1
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Tano-Menka R, Singh NK, Muzhingi I, Li X, Mandanas MV, Kaseke C, Crain CR, Zhang A, Ogunshola FJ, Vecchiarello L, Piechocka-Trocha A, Bashirova A, Birnbaum ME, Carrington M, Walker BD, Gaiha GD. Polymorphic residues in HLA-B that mediate HIV control distinctly modulate peptide interactions with both TCR and KIR molecules. Structure 2024:S0969-2126(24)00141-2. [PMID: 38733995 DOI: 10.1016/j.str.2024.04.015] [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] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/27/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024]
Abstract
Immunogenetic studies have shown that specific HLA-B residues (67, 70, 97, and 156) mediate the impact of HLA class I on HIV infection, but the molecular basis is not well understood. Here we evaluate the function of these residues within the protective HLA-B∗5701 allele. While mutation of Met67, Ser70, and Leu156 disrupt CD8+ T cell recognition, substitution of Val97 had no significant impact. Thermal denaturation of HLA-B∗5701-peptide complexes revealed that Met67 and Leu156 maintain HLA-peptide stability, while Ser70 and Leu156 facilitate T cell receptor (TCR) interactions. Analyses of existing structures and structural models suggested that Val97 mediates HLA-peptide binding to inhibitory KIR3DL1 molecules, which was confirmed by experimental assays. These data thereby demonstrate that the genetic basis by which host immunity impacts HIV outcomes occurs by modulating HLA-B-peptide stability and conformation for interaction with TCR and killer immunoglobulin receptor (KIR) molecules. Moreover, they indicate a key role for epitope specificity and HLA-KIR interactions to HIV control.
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Affiliation(s)
- Rhoda Tano-Menka
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Nishant K Singh
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Itai Muzhingi
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Xiaolong Li
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; The First Affiliated School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Michael V Mandanas
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Charles R Crain
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Angela Zhang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Funsho J Ogunshola
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael E Birnbaum
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.
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2
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Viard M, O'hUigin C, Yuki Y, Bashirova AA, Collins DR, Urbach JM, Wolinsky S, Buchbinder S, Kirk GD, Goedert JJ, Michael NL, Haas DW, Deeks SG, Walker BD, Yu X, Carrington M. Impact of HLA class I functional divergence on HIV control. Science 2024; 383:319-325. [PMID: 38236978 DOI: 10.1126/science.adk0777] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024]
Abstract
Heterozygosity of Human leukocyte antigen (HLA) class I genes is linked to beneficial outcomes after HIV infection, presumably through greater breadth of HIV epitope presentation and cytotoxic T cell response. Distinct allotype pairs, however, differ in the extent to which they bind shared sets of peptides. We developed a functional divergence metric that measures pairwise complementarity of allotype-associated peptide binding profiles. Greater functional divergence for pairs of HLA-A and/or HLA-B allotypes was associated with slower AIDS progression and independently with enhanced viral load control. The metric predicts immune breadth at the peptide level rather than gene level and redefines HLA heterozygosity as a continuum differentially affecting disease outcome. Functional divergence may affect response to additional infections, vaccination, immunotherapy, and other diseases where HLA heterozygote advantage occurs.
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Affiliation(s)
- Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - Colm O'hUigin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
| | - David R Collins
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Jonathan M Urbach
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Steven Wolinsky
- Division of Infectious Diseases, Department of Medicine, The Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, USA
- Department of Medicine, Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Gregory D Kirk
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Xu Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute Bethesda, MD, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
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3
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Zonozi R, Walters LC, Shulkin A, Naranbhai V, Nithagon P, Sauvage G, Kaeske C, Cosgrove K, Nathan A, Tano-Menka R, Gayton AC, Getz MA, Senjobe F, Worrall D, Iafrate AJ, Fromson C, Montesi SB, Rao DA, Sparks JA, Wallace ZS, Farmer JR, Walker BD, Charles RC, Laliberte K, Niles JL, Gaiha GD. T cell responses to SARS-CoV-2 infection and vaccination are elevated in B cell deficiency and reduce risk of severe COVID-19. Sci Transl Med 2023; 15:eadh4529. [PMID: 38019932 DOI: 10.1126/scitranslmed.adh4529] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 03/04/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023]
Abstract
Individuals with primary and pharmacologic B cell deficiencies have high rates of severe disease and mortality from coronavirus disease 2019 (COVID-19), but the immune responses and clinical outcomes after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and vaccination have yet to be fully defined. Here, we evaluate the cellular immune responses after both SARS-CoV-2 infection and vaccination in patients receiving the anti-CD20 therapy rituximab (RTX) and those with low B cell counts due to common variable immune deficiency (CVID) disease. Assessment of effector and memory CD4+ and CD8+ T cell responses to SARS-CoV-2 revealed elevated reactivity and proliferative capacity after both infection and vaccination in B cell-deficient individuals, particularly within the CD8+ T cell compartment, in comparison with healthy controls. Evaluation of clinical outcomes demonstrates that vaccination of RTX-treated individuals was associated with about 4.8-fold reduced odds of moderate or severe COVID-19 in the absence of vaccine-induced antibodies. Analysis of T cell differentiation demonstrates that RTX administration increases the relative frequency of naïve CD8+ T cells, potentially by depletion of CD8+CD20dim T cells, which are primarily of an effector memory or terminal effector memory (TEMRA) phenotype. However, this also leads to a reduction in preexisting antiviral T cell immunity. Collectively, these data indicate that individuals with B cell deficiencies have enhanced T cell immunity after both SARS-CoV-2 infection and vaccination that potentially accounts for reduced hospitalization and severe disease from subsequent SARS-CoV-2 infection.
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Affiliation(s)
- Reza Zonozi
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lucy C Walters
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Aaron Shulkin
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
- Monash University, Melbourne, VIC 3022, Australia
| | - Pravarut Nithagon
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gabriel Sauvage
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Clarety Kaeske
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Katherine Cosgrove
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anusha Nathan
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Rhoda Tano-Menka
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Alton C Gayton
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Matthew A Getz
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Fernando Senjobe
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Daniel Worrall
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Caroline Fromson
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sydney B Montesi
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zachary S Wallace
- Division of Rheumatology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jocelyn R Farmer
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Division of Allergy and Inflammation, Beth Israel Lahey Health, Boston, MA 02215, USA
| | - Bruce D Walker
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
- Broad Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Karen Laliberte
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John L Niles
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gaurav D Gaiha
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
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4
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McLaren PJ, Porreca I, Iaconis G, Mok HP, Mukhopadhyay S, Karakoc E, Cristinelli S, Pomilla C, Bartha I, Thorball CW, Tough RH, Angelino P, Kiar CS, Carstensen T, Fatumo S, Porter T, Jarvis I, Skarnes WC, Bassett A, DeGorter MK, Sathya Moorthy MP, Tuff JF, Kim EY, Walter M, Simons LM, Bashirova A, Buchbinder S, Carrington M, Cossarizza A, De Luca A, Goedert JJ, Goldstein DB, Haas DW, Herbeck JT, Johnson EO, Kaleebu P, Kilembe W, Kirk GD, Kootstra NA, Kral AH, Lambotte O, Luo M, Mallal S, Martinez-Picado J, Meyer L, Miro JM, Moodley P, Motala AA, Mullins JI, Nam K, Obel N, Pirie F, Plummer FA, Poli G, Price MA, Rauch A, Theodorou I, Trkola A, Walker BD, Winkler CA, Zagury JF, Montgomery SB, Ciuffi A, Hultquist JF, Wolinsky SM, Dougan G, Lever AML, Gurdasani D, Groom H, Sandhu MS, Fellay J. Author Correction: Africa-specific human genetic variation near CHD1L associates with HIV-1 load. Nature 2023; 621:E42. [PMID: 37670157 DOI: 10.1038/s41586-023-06591-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Affiliation(s)
- Paul J McLaren
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.
| | | | - Gennaro Iaconis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Hoi Ping Mok
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Subhankar Mukhopadhyay
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - István Bartha
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christian W Thorball
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Riley H Tough
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Paolo Angelino
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Cher S Kiar
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Tommy Carstensen
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Department of Non-Communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Isobel Jarvis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Marianne K DeGorter
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mohana Prasad Sathya Moorthy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey F Tuff
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Eun-Young Kim
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Miriam Walter
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lacy M Simons
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea De Luca
- University Division of Infectious Diseases, Siena University Hospital, Siena, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - James J Goedert
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Eric O Johnson
- GenOmics and Translational Research Center and Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Alex H Kral
- Community Health Research Division, RTI International, Berkeley, CA, USA
| | - Olivier Lambotte
- Université Paris Saclay, Inserm UMR1184, CEA, Le Kremlin-Bicêtre, France
- APHP, Department of Clinical Immunology, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Vaccine and Therapeutics Laboratory, Medical and Scientific Affairs, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Simon Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Javier Martinez-Picado
- University of Vic-Central University of Catalonia, Vic, Spain
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Laurence Meyer
- INSERM U1018, Université Paris-Saclay, Le Kremlin Bicêtre, France
- AP-HP, Hôpital de Bicêtre, Département d'Épidémiologie, Le Kremlin Bicêtre, France
| | - José M Miro
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases Service, Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Pravi Moodley
- National Health Laboratory Service, South Africa and University of KwaZulu-Natal, Durban, South Africa
| | - Ayesha A Motala
- Department of Diabetes and Endocrinology, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kireem Nam
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Niels Obel
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Fraser Pirie
- Department of Diabetes and Endocrinology, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Guido Poli
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Matthew A Price
- International AIDS Vaccine Initiative, New York, NY, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ioannis Theodorou
- Laboratoire d'Immunologie, Hôpital Robert Debré Paris, Paris, France
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Frederick National Laboratory for Cancer Research and Cancer Innovative Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Judd F Hultquist
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Deepti Gurdasani
- Queen Mary University of London, London, UK
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Harriet Groom
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Manjinder S Sandhu
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, UK.
