 21:e13098. [DOI: 10.1111/cmi.13098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 08/08/2019] [Accepted: 08/10/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Céline Michard
- Department of Microbiology, Immunology, and Cancer BiologyUniversity of Virginia Charlottesville Virginia
| | - Lauren K. Yum
- Department of Microbiology, Immunology, and Cancer BiologyUniversity of Virginia Charlottesville Virginia
| | - Hervé Agaisse
- Department of Microbiology, Immunology, and Cancer BiologyUniversity of Virginia Charlottesville Virginia
| |
Collapse
|
5
|
Yum LK, Byndloss MX, Feldman SH, Agaisse H. Critical role of bacterial dissemination in an infant rabbit model of bacillary dysentery. Nat Commun 2019; 10:1826. [PMID: 31015451 PMCID: PMC6478941 DOI: 10.1038/s41467-019-09808-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 12/28/2018] [Accepted: 03/28/2019] [Indexed: 11/09/2022] Open
Abstract
The bacterial pathogen Shigella flexneri causes 270 million cases of bacillary dysentery (blood in stool) worldwide every year, resulting in more than 200,000 deaths. A major challenge in combating bacillary dysentery is the lack of a small-animal model that recapitulates the symptoms observed in infected individuals, including bloody diarrhea. Here, we show that similar to humans, infant rabbits infected with S. flexneri experience severe inflammation, massive ulceration of the colonic mucosa, and bloody diarrhea. T3SS-dependent invasion of epithelial cells is necessary and sufficient for mediating immune cell infiltration and vascular lesions. However, massive ulceration of the colonic mucosa, bloody diarrhea, and dramatic weight loss are strictly contingent on the ability of the bacteria to spread from cell to cell. The infant rabbit model features bacterial dissemination as a critical determinant of S. flexneri pathogenesis and provides a unique small-animal model for research and development of therapeutic interventions.
Collapse
Affiliation(s)
- Lauren K Yum
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA
| | - Mariana X Byndloss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sanford H Feldman
- Center for Comparative Medicine, University of Virginia, Charlottesville, VA, USA
| | - Hervé Agaisse
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA.
| |
Collapse
|
6
|
Q.S. Medeiros PH, Ledwaba SE, Bolick DT, Giallourou N, Yum LK, Costa DV, Oriá RB, Barry EM, Swann JR, Lima AÂM, Agaisse H, Guerrant RL. A murine model of diarrhea, growth impairment and metabolic disturbances with Shigella flexneri infection and the role of zinc deficiency. Gut Microbes 2019; 10:615-630. [PMID: 30712505 PMCID: PMC6748602 DOI: 10.1080/19490976.2018.1564430] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Shigella is one of the major enteric pathogens worldwide. We present a murine model of S. flexneri infection and investigate the role of zinc deficiency (ZD). C57BL/6 mice fed either standard chow (HC) or ZD diets were pretreated with an antibiotic cocktail and received S. flexneri strain 2457T orally. Antibiotic pre-treated ZD mice showed higher S. flexneri colonization than non-treated mice. ZD mice showed persistent colonization for at least 50 days post-infection (pi). S. flexneri-infected mice showed significant weight loss, diarrhea and increased levels of fecal MPO and LCN in both HC and ZD fed mice. S. flexneri preferentially colonized the colon, caused epithelial disruption and inflammatory cell infiltrate, and promoted cytokine production which correlated with weight loss and histopathological changes. Infection with S. flexneri ΔmxiG (critical for type 3 secretion system) did not cause weight loss or diarrhea, and had decreased stool shedding duration and tissue burden. Several biochemical changes related to energy, inflammation and gut-microbial metabolism were observed. Zinc supplementation increased weight gains and reduced intestinal inflammation and stool shedding in ZD infected mice. In conclusion, young antibiotic-treated mice provide a new model of oral S. flexneri infection, with ZD promoting prolonged infection outcomes.
Collapse
Affiliation(s)
- Pedro Henrique Q.S. Medeiros
- Center for Global Health, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, USA,Institute of Biomedicine, Federal University of Ceara, Fortaleza, Brazil,CONTACT Pedro Henrique Q.S. Medeiros Center for Global Health, Division of Infectious Diseases and International Health, University of Virginia, 345 Crispell Drive, MR6 Room 2711, Charlottesville, VA, USA
| | - Solanka E. Ledwaba
- Center for Global Health, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, USA
| | - David T. Bolick
- Center for Global Health, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, USA
| | - Natasa Giallourou
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Lauren K. Yum
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, USA
| | - Deiziane V.S. Costa
- Center for Global Health, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, USA,Institute of Biomedicine, Federal University of Ceara, Fortaleza, Brazil
| | - Reinaldo B. Oriá
- Center for Global Health, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, USA,Institute of Biomedicine, Federal University of Ceara, Fortaleza, Brazil
| | - Eileen M. Barry
- Center for Vaccine Development, University of Maryland, Baltimore, USA
| | - Jonathan R. Swann
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | | | - Hervé Agaisse
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, USA
| | - Richard L. Guerrant
- Center for Global Health, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, USA
| |
Collapse
|
7
|
Röthig T, Yum LK, Kremb SG, Roik A, Voolstra CR. Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment. Sci Rep 2017; 7:44714. [PMID: 28303925 PMCID: PMC5356181 DOI: 10.1038/srep44714] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/13/2017] [Indexed: 11/16/2022] Open
Abstract
Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L-1) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment.
Collapse
Affiliation(s)
- Till Röthig
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Lauren K. Yum
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Stephan G. Kremb
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Anna Roik
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Christian R. Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|