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.
- Omnigen Biodata, Cambridge, UK.
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland.
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5
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McLaren PJ, Porreca I, Iaconis G, Mok HP, Mukhopadhyay S, Karakoc E, Cristinelli S, Pomilla C, Bartha I, Thorball CW, Tough RH, Angelino P, Kiar CS, Carstensen T, Fatumo S, Porter T, Jarvis I, Skarnes WC, Bassett A, DeGorter MK, Sathya Moorthy MP, Tuff JF, Kim EY, Walter M, Simons LM, Bashirova A, Buchbinder S, Carrington M, Cossarizza A, De Luca A, Goedert JJ, Goldstein DB, Haas DW, Herbeck JT, Johnson EO, Kaleebu P, Kilembe W, Kirk GD, Kootstra NA, Kral AH, Lambotte O, Luo M, Mallal S, Martinez-Picado J, Meyer L, Miro JM, Moodley P, Motala AA, Mullins JI, Nam K, Obel N, Pirie F, Plummer FA, Poli G, Price MA, Rauch A, Theodorou I, Trkola A, Walker BD, Winkler CA, Zagury JF, Montgomery SB, Ciuffi A, Hultquist JF, Wolinsky SM, Dougan G, Lever AML, Gurdasani D, Groom H, Sandhu MS, Fellay J. Africa-specific human genetic variation near CHD1L associates with HIV-1 load. Nature 2023; 620:1025-1030. [PMID: 37532928 PMCID: PMC10848312 DOI: 10.1038/s41586-023-06370-4] [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: 11/28/2018] [Accepted: 06/26/2023] [Indexed: 08/04/2023]
Abstract
HIV-1 remains a global health crisis1, highlighting the need to identify new targets for therapies. Here, given the disproportionate HIV-1 burden and marked human genome diversity in Africa2, we assessed the genetic determinants of control of set-point viral load in 3,879 people of African ancestries living with HIV-1 participating in the international collaboration for the genomics of HIV3. We identify a previously undescribed association signal on chromosome 1 where the peak variant associates with an approximately 0.3 log10-transformed copies per ml lower set-point viral load per minor allele copy and is specific to populations of African descent. The top associated variant is intergenic and lies between a long intergenic non-coding RNA (LINC00624) and the coding gene CHD1L, which encodes a helicase that is involved in DNA repair4. Infection assays in iPS cell-derived macrophages and other immortalized cell lines showed increased HIV-1 replication in CHD1L-knockdown and CHD1L-knockout cells. We provide evidence from population genetic studies that Africa-specific genetic variation near CHD1L associates with HIV replication in vivo. Although experimental studies suggest that CHD1L is able to limit HIV infection in some cell types in vitro, further investigation is required to understand the mechanisms underlying our observations, including any potential indirect effects of CHD1L on HIV spread in vivo that our cell-based assays cannot recapitulate.
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Affiliation(s)
- Paul J McLaren
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.
| | | | - Gennaro Iaconis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Hoi Ping Mok
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Subhankar Mukhopadhyay
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | | | - Sara Cristinelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - István Bartha
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Christian W Thorball
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Riley H Tough
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Paolo Angelino
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Cher S Kiar
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King's College London, London, UK
| | - Tommy Carstensen
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Department of Non-Communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Isobel Jarvis
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Marianne K DeGorter
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mohana Prasad Sathya Moorthy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey F Tuff
- Sexually Transmitted and Blood-Borne Infections Division at JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Eun-Young Kim
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Miriam Walter
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lacy M Simons
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Susan Buchbinder
- Bridge HIV, San Francisco Department of Public Health, San Francisco, CA, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea De Luca
- University Division of Infectious Diseases, Siena University Hospital, Siena, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - James J Goedert
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - David W Haas
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joshua T Herbeck
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Eric O Johnson
- GenOmics and Translational Research Center and Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Alex H Kral
- Community Health Research Division, RTI International, Berkeley, CA, USA
| | - Olivier Lambotte
- Université Paris Saclay, Inserm UMR1184, CEA, Le Kremlin-Bicêtre, France
- APHP, Department of Clinical Immunology, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Ma Luo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
- Vaccine and Therapeutics Laboratory, Medical and Scientific Affairs, National Microbiology Laboratory Branch, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Simon Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Javier Martinez-Picado
- University of Vic-Central University of Catalonia, Vic, Spain
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Laurence Meyer
- INSERM U1018, Université Paris-Saclay, Le Kremlin Bicêtre, France
- AP-HP, Hôpital de Bicêtre, Département d'Épidémiologie, Le Kremlin Bicêtre, France
| | - José M Miro
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
- Infectious Diseases Service, Hospital Clinic-Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Pravi Moodley
- National Health Laboratory Service, South Africa and University of KwaZulu-Natal, Durban, South Africa
| | - Ayesha A Motala
- Department of Diabetes and Endocrinology, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James I Mullins
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Kireem Nam
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Niels Obel
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Fraser Pirie
- Department of Diabetes and Endocrinology, School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Francis A Plummer
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Guido Poli
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Matthew A Price
- International AIDS Vaccine Initiative, New York, NY, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ioannis Theodorou
- Laboratoire d'Immunologie, Hôpital Robert Debré Paris, Paris, France
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Frederick National Laboratory for Cancer Research and Cancer Innovative Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique et Chimie Moléculaire, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Angela Ciuffi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Judd F Hultquist
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Andrew M L Lever
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Deepti Gurdasani
- Queen Mary University of London, London, UK
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Harriet Groom
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Manjinder S Sandhu
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, UK.
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.
- Omnigen Biodata, Cambridge, UK.
| | - Jacques Fellay
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland.
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6
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Allard-Chamard H, Kaneko N, Bertocchi A, Sun N, Boucau J, Kuo HH, Farmer JR, Perugino C, Mahajan VS, Murphy SJH, Premo K, Diefenbach T, Ghebremichael M, Yuen G, Kotta A, Akman Z, Lichterfeld M, Walker BD, Yu XG, Moriyama M, Maehara T, Nakamura S, Stone JH, Padera RF, Pillai S. Extrafollicular IgD -CD27 -CXCR5 -CD11c - DN3 B cells infiltrate inflamed tissues in autoimmune fibrosis and in severe COVID-19. Cell Rep 2023; 42:112630. [PMID: 37300833 PMCID: PMC10227203 DOI: 10.1016/j.celrep.2023.112630] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 12/19/2022] [Revised: 04/30/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Although therapeutic B cell depletion dramatically resolves inflammation in many diseases in which antibodies appear not to play a central role, distinct extrafollicular pathogenic B cell subsets that accumulate in disease lesions have hitherto not been identified. The circulating immunoglobulin D (IgD)-CD27-CXCR5-CD11c+ DN2 B cell subset has been previously studied in some autoimmune diseases. A distinct IgD-CD27-CXCR5-CD11c- DN3 B cell subset accumulates in the blood both in IgG4-related disease, an autoimmune disease in which inflammation and fibrosis can be reversed by B cell depletion, and in severe COVID-19. These DN3 B cells prominently accumulate in the end organs of IgG4-related disease and in lung lesions in COVID-19, and double-negative B cells prominently cluster with CD4+ T cells in these lesions. Extrafollicular DN3 B cells may participate in tissue inflammation and fibrosis in autoimmune fibrotic diseases, as well as in COVID-19.
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Affiliation(s)
- Hugues Allard-Chamard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Rheumatology, Faculté de médecine et des sciences de la santé de l'Université de Sherbrooke et Centre de Recherche Clinique Étienne-Le Bel, Sherbrooke, QC J1K 2R1, Canada
| | - Naoki Kaneko
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Alice Bertocchi
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Na Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hsiao-Hsuan Kuo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jocelyn R Farmer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Cory Perugino
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Rheumatology Allergy and Immunology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vinay S Mahajan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Katherine Premo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | | | - Grace Yuen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Alekhya Kotta
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Zafer Akman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology and Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Masafumi Moriyama
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Takashi Maehara
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Seiji Nakamura
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - John H Stone
- Division of Rheumatology Allergy and Immunology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robert F Padera
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Shiv Pillai
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
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7
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Li X, Singh NK, Collins DR, Ng R, Zhang A, Lamothe-Molina PA, Shahinian P, Xu S, Tan K, Piechocka-Trocha A, Urbach JM, Weber JK, Gaiha GD, Takou Mbah OC, Huynh T, Cheever S, Chen J, Birnbaum M, Zhou R, Walker BD, Wang JH. Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide. Nat Commun 2023; 14:2929. [PMID: 37217466 DOI: 10.1038/s41467-023-38573-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
Cytotoxic-T-lymphocyte (CTL) mediated control of HIV-1 is enhanced by targeting highly networked epitopes in complex with human-leukocyte-antigen-class-I (HLA-I). However, the extent to which the presenting HLA allele contributes to this process is unknown. Here we examine the CTL response to QW9, a highly networked epitope presented by the disease-protective HLA-B57 and disease-neutral HLA-B53. Despite robust targeting of QW9 in persons expressing either allele, T cell receptor (TCR) cross-recognition of the naturally occurring variant QW9_S3T is consistently reduced when presented by HLA-B53 but not by HLA-B57. Crystal structures show substantial conformational changes from QW9-HLA to QW9_S3T-HLA by both alleles. The TCR-QW9-B53 ternary complex structure manifests how the QW9-B53 can elicit effective CTLs and suggests sterically hindered cross-recognition by QW9_S3T-B53. We observe populations of cross-reactive TCRs for B57, but not B53 and also find greater peptide-HLA stability for B57 in comparison to B53. These data demonstrate differential impacts of HLAs on TCR cross-recognition and antigen presentation of a naturally arising variant, with important implications for vaccine design.
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Affiliation(s)
- Xiaolong Li
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
| | - Nishant Kumar Singh
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - David R Collins
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Robert Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Angela Zhang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | | | - Peter Shahinian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Shutong Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
| | - Kemin Tan
- Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | | | - Jeffrey K Weber
- IBM Thomas J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY, 10598, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | | | - Tien Huynh
- IBM Thomas J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY, 10598, USA
| | - Sophia Cheever
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - James Chen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Michael Birnbaum
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, 02142, USA
| | - Ruhong Zhou
- IBM Thomas J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY, 10598, USA
- Department of Chemistry, Columbia University, New York, NY, 10025, USA
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
- Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Jia-Huai Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02215, USA.
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8
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Collins DR, Hitschfel J, Urbach JM, Mylvaganam GH, Ly NL, Arshad U, Racenet ZJ, Yanez AG, Diefenbach TJ, Walker BD. Cytolytic CD8 + T cells infiltrate germinal centers to limit ongoing HIV replication in spontaneous controller lymph nodes. Sci Immunol 2023; 8:eade5872. [PMID: 37205767 DOI: 10.1126/sciimmunol.ade5872] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/26/2023] [Indexed: 05/21/2023]
Abstract
Follicular CD8+ T cells (fCD8) mediate surveillance in lymph node (LN) germinal centers against lymphotropic infections and cancers, but the precise mechanisms by which these cells mediate immune control remain incompletely resolved. To address this, we investigated functionality, clonotypic compartmentalization, spatial localization, phenotypic characteristics, and transcriptional profiles of LN-resident virus-specific CD8+ T cells in persons who control HIV without medications. Antigen-induced proliferative and cytolytic potential consistently distinguished spontaneous controllers from noncontrollers. T cell receptor analysis revealed complete clonotypic overlap between peripheral and LN-resident HIV-specific CD8+ T cells. Transcriptional analysis of LN CD8+ T cells revealed gene signatures of inflammatory chemotaxis and antigen-induced effector function. In HIV controllers, the cytotoxic effectors perforin and granzyme B were elevated among virus-specific CXCR5+ fCD8s proximate to foci of HIV RNA within germinal centers. These results provide evidence consistent with cytolytic control of lymphotropic infection supported by inflammatory recruitment, antigen-specific proliferation, and cytotoxicity of fCD8s.
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Affiliation(s)
- David R Collins
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Julia Hitschfel
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Institute of Clinical and Molecular Virology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Geetha H Mylvaganam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ngoc L Ly
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Umar Arshad
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Adrienne G Yanez
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Medical Engineering and Sciences and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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9
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Vieira V, Lim N, Singh A, Leitman E, Dsouza R, Adland E, Muenchhoff M, Roider J, Marin Lopez M, Carabelli J, Giandhari J, Groll A, Jooste P, Prado JG, Thobakgale C, Dong K, Kiepiela P, Prendergast AJ, Tudor-Williams G, Frater J, Walker BD, Ndung’u T, Ramsuran V, Leslie A, Kløverpris HN, Goulder P. Slow progression of pediatric HIV associates with early CD8+ T cell PD-1 expression and a stem-like phenotype. JCI Insight 2023; 8:e156049. [PMID: 36602861 PMCID: PMC9977437 DOI: 10.1172/jci.insight.156049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
HIV nonprogression despite persistent viremia is rare among adults who are naive to antiretroviral therapy (ART) but relatively common among ART-naive children. Previous studies indicate that ART-naive pediatric slow progressors (PSPs) adopt immune evasion strategies similar to those described in natural hosts of SIV. However, the mechanisms underlying this immunophenotype are not well understood. In a cohort of early-treated infants who underwent analytical treatment interruption (ATI) after 12 months of ART, expression of PD-1 on CD8+ T cells immediately before ATI was the main predictor of slow progression during ATI. PD-1+CD8+ T cell frequency was also negatively correlated with CCR5 and HLA-DR expression on CD4+ T cells and predicted stronger HIV-specific T lymphocyte responses. In the CD8+ T cell compartment of PSPs, we identified an enrichment of stem-like TCF-1+PD-1+ memory cells, whereas pediatric progressors and viremic adults had a terminally exhausted PD-1+CD39+ population. TCF-1+PD-1+ expression on CD8+ T cells was associated with higher proliferative activity and stronger Gag-specific effector functionality. These data prompted the hypothesis that the proliferative burst potential of stem-like HIV-specific cytotoxic cells could be exploited in therapeutic strategies to boost the antiviral response and facilitate remission in infants who received early ART with a preserved and nonexhausted T cell compartment.
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Affiliation(s)
- Vinicius Vieira
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Nicholas Lim
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Alveera Singh
- Africa Health Research Institute, Durban, South Africa
| | - Ellen Leitman
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Reena Dsouza
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Maximilian Muenchhoff
- Max von Pettenkofer-Institute, Department of Virology, Ludwig-Maximilians-University, Munich, Germany
- German Center for Infection Research, Munich, Germany
| | - Julia Roider
- German Center for Infection Research, Munich, Germany
- Department of Infectious Diseases, Ludwig-Maximilians-University, Munich, Germany
| | | | | | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Andreas Groll
- Department of Statistics, TU Dortmund University, Dortmund, Germany
| | - Pieter Jooste
- Department of Paediatrics, Kimberley Hospital, Kimberley, South Africa
| | - Julia G. Prado
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute, Badalona, Spain; Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Christina Thobakgale
- Faculty of Health Sciences, Centre for HIV and STIs, National Institute for Communicable Diseases, University of the Witwatersrand, Johannesburg, South Africa
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Krista Dong
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Photini Kiepiela
- South African Medical Research Council, Durban, South Africa
- Wits Health Consortium, Johannesburg, South Africa
| | - Andrew J. Prendergast
- Blizard Institute, Queen Mary University of London, London, United Kingdom
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
| | - Gareth Tudor-Williams
- Centre for Paediatrics and Child Health, Imperial College London, London, United Kingdom
| | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford, United Kingdom
| | - Bruce D. Walker
- Africa Health Research Institute, Durban, South Africa
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Thumbi Ndung’u
- Africa Health Research Institute, Durban, South Africa
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Alasdair Leslie
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Henrik N. Kløverpris
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, United Kingdom
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
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10
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Sun W, Gao C, Hartana CA, Osborn MR, Einkauf KB, Lian X, Bone B, Bonheur N, Chun TW, Rosenberg ES, Walker BD, Yu XG, Lichterfeld M. Phenotypic signatures of immune selection in HIV-1 reservoir cells. Nature 2023; 614:309-317. [PMID: 36599977 PMCID: PMC9908552 DOI: 10.1038/s41586-022-05538-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 11/08/2022] [Indexed: 01/06/2023]
Abstract
Human immunodeficiency virus 1 (HIV-1) reservoir cells persist lifelong despite antiretroviral treatment1,2 but may be vulnerable to host immune responses that could be exploited in strategies to cure HIV-1. Here we used a single-cell, next-generation sequencing approach for the direct ex vivo phenotypic profiling of individual HIV-1-infected memory CD4+ T cells from peripheral blood and lymph nodes of people living with HIV-1 and receiving antiretroviral treatment for approximately 10 years. We demonstrate that in peripheral blood, cells harbouring genome-intact proviruses and large clones of virally infected cells frequently express ensemble signatures of surface markers conferring increased resistance to immune-mediated killing by cytotoxic T and natural killer cells, paired with elevated levels of expression of immune checkpoint markers likely to limit proviral gene transcription; this phenotypic profile might reduce HIV-1 reservoir cell exposure to and killing by cellular host immune responses. Viral reservoir cells harbouring intact HIV-1 from lymph nodes exhibited a phenotypic signature primarily characterized by upregulation of surface markers promoting cell survival, including CD44, CD28, CD127 and the IL-21 receptor. Together, these results suggest compartmentalized phenotypic signatures of immune selection in HIV-1 reservoir cells, implying that only small subsets of infected cells with optimal adaptation to their anatomical immune microenvironment are able to survive during long-term antiretroviral treatment. The identification of phenotypic markers distinguishing viral reservoir cells may inform future approaches for strategies to cure and eradicate HIV-1.
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Affiliation(s)
- Weiwei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Kevin B Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Benjamin Bone
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Tae-Wook Chun
- National Institute of Allergies and Infectious Diseases, Bethesda, MD, USA
| | - Eric S Rosenberg
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Medical Engineering and Sciences and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
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11
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Barnes CO, Schoofs T, Gnanapragasam PN, Golijanin J, Huey-Tubman KE, Gruell H, Schommers P, Suh-Toma N, Lee YE, Cetrulo Lorenzi JC, Piechocka-Trocha A, Scheid JF, West AP, Walker BD, Seaman MS, Klein F, Nussenzweig MC, Bjorkman PJ. A naturally arising broad and potent CD4-binding site antibody with low somatic mutation. Sci Adv 2022; 8:eabp8155. [PMID: 35960796 PMCID: PMC9374330 DOI: 10.1126/sciadv.abp8155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 06/29/2022] [Indexed: 05/05/2023]
Abstract
The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, including insertions and deletions, which make their induction challenging. VRC01-class bNAbs not only exhibit extraordinary breadth and potency but also rank among the most highly somatically mutated bNAbs. Here, we describe a VRC01-class antibody isolated from a viremic controller, BG24, that is much less mutated than most relatives of its class while achieving comparable breadth and potency. A 3.8-Å x-ray crystal structure of a BG24-BG505 Env trimer complex revealed conserved contacts at the gp120 interface characteristic of the VRC01-class Abs, despite lacking common CDR3 sequence motifs. The existence of moderately mutated CD4-binding site (CD4bs) bNAbs such as BG24 provides a simpler blueprint for CD4bs antibody induction by a vaccine, raising the prospect that such an induction might be feasible with a germline-targeting approach.
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Affiliation(s)
- Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Till Schoofs
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
| | | | - Jovana Golijanin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Kathryn E. Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nina Suh-Toma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yu Erica Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
| | - Johannes F. Scheid
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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12
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Baiyegunhi OO, Mann J, Khaba T, Nkosi T, Mbatha A, Ogunshola F, Chasara C, Ismail N, Ngubane T, Jajbhay I, Pansegrouw J, Dong KL, Walker BD, Ndung'u T, Ndhlovu ZM. CD8 lymphocytes mitigate HIV-1 persistence in lymph node follicular helper T cells during hyperacute-treated infection. Nat Commun 2022; 13:4041. [PMID: 35831418 PMCID: PMC9279299 DOI: 10.1038/s41467-022-31692-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 11/08/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
HIV persistence in tissue sites despite ART is a major barrier to HIV cure. Detailed studies of HIV-infected cells and immune responses in native lymph node tissue environment is critical for gaining insight into immune mechanisms impacting HIV persistence and clearance in tissue sanctuary sites. We compared HIV persistence and HIV-specific T cell responses in lymph node biopsies obtained from 14 individuals who initiated therapy in Fiebig stages I/II, 5 persons treated in Fiebig stages III-V and 17 late treated individuals who initiated ART in Fiebig VI and beyond. Using multicolor immunofluorescence staining and in situ hybridization, we detect HIV RNA and/or protein in 12 of 14 Fiebig I/II treated persons on suppressive therapy for 1 to 55 months, and in late treated persons with persistent antigens. CXCR3+ T follicular helper cells harbor the greatest amounts of gag mRNA transcripts. Notably, HIV-specific CD8+ T cells responses are associated with lower HIV antigen burden, suggesting that these responses may contribute to HIV suppression in lymph nodes during therapy. These results reveal HIV persistence despite the initiation of ART in hyperacute infection and highlight the contribution of virus-specific responses to HIV suppression in tissue sanctuaries during suppressive ART.
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Affiliation(s)
- Omolara O Baiyegunhi
- Africa Health Research Institute (AHRI), Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Jaclyn Mann
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Trevor Khaba
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thandeka Nkosi
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Anele Mbatha
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Funsho Ogunshola
- Africa Health Research Institute (AHRI), Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA
| | | | - Nasreen Ismail
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Thandekile Ngubane
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Krista L Dong
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA
| | - Bruce D Walker
- Africa Health Research Institute (AHRI), Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA
- Institute for Medical Sciences and Engineering and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Thumbi Ndung'u
- Africa Health Research Institute (AHRI), Durban, South Africa
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA
- Max Planck Institute for Infection Biology, Berlin, Germany
- Division of Infection and Immunity, University College London, London, UK
| | - Zaza M Ndhlovu
- Africa Health Research Institute (AHRI), Durban, South Africa.
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, USA.
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13
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Gaebler C, Nogueira L, Stoffel E, Oliveira TY, Breton G, Millard KG, Turroja M, Butler A, Ramos V, Seaman MS, Reeves JD, Petroupoulos CJ, Shimeliovich I, Gazumyan A, Jiang CS, Jilg N, Scheid JF, Gandhi R, Walker BD, Sneller MC, Fauci A, Chun TW, Caskey M, Nussenzweig MC. Prolonged viral suppression with anti-HIV-1 antibody therapy. Nature 2022; 606:368-374. [PMID: 35418681 PMCID: PMC9177424 DOI: 10.1038/s41586-022-04597-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [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: 11/14/2021] [Accepted: 02/28/2022] [Indexed: 01/26/2023]
Abstract
HIV-1 infection remains a public health problem with no cure. Anti-retroviral therapy (ART) is effective but requires lifelong drug administration owing to a stable reservoir of latent proviruses integrated into the genome of CD4+ T cells1. Immunotherapy with anti-HIV-1 antibodies has the potential to suppress infection and increase the rate of clearance of infected cells2,3. Here we report on a clinical study in which people living with HIV received seven doses of a combination of two broadly neutralizing antibodies over 20 weeks in the presence or absence of ART. Without pre-screening for antibody sensitivity, 76% (13 out of 17) of the volunteers maintained virologic suppression for at least 20 weeks off ART. Post hoc sensitivity analyses were not predictive of the time to viral rebound. Individuals in whom virus remained suppressed for more than 20 weeks showed rebound viraemia after one of the antibodies reached serum concentrations below 10 µg ml-1. Two of the individuals who received all seven antibody doses maintained suppression after one year. Reservoir analysis performed after six months of antibody therapy revealed changes in the size and composition of the intact proviral reservoir. By contrast, there was no measurable decrease in the defective reservoir in the same individuals. These data suggest that antibody administration affects the HIV-1 reservoir, but additional larger and longer studies will be required to define the precise effect of antibody immunotherapy on the reservoir.
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Affiliation(s)
- Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Elina Stoffel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
- Columbia University Irving Medical Center, New York, NY, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Gaëlle Breton
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Allison Butler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | | | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Caroline S Jiang
- Center for Clinical and Translational Science, The Rockefeller University, New York, NY, USA
| | - Nikolaus Jilg
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Johannes F Scheid
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Rajesh Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Michael C Sneller
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Anthony Fauci
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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14
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Kaneko N, Boucau J, Kuo HH, Perugino C, Mahajan VS, Farmer JR, Liu H, Diefenbach TJ, Piechocka-Trocha A, Lefteri K, Waring MT, Premo KR, Walker BD, Li JZ, Gaiha G, Yu XG, Lichterfeld M, Padera RF, Pillai S. Temporal changes in T cell subsets and expansion of cytotoxic CD4+ T cells in the lungs in severe COVID-19. Clin Immunol 2022; 237:108991. [PMID: 35364330 PMCID: PMC8961941 DOI: 10.1016/j.clim.2022.108991] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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: 03/15/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023]
Abstract
Many studies have been performed in severe COVID-19 on immune cells in the circulation and on cells obtained by bronchoalveolar lavage. Most studies have tended to provide relative information rather than a quantitative view, and it is a combination of approaches by various groups that is helping the field build a picture of the mechanisms that drive severe lung disease. Approaches employed to date have not revealed information on lung parenchymal T cell subsets in severe COVID-19. Therefore, we sought to examine early and late T cell subset alterations in the lungs and draining lymph nodes in severe COVID-19 using a rapid autopsy protocol and quantitative imaging approaches. Here, we have established that cytotoxic CD4+ T cells (CD4 + CTLs) increase in the lungs, draining lymph nodes and blood as COVID-19 progresses. CD4 + CTLs are prominently expanded in the lung parenchyma in severe COVID-19. In contrast CD8+ T cells are not prominent, exhibit increased PD-1 expression, and no obvious increase is seen in the number of Granzyme B+ CD8+ T cells in the lung parenchyma in severe COVID-19. Based on quantitative evidence for re-activation in the lung milieu, CD4 + CTLs may be as likely to drive viral clearance as CD8+ T cells and may also be contributors to lung inflammation and eventually to fibrosis in severe COVID-19.
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Affiliation(s)
- Naoki Kaneko
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hsiao-Hsuan Kuo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Cory Perugino
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Rheumatology Allergy and Immunology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vinay S Mahajan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jocelyn R Farmer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Rheumatology Allergy and Immunology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hang Liu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Kristina Lefteri
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Michael T Waring
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA; Department of Biology and Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan Z Li
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Gaurav Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Robert F Padera
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Shiv Pillai
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
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15
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Naranbhai V, Nathan A, Kaseke C, Berrios C, Khatri A, Choi S, Getz MA, Tano-Menka R, Ofoman O, Gayton A, Senjobe F, Zhao Z, St Denis KJ, Lam EC, Carrington M, Garcia-Beltran WF, Balazs AB, Walker BD, Iafrate AJ, Gaiha GD. T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals. Cell 2022; 185:1259. [PMID: 35364034 PMCID: PMC8969090 DOI: 10.1016/j.cell.2022.03.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Naranbhai V, Nathan A, Kaseke C, Berrios C, Khatri A, Choi S, Getz MA, Tano-Menka R, Ofoman O, Gayton A, Senjobe F, Zhao Z, St Denis KJ, Lam EC, Carrington M, Garcia-Beltran WF, Balazs AB, Walker BD, Iafrate AJ, Gaiha GD. T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals. Cell 2022; 185:1041-1051.e6. [PMID: 35202566 PMCID: PMC8810349 DOI: 10.1016/j.cell.2022.01.029] [Citation(s) in RCA: 160] [Impact Index Per Article: 80.0] [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: 01/04/2022] [Revised: 01/04/2022] [Accepted: 01/28/2022] [Indexed: 01/11/2023]
Abstract
The SARS-CoV-2 Omicron variant (B.1.1.529) contains mutations that mediate escape from antibody responses, although the extent to which these substitutions in spike and non-spike proteins affect T cell recognition is unknown. In this study, we show that T cell responses in individuals with prior infection, vaccination, both prior infection and vaccination, and boosted vaccination are largely preserved to Omicron spike and non-spike proteins. However, we also identify a subset of individuals (∼21%) with a >50% reduction in T cell reactivity to the Omicron spike. Evaluation of functional CD4+ and CD8+ memory T cell responses confirmed these findings and revealed that reduced recognition to Omicron spike is primarily observed within the CD8+ T cell compartment potentially due to escape from HLA binding. Booster vaccination enhanced T cell responses to Omicron spike. In contrast to neutralizing immunity, these findings suggest preservation of T cell responses to the Omicron variant, although with reduced reactivity in some individuals.
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Affiliation(s)
- Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa.
| | - Anusha Nathan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Program in Health Sciences & Technology, Harvard Medical School, Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Cristhian Berrios
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ashok Khatri
- Massachusetts General Hospital Endocrine Division and Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Shawn Choi
- Massachusetts General Hospital Endocrine Division and Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Matthew A Getz
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Rhoda Tano-Menka
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Onosereme Ofoman
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alton Gayton
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Fernando Senjobe
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Zezhou Zhao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Program in Health Sciences & Technology, Harvard Medical School, Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Kerri J St Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Evan C Lam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Wilfredo F Garcia-Beltran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Bruce D Walker
- Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; The Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Institute for Medical Engineering and Science, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.
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17
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Silverstein NJ, Wang Y, Manickas-Hill Z, Carbone C, Dauphin A, Boribong BP, Loiselle M, Davis J, Leonard MM, Kuri-Cervantes L, Meyer NJ, Betts MR, Li JZ, Walker BD, Yu XG, Yonker LM, Luban J. Innate lymphoid cells and COVID-19 severity in SARS-CoV-2 infection. eLife 2022; 11:e74681. [PMID: 35275061 PMCID: PMC9038195 DOI: 10.7554/elife.74681] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [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: 10/14/2021] [Accepted: 03/11/2022] [Indexed: 11/21/2022] Open
Abstract
Background Risk of severe COVID-19 increases with age, is greater in males, and is associated with lymphopenia, but not with higher burden of SARS-CoV-2. It is unknown whether effects of age and sex on abundance of specific lymphoid subsets explain these correlations. Methods Multiple regression was used to determine the relationship between abundance of specific blood lymphoid cell types, age, sex, requirement for hospitalization, duration of hospitalization, and elevation of blood markers of systemic inflammation, in adults hospitalized for severe COVID-19 (n = 40), treated for COVID-19 as outpatients (n = 51), and in uninfected controls (n = 86), as well as in children with COVID-19 (n = 19), recovering from COVID-19 (n = 14), MIS-C (n = 11), recovering from MIS-C (n = 7), and pediatric controls (n = 17). Results This observational study found that the abundance of innate lymphoid cells (ILCs) decreases more than 7-fold over the human lifespan - T cell subsets decrease less than 2-fold - and is lower in males than in females. After accounting for effects of age and sex, ILCs, but not T cells, were lower in adults hospitalized with COVID-19, independent of lymphopenia. Among SARS-CoV-2-infected adults, the abundance of ILCs, but not of T cells, correlated inversely with odds and duration of hospitalization, and with severity of inflammation. ILCs were also uniquely decreased in pediatric COVID-19 and the numbers of these cells did not recover during follow-up. In contrast, children with MIS-C had depletion of both ILCs and T cells, and both cell types increased during follow-up. In both pediatric COVID-19 and MIS-C, ILC abundance correlated inversely with inflammation. Blood ILC mRNA and phenotype tracked closely with ILCs from lung. Importantly, blood ILCs produced amphiregulin, a protein implicated in disease tolerance and tissue homeostasis. Among controls, the percentage of ILCs that produced amphiregulin was higher in females than in males, and people hospitalized with COVID-19 had a lower percentage of ILCs that produced amphiregulin than did controls. Conclusions These results suggest that, by promoting disease tolerance, homeostatic ILCs decrease morbidity and mortality associated with SARS-CoV-2 infection, and that lower ILC abundance contributes to increased COVID-19 severity with age and in males. Funding This work was supported in part by the Massachusetts Consortium for Pathogen Readiness and NIH grants R37AI147868, R01AI148784, F30HD100110, 5K08HL143183.
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Affiliation(s)
- Noah J Silverstein
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
- Medical Scientist Training Program, University of Massachusetts Medical SchoolWorcesterUnited States
- Massachusetts Consortium on Pathogen ReadinessBostonUnited States
| | - Yetao Wang
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
- Massachusetts Consortium on Pathogen ReadinessBostonUnited States
| | - Zachary Manickas-Hill
- Massachusetts Consortium on Pathogen ReadinessBostonUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | - Claudia Carbone
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Brittany P Boribong
- Massachusetts General Hospital, Mucosal Immunology and Biology Research CenterBostonUnited States
- Massachusetts General Hospital, Department of PediatricsBostonUnited States
- Harvard Medical SchoolBostonUnited States
| | - Maggie Loiselle
- Massachusetts General Hospital, Mucosal Immunology and Biology Research CenterBostonUnited States
| | - Jameson Davis
- Massachusetts General Hospital, Mucosal Immunology and Biology Research CenterBostonUnited States
| | - Maureen M Leonard
- Massachusetts General Hospital, Mucosal Immunology and Biology Research CenterBostonUnited States
- Massachusetts General Hospital, Department of PediatricsBostonUnited States
- Harvard Medical SchoolBostonUnited States
| | - Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Institute for Immunology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Nuala J Meyer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
- Institute for Immunology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Jonathan Z Li
- Massachusetts Consortium on Pathogen ReadinessBostonUnited States
- Department of Medicine, Brigham and Women’s HospitalBostonUnited States
| | - Bruce D Walker
- Massachusetts Consortium on Pathogen ReadinessBostonUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
- Department of Biology and Institute of Medical Engineering and Science, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Xu G Yu
- Massachusetts Consortium on Pathogen ReadinessBostonUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Medicine, Brigham and Women’s HospitalBostonUnited States
| | - Lael M Yonker
- Massachusetts General Hospital, Mucosal Immunology and Biology Research CenterBostonUnited States
- Massachusetts General Hospital, Department of PediatricsBostonUnited States
- Harvard Medical SchoolBostonUnited States
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
- Massachusetts Consortium on Pathogen ReadinessBostonUnited States
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical SchoolWorcesterUnited States
- Broad Institute of Harvard and MITCambridgeUnited States
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18
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Lorin V, Fernández I, Masse-Ranson G, Bouvin-Pley M, Molinos-Albert LM, Planchais C, Hieu T, Péhau-Arnaudet G, Hrebík D, Girelli-Zubani G, Fiquet O, Guivel-Benhassine F, Sanders RW, Walker BD, Schwartz O, Scheid JF, Dimitrov JD, Plevka P, Braibant M, Seaman MS, Bontems F, Di Santo JP, Rey FA, Mouquet H. Epitope convergence of broadly HIV-1 neutralizing IgA and IgG antibody lineages in a viremic controller. J Exp Med 2022; 219:213042. [PMID: 35230385 PMCID: PMC8932546 DOI: 10.1084/jem.20212045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 10/01/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
Decrypting the B cell ontogeny of HIV-1 broadly neutralizing antibodies (bNAbs) is paramount for vaccine design. Here, we characterized IgA and IgG bNAbs of three distinct B cell lineages in a viremic controller, two of which comprised only IgG+ or IgA+ blood memory B cells; the third combined both IgG and IgA clonal variants. 7-269 bNAb in the IgA-only lineage displayed the highest neutralizing capacity despite limited somatic mutation, and delayed viral rebound in humanized mice. bNAbs in all three lineages targeted the N332 glycan supersite. The 2.8-Å resolution cryo-EM structure of 7-269-BG505 SOSIP.664 complex showed a similar pose as 2G12, on an epitope mainly composed of sugar residues comprising the N332 and N295 glycans. Binding and cryo-EM structural analyses showed that antibodies from the two other lineages interact mostly with glycans N332 and N386. Hence, multiple B cell lineages of IgG and IgA bNAbs focused on a unique HIV-1 site of vulnerability can codevelop in HIV-1 viremic controllers.
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Affiliation(s)
- Valérie Lorin
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Ignacio Fernández
- Structural Virology Unit, Department of Virology, Institut Pasteur, Paris, France.,Centre national de la recherche scientifique URA3015, Paris, France
| | - Guillemette Masse-Ranson
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Mélanie Bouvin-Pley
- Université de Tours, Institut national de la santé et de la recherche médicale U1259, Tours, France
| | - Luis M Molinos-Albert
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France
| | - Cyril Planchais
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France
| | - Thierry Hieu
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France
| | - Gérard Péhau-Arnaudet
- Imagopole, Plate-Forme de Microscopie Ultrastructurale and UMR 3528, Institut Pasteur, Paris, France
| | - Dominik Hrebík
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Giulia Girelli-Zubani
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Oriane Fiquet
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Florence Guivel-Benhassine
- Centre national de la recherche scientifique URA3015, Paris, France.,Virus and Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam Infection and Immunity Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.,Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA.,Partners AIDS Research Center, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA
| | - Olivier Schwartz
- Centre national de la recherche scientifique URA3015, Paris, France.,Virus and Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Johannes F Scheid
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Jordan D Dimitrov
- Centre de Recherche des Cordeliers, Institut national de la santé et de la recherche médicale, Sorbonne Université, Université de Paris, Paris, France
| | - Pavel Plevka
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Martine Braibant
- Université de Tours, Institut national de la santé et de la recherche médicale U1259, Tours, France
| | | | - François Bontems
- Structural Virology Unit, Department of Virology, Institut Pasteur, Paris, France.,Institut de Chimie des Substances Naturelles, Centre national de la recherche scientifique, Université Paris Saclay, Gif-sur-Yvette, France
| | - James P Di Santo
- Innate Immunity Unit, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1223, Paris, France
| | - Félix A Rey
- Structural Virology Unit, Department of Virology, Institut Pasteur, Paris, France.,Centre national de la recherche scientifique URA3015, Paris, France
| | - Hugo Mouquet
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, Paris, France.,Institut national de la santé et de la recherche médicale U1222, Paris, France
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19
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Zhang A, Piechocka-Trocha A, Li X, Walker BD. A Leucine Zipper Dimerization Strategy to Generate Soluble T Cell Receptors Using the Escherichia coli Expression System. Cells 2022; 11:cells11030312. [PMID: 35159122 PMCID: PMC8834513 DOI: 10.3390/cells11030312] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 12/10/2022] Open
Abstract
T cell-mediated adaptive immunity plays a key role in immunological surveillance and host control of infectious diseases. A better understanding of T cell receptor (TCR) recognition of pathogen-derived epitopes or cancer-associated neoantigens is the basis for developing T cell-based vaccines and immunotherapies. Studies on the interaction between soluble TCR α:β heterodimers and peptide-bound major histocompatibility complexes (pMHCs) inform underlying mechanisms driving TCR recognition, but not every isolated TCR can be prepared in soluble form for structural and functional studies using conventional methods. Here, taking a challenging HIV-specific TCR as a model, we designed a general leucine zipper (LZ) dimerization strategy for soluble TCR preparation using the Escherichia coli expression system. We report details of TCR construction, inclusion body expression and purification, and protein refolding and purification. Measurements of binding affinity between the TCR and its specific pMHC using surface plasmon resonance (SPR) verify its activity. We conclude that this is a feasible approach to produce challenging TCRs in soluble form, needed for studies related to T cell recognition.
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Affiliation(s)
- Angela Zhang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Xiaolong Li
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Correspondence: (X.L.); (B.D.W.)
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Institute for Medical Engineering and Science (IMES) and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Correspondence: (X.L.); (B.D.W.)
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20
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Naranbhai V, Nathan A, Kaseke C, Berrios C, Khatri A, Choi S, Getz MA, Tano-Menka R, Ofoman O, Gayton A, Senjobe F, Denis KJS, Lam EC, Garcia-Beltran WF, Balazs AB, Walker BD, Iafrate AJ, Gaiha GD. T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all prior infected and vaccinated individuals. medRxiv 2022:2022.01.04.21268586. [PMID: 35018386 PMCID: PMC8750712 DOI: 10.1101/2022.01.04.21268586] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The SARS-CoV-2 Omicron variant (B.1.1.529) contains mutations that mediate escape from infection and vaccine-induced antibody responses, although the extent to which these substitutions in spike and non-spike proteins affect T cell recognition is unknown. Here we show that T cell responses in individuals with prior infection, vaccination, both prior infection and vaccination, and boosted vaccination are largely preserved to Omicron spike and non-spike proteins. However, we also identify a subset of individuals (∼21%) with a >50% reduction in T cell reactivity to the Omicron spike. Evaluation of functional CD4 + and CD8 + memory T cell responses confirmed these findings and reveal that reduced recognition to Omicron spike is primarily observed within the CD8 + T cell compartment. Booster vaccination substantially enhanced T cell responses to Omicron spike. In contrast to neutralizing immunity, these findings suggest preservation of T cell responses to the Omicron variant, although with reduced reactivity in some individuals.
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21
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Turk G, Seiger K, Lian X, Sun W, Parsons EM, Gao C, Rassadkina Y, Polo ML, Czernikier A, Ghiglione Y, Vellicce A, Varriale J, Lai J, Yuki Y, Martin M, Rhodes A, Lewin SR, Walker BD, Carrington M, Siliciano R, Siliciano J, Lichterfeld M, Laufer N, Yu XG. A Possible Sterilizing Cure of HIV-1 Infection Without Stem Cell Transplantation. Ann Intern Med 2022; 175:95-100. [PMID: 34781719 PMCID: PMC9215120 DOI: 10.7326/l21-0297] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND A sterilizing cure of HIV-1 infection has been reported in 2 persons living with HIV-1 who underwent allogeneic hematopoietic stem cell transplantations from donors who were homozygous for the CCR5Δ32 gene polymorphism. However, this has been considered elusive during natural infection. OBJECTIVE To evaluate persistent HIV-1 reservoir cells in an elite controller with undetectable HIV-1 viremia for more than 8 years in the absence of antiretroviral therapy. DESIGN Detailed investigation of virologic and immunologic characteristics. SETTING Tertiary care centers in Buenos Aires, Argentina, and Boston, Massachusetts. PATIENT A patient with HIV-1 infection and durable drug-free suppression of HIV-1 replication. MEASUREMENTS Analysis of genome-intact and replication-competent HIV-1 using near-full-length individual proviral sequencing and viral outgrowth assays, respectively; analysis of HIV-1 plasma RNA by ultrasensitive HIV-1 viral load testing. RESULTS No genome-intact HIV-1 proviruses were detected in analysis of a total of 1.188 billion peripheral blood mononuclear cells and 503 million mononuclear cells from placental tissues. Seven defective proviruses, some of them derived from clonally expanded cells, were detected. A viral outgrowth assay failed to retrieve replication-competent HIV-1 from 150 million resting CD4+ T cells. No HIV-1 RNA was detected in 4.5 mL of plasma. LIMITATIONS Absence of evidence for intact HIV-1 proviruses in large numbers of cells is not evidence of absence of intact HIV-1 proviruses. A sterilizing cure of HIV-1 can never be empirically proved. CONCLUSION Genome-intact and replication-competent HIV-1 were not detected in an elite controller despite analysis of massive numbers of cells from blood and tissues, suggesting that this patient may have naturally achieved a sterilizing cure of HIV-1 infection. These observations raise the possibility that a sterilizing cure may be an extremely rare but possible outcome of HIV-1 infection. PRIMARY FUNDING SOURCE National Institutes of Health and Bill & Melinda Gates Foundation.
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Affiliation(s)
- Gabriela Turk
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET - Universidad de Buenos Aires, and Facultad de Medicina, Departamento de Microbiología, Parasitología e Inmunología, Universidad de Buenos Aires, Buenos Aires, Argentina (G.T., N.L.)
| | - Kyra Seiger
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, and Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts (K.S., X.L., W.S., E.M.P., C.G., M.L., X.G.Y.)
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, and Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts (K.S., X.L., W.S., E.M.P., C.G., M.L., X.G.Y.)
| | - Weiwei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, and Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts (K.S., X.L., W.S., E.M.P., C.G., M.L., X.G.Y.)
| | - Elizabeth M Parsons
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, and Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts (K.S., X.L., W.S., E.M.P., C.G., M.L., X.G.Y.)
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, and Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts (K.S., X.L., W.S., E.M.P., C.G., M.L., X.G.Y.)
| | | | - Maria Laura Polo
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET - Universidad de Buenos Aires, and Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina (M.L.P., A.C., Y.G.)
| | - Alejandro Czernikier
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET - Universidad de Buenos Aires, and Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina (M.L.P., A.C., Y.G.)
| | - Yanina Ghiglione
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET - Universidad de Buenos Aires, and Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina (M.L.P., A.C., Y.G.)
| | - Alejandra Vellicce
- Department of Hematology, Hospital de Clínicas José de San Martín, Universidad de Buenos Aires, Buenos Aires, Argentina (A.V.)
| | - Joseph Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland (J.V., J.L., R.S., J.S.)
| | - Jun Lai
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland (J.V., J.L., R.S., J.S.)
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland (Y.Y., M.M.)
| | - Maureen Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland (Y.Y., M.M.)
| | - Ajantha Rhodes
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia (A.R.)
| | - Sharon R Lewin
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, and Department of Infectious Diseases, Alfred Health and Monash University, Melbourne, Victoria, Australia (S.R.L.)
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts (Y.R., B.D.W.)
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland (M.C.)
| | - Robert Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland (J.V., J.L., R.S., J.S.)
| | - Janet Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland (J.V., J.L., R.S., J.S.)
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, and Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts (K.S., X.L., W.S., E.M.P., C.G., M.L., X.G.Y.)
| | - Natalia Laufer
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), CONICET - Universidad de Buenos Aires, and Facultad de Medicina, Departamento de Microbiología, Parasitología e Inmunología, Universidad de Buenos Aires, Buenos Aires, Argentina (G.T., N.L.)
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, and Infectious Disease Division, Brigham and Women's Hospital, Boston, Massachusetts (K.S., X.L., W.S., E.M.P., C.G., M.L., X.G.Y.)
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22
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Lian X, Gao C, Sun X, Jiang C, Einkauf KB, Seiger KW, Chevalier JM, Yuki Y, Martin M, Hoh R, Peluso MJ, Carrington M, Ruiz-Mateos E, Deeks SG, Rosenberg ES, Walker BD, Lichterfeld M, Yu XG. Signatures of immune selection in intact and defective proviruses distinguish HIV-1 elite controllers. Sci Transl Med 2021; 13:eabl4097. [PMID: 34910552 DOI: 10.1126/scitranslmed.abl4097] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Chenyang Jiang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kevin B Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kyra W Seiger
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Joshua M Chevalier
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Maureen Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Rebecca Hoh
- University of California at San Francisco, San Francisco, CA 94143, USA
| | - Michael J Peluso
- University of California at San Francisco, San Francisco, CA 94143, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ezequiel Ruiz-Mateos
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, Seville 41013, Spain
| | - Steven G Deeks
- University of California at San Francisco, San Francisco, CA 94143, USA
| | - Eric S Rosenberg
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Institute for Medical Engineering and Sciences and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA
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23
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Vieira VA, Adland E, Malone DFG, Martin MP, Groll A, Ansari MA, Garcia-Guerrero MC, Puertas MC, Muenchhoff M, Guash CF, Brander C, Martinez-Picado J, Bamford A, Tudor-Williams G, Ndung’u T, Walker BD, Ramsuran V, Frater J, Jooste P, Peppa D, Carrington M, Goulder PJR. An HLA-I signature favouring KIR-educated Natural Killer cells mediates immune control of HIV in children and contrasts with the HLA-B-restricted CD8+ T-cell-mediated immune control in adults. PLoS Pathog 2021; 17:e1010090. [PMID: 34793581 PMCID: PMC8639058 DOI: 10.1371/journal.ppat.1010090] [Citation(s) in RCA: 11] [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: 08/31/2021] [Revised: 12/02/2021] [Accepted: 11/04/2021] [Indexed: 12/30/2022] Open
Abstract
Natural Killer (NK) cells contribute to HIV control in adults, but HLA-B-mediated T-cell activity has a more substantial impact on disease outcome. However, the HLA-B molecules influencing immune control in adults have less impact on paediatric infection. To investigate the contribution NK cells make to immune control, we studied >300 children living with HIV followed over two decades in South Africa. In children, HLA-B alleles associated with adult protection or disease-susceptibility did not have significant effects, whereas Bw4 (p = 0.003) and low HLA-A expression (p = 0.002) alleles were strongly associated with immunological and viral control. In a comparator adult cohort, Bw4 and HLA-A expression contributions to HIV disease outcome were dwarfed by those of protective and disease-susceptible HLA-B molecules. We next investigated the immunophenotype and effector functions of NK cells in a subset of these children using flow cytometry. Slow progression and better plasma viraemic control were also associated with high frequencies of less terminally differentiated NKG2A+NKp46+CD56dim NK cells strongly responsive to cytokine stimulation and linked with the immunogenetic signature identified. Future studies are indicated to determine whether this signature associated with immune control in early life directly facilitates functional cure in children. In adults, immune control of HIV is strongly influenced by antiviral CD8+ T-cell responses restricted by ‘protective’ HLA class I molecules, such as HLA-B*57, and by ‘disease-susceptible’ HLA class I molecules such as HLA-B*58:02. By contrast, Natural Killer (NK) cells responses make a smaller, albeit significant, contribution. In this study, we evaluate in children living with HIV the contribution of NK cell responses to immune control of HIV, in an age group where HIV-specific CD8+ T-cell responses have less impact on disease outcome. A cohort of >300 therapy-naïve children living with HIV shows that a genetic signature favouring a KIR-education on NK cells is associated with slow progression and better viraemic control. Consistent with this, we observed control of HIV viraemia and lower total HIV DNA levels among children was associated with a less differentiated NKG2A+NKp46+ CD56dim NK cell population that functionally was highly responsive to cytokine stimulation. Thus, the study identifies a signature that can impact future therapeutic strategies to achieve remission in children.
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Affiliation(s)
- Vinicius A. Vieira
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Emily Adland
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | | | - Maureen P. Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Andreas Groll
- Department of Statistics, TU Dortmund University, Dortmund, Germany
| | - M. Azim Ansari
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Mari C. Puertas
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBER en Enfermedades Infecciosas, Madrid, Spain
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Claudia Fortuny Guash
- Infectious Diseases and Systemic Inflammatory Response in Pediatrics, Infectious Diseases Unit, Department of Pediatrics, Sant Joan de Déu Hospital Research Foundation, Barcelona, Spain
- Center for Biomedical Network Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Pediatrics, University of Barcelona, Barcelona, Spain
- Translational Research Network in Pediatric Infectious Diseases (RITIP), Madrid, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBER en Enfermedades Infecciosas, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBER en Enfermedades Infecciosas, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Alasdair Bamford
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | | | - Thumbi Ndung’u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute (AHRI), Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
- Max Planck Institute for Infection Biology, Chariteplatz, Berlin, Germany
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Bruce D. Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute (AHRI), Durban, South Africa
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - John Frater
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, Oxford, United Kingdom
| | - Pieter Jooste
- Department of Paediatrics, Kimberley Hospital, Kimberley, South Africa
| | - Dimitra Peppa
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD and Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Philip J. R. Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- * E-mail:
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24
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Collins DR, Urbach JM, Racenet ZJ, Arshad U, Power KA, Newman RM, Mylvaganam GH, Ly NL, Lian X, Rull A, Rassadkina Y, Yanez AG, Peluso MJ, Deeks SG, Vidal F, Lichterfeld M, Yu XG, Gaiha GD, Allen TM, Walker BD. Functional impairment of HIV-specific CD8 + T cells precedes aborted spontaneous control of viremia. Immunity 2021; 54:2372-2384.e7. [PMID: 34496223 PMCID: PMC8516715 DOI: 10.1016/j.immuni.2021.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 04/20/2021] [Revised: 06/21/2021] [Accepted: 08/09/2021] [Indexed: 12/14/2022]
Abstract
Spontaneous control of HIV infection has been repeatedly linked to antiviral CD8+ T cells but is not always permanent. To address mechanisms of durable and aborted control of viremia, we evaluated immunologic and virologic parameters longitudinally among 34 HIV-infected subjects with differential outcomes. Despite sustained recognition of autologous virus, HIV-specific proliferative and cytolytic T cell effector functions became selectively and intrinsically impaired prior to aborted control. Longitudinal transcriptomic profiling of functionally impaired HIV-specific CD8+ T cells revealed altered expression of genes related to activation, cytokine-mediated signaling, and cell cycle regulation, including increased expression of the antiproliferative transcription factor KLF2 but not of genes associated with canonical exhaustion. Lymphoid HIV-specific CD8+ T cells also exhibited poor functionality during aborted control relative to durable control. Our results identify selective functional impairment of HIV-specific CD8+ T cells as prognostic of impending aborted HIV control, with implications for clinical monitoring and immunotherapeutic strategies.
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Affiliation(s)
- David R Collins
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | - Umar Arshad
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Karen A Power
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Ruchi M Newman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Geetha H Mylvaganam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Ngoc L Ly
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Anna Rull
- Joan XXIII University Hospital, Pere Virgili Institute (IISPV), Rovira i Virgili University, Tarragona, Spain
| | - Yelizaveta Rassadkina
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Adrienne G Yanez
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, CA, USA
| | - Francesc Vidal
- Joan XXIII University Hospital, Pere Virgili Institute (IISPV), Rovira i Virgili University, Tarragona, Spain
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Todd M Allen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Institute for Medical Engineering and Sciences and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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25
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Kaseke C, Park RJ, Singh NK, Koundakjian D, Bashirova A, Garcia Beltran WF, Takou Mbah OC, Ma J, Senjobe F, Urbach JM, Nathan A, Rossin EJ, Tano-Menka R, Khatri A, Piechocka-Trocha A, Waring MT, Birnbaum ME, Baker BM, Carrington M, Walker BD, Gaiha GD. HLA class-I-peptide stability mediates CD8 + T cell immunodominance hierarchies and facilitates HLA-associated immune control of HIV. Cell Rep 2021; 36:109378. [PMID: 34260940 PMCID: PMC8293625 DOI: 10.1016/j.celrep.2021.109378] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/24/2021] [Accepted: 06/18/2021] [Indexed: 11/29/2022] Open
Abstract
Defining factors that govern CD8+ T cell immunodominance is critical for the rational design of vaccines for viral pathogens. Here, we assess the contribution of human leukocyte antigen (HLA) class-I-peptide stability for 186 optimal HIV epitopes across 18 HLA alleles using transporter associated with antigen processing (TAP)-deficient mono-allelic HLA-expressing cell lines. We find that immunodominant HIV epitopes increase surface stabilization of HLA class-I molecules in comparison to subdominant epitopes. HLA class-I-peptide stability is also strongly correlated with overall immunodominance hierarchies, particularly for epitopes from high-abundance proteins (e.g., Gag). Moreover, HLA alleles associated with HIV protection are preferentially stabilized by epitopes derived from topologically important viral regions at a greater frequency than neutral and risk alleles. These findings indicate that relative stabilization of HLA class-I is a key factor for CD8+ T cell epitope immunodominance hierarchies, with implications for HIV control and the design of T-cell-based vaccines. TAP-deficient HLA-expressing cells provide rapid assessment of HLA-peptide stability Immunodominant HIV CD8+ T cell epitopes are superior stabilizers of HLA molecules HLA class-I-peptide stability correlates with overall immunodominance hierarchies Protective HLA alleles are preferentially stabilized by highly networked epitopes
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Affiliation(s)
- Clarety Kaseke
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ryan J Park
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Harvard Radiation Oncology Program, Boston, MA 02114, USA
| | - Nishant K Singh
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Wilfredo F Garcia Beltran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Jiaqi Ma
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46556, USA
| | - Fernando Senjobe
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Program in Virology, Harvard Medical School, Boston, MA 02114, USA
| | | | - Anusha Nathan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elizabeth J Rossin
- Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA 02114, USA; The Broad Institute, Cambridge, MA 02142, USA
| | - Rhoda Tano-Menka
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashok Khatri
- Massachusetts General Hospital Endocrine Unit and Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Michael T Waring
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Michael E Birnbaum
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Harper Cancer Research Institute, University of Notre Dame, South Bend, IN 46556, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; The Broad Institute, Cambridge, MA 02142, USA; Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa; Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.
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26
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Nathan A, Rossin EJ, Kaseke C, Park RJ, Khatri A, Koundakjian D, Urbach JM, Singh NK, Bashirova A, Tano-Menka R, Senjobe F, Waring MT, Piechocka-Trocha A, Garcia-Beltran WF, Iafrate AJ, Naranbhai V, Carrington M, Walker BD, Gaiha GD. Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses. Cell 2021; 184:4401-4413.e10. [PMID: 34265281 PMCID: PMC8241654 DOI: 10.1016/j.cell.2021.06.029] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/02/2021] [Accepted: 06/24/2021] [Indexed: 12/05/2022]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that escape convalescent and vaccine-induced antibody responses has renewed focus on the development of broadly protective T-cell-based vaccines. Here, we apply structure-based network analysis and assessments of HLA class I peptide stability to define mutationally constrained CD8+ T cell epitopes across the SARS-CoV-2 proteome. Highly networked residues are conserved temporally among circulating variants and sarbecoviruses and disproportionately impair spike pseudotyped lentivirus infectivity when mutated. Evaluation of HLA class I stabilizing activity for 18 globally prevalent alleles identifies CD8+ T cell epitopes within highly networked regions with limited mutational frequencies in circulating SARS-CoV-2 variants and deep-sequenced primary isolates. Moreover, these epitopes elicit demonstrable CD8+ T cell reactivity in convalescent individuals but reduced recognition in recipients of mRNA-based vaccines. These data thereby elucidate key mutationally constrained regions and immunogenic epitopes in the SARS-CoV-2 proteome for a global T-cell-based vaccine against emerging variants and SARS-like coronaviruses.
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Affiliation(s)
- Anusha Nathan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Elizabeth J Rossin
- The Broad Institute, Cambridge, MA 02142, USA; Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ryan J Park
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Harvard Radiation Oncology Program, Boston, MA 02114, USA
| | - Ashok Khatri
- Massachusetts General Hospital Endocrine Division and Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | | | | | - Nishant K Singh
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA
| | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Rhoda Tano-Menka
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Fernando Senjobe
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael T Waring
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Wilfredo F Garcia-Beltran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, MA 02115, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, MA 02115, USA
| | - Vivek Naranbhai
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; The Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa; Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.
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27
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Abstract
In the evolutionary battle between virus and host, a genetic alteration in cytomegalovirus caused by an inversion-deletion event during tissue culture passage opens an unconventional path toward an HIV vaccine (see the related Research Articles by Malouli et al., Yang et al., and Verweij et al.).
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Affiliation(s)
- Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA 02139, USA.
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28
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McCann CD, van Dorp CH, Danesh A, Ward AR, Dilling TR, Mota TM, Zale E, Stevenson EM, Patel S, Brumme CJ, Dong W, Jones DS, Andresen TL, Walker BD, Brumme ZL, Bollard CM, Perelson AS, Irvine DJ, Jones RB. A participant-derived xenograft model of HIV enables long-term evaluation of autologous immunotherapies. J Exp Med 2021; 218:212105. [PMID: 33988715 PMCID: PMC8129803 DOI: 10.1084/jem.20201908] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 02/15/2021] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
HIV-specific CD8+ T cells partially control viral replication and delay disease progression, but they rarely provide lasting protection, largely due to immune escape. Here, we show that engrafting mice with memory CD4+ T cells from HIV+ donors uniquely allows for the in vivo evaluation of autologous T cell responses while avoiding graft-versus-host disease and the need for human fetal tissues that limit other models. Treating HIV-infected mice with clinically relevant HIV-specific T cell products resulted in substantial reductions in viremia. In vivo activity was significantly enhanced when T cells were engineered with surface-conjugated nanogels carrying an IL-15 superagonist, but it was ultimately limited by the pervasive selection of a diverse array of escape mutations, recapitulating patterns seen in humans. By applying mathematical modeling, we show that the kinetics of the CD8+ T cell response have a profound impact on the emergence and persistence of escape mutations. This “participant-derived xenograft” model of HIV provides a powerful tool for studying HIV-specific immunological responses and facilitating the development of effective cell-based therapies.
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Affiliation(s)
- Chase D McCann
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY.,Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | | | - Ali Danesh
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Adam R Ward
- Department of Microbiology, Immunology & Tropical Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC.,PhD Program in Epidemiology, Milken Institute School of Public Health, The George Washington University, Washington, DC
| | - Thomas R Dilling
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Talia M Mota
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Elizabeth Zale
- Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - Eva M Stevenson
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Shabnum Patel
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC.,George Washington University Cancer Center, George Washington University, Washington, DC
| | - Chanson J Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | - Winnie Dong
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | | | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Boston, MA.,Institute for Medical and Engineering Sciences, Massachusetts Institute of Technology, Cambridge, MA.,Howard Hughes Medical Institute, Chevy Chase, MD
| | - Zabrina L Brumme
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Catherine M Bollard
- Center for Cancer and Immunology Research, Children's National Health System, Washington, DC.,George Washington University Cancer Center, George Washington University, Washington, DC
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM
| | - Darrell J Irvine
- Howard Hughes Medical Institute, Chevy Chase, MD.,Department of Material Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | - R Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, NY.,Immunology & Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY
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Singh R, Ramsuran V, Naranbhai V, Yende-Zuma N, Garrett N, Mlisana K, Dong KL, Walker BD, Abdool Karim SS, Carrington M, Ndung'u T. Epigenetic Regulation of BST-2 Expression Levels and the Effect on HIV-1 Pathogenesis. Front Immunol 2021; 12:669241. [PMID: 34025670 PMCID: PMC8131512 DOI: 10.3389/fimmu.2021.669241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 02/18/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
HIV-1 must overcome host antiviral restriction factors for efficient replication. We hypothesized that elevated levels of bone marrow stromal cell antigen 2 (BST-2), a potent host restriction factor that interferes with HIV-1 particle release in some human cells and is antagonized by the viral protein Vpu, may associate with viral control. Using cryopreserved samples, from HIV-1 seronegative and seropositive Black women, we measured in vitro expression levels of BST-2 mRNA using a real-time PCR assay and protein levels were validated by Western blotting. The expression level of BST-2 showed an association with viral control within two independent cohorts of Black HIV infected females (r=-0.53, p=0.015, [n =21]; and r=-0.62, p=0.0006, [n=28]). DNA methylation was identified as a mechanism regulating BST-2 levels, where increased BST-2 methylation results in lower expression levels and associates with worse HIV disease outcome. We further demonstrate the ability to regulate BST-2 levels using a DNA hypomethylation drug. Our results suggest BST-2 as a factor for potential therapeutic intervention against HIV and other diseases known to involve BST-2.
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Affiliation(s)
- Ravesh Singh
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Vivek Naranbhai
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Koleka Mlisana
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Krista L Dong
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Bruce D Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Mary Carrington
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Max Planck Institute for Infection Biology, Chariteplatz, Berlin, Germany.,Division of Infection and Immunity, University College London, London, United Kingdom
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30
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Hartana CA, Rassadkina Y, Gao C, Martin-Gayo E, Walker BD, Lichterfeld M, Yu XG. Long noncoding RNA MIR4435-2HG enhances metabolic function of myeloid dendritic cells from HIV-1 elite controllers. J Clin Invest 2021; 131:146136. [PMID: 33938445 PMCID: PMC8087208 DOI: 10.1172/jci146136] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 11/16/2020] [Accepted: 03/11/2021] [Indexed: 12/24/2022] Open
Abstract
Restriction of HIV-1 replication in elite controllers (ECs) is frequently attributed to T cell-mediated immune responses, while the specific contribution of innate immune cells is less clear. Here, we demonstrate an upregulation of the host long noncoding RNA (lncRNA) MIR4435-2HG in primary myeloid dendritic cells (mDCs) from ECs. Elevated expression of this lncRNA in mDCs was associated with a distinct immunometabolic profile, characterized by increased oxidative phosphorylation and glycolysis activities in response to TLR3 stimulation. Using functional assays, we show that MIR4435-2HG directly influenced the metabolic state of mDCs, likely through epigenetic mechanisms involving H3K27ac enrichment at an intronic enhancer in the RPTOR gene locus, the main component of the mammalian target of rapamycin complex 1 (mTORC1). Together, these results suggest a role of MIR4435-2HG for enhancing immunometabolic activities of mDCs in ECs through targeted epigenetic modifications of a member of the mTOR signaling pathway.
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Affiliation(s)
| | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Enrique Martin-Gayo
- Immunology Unit, Universidad Autónoma de Madrid, Hospital Universitario la Princesa, Madrid, Spain
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Institute for Medical Engineering and Sciences, and
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
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31
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Kazer SW, Walker BD, Shalek AK. Evolution and Diversity of Immune Responses during Acute HIV Infection. Immunity 2021; 53:908-924. [PMID: 33207216 DOI: 10.1016/j.immuni.2020.10.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [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: 05/28/2020] [Revised: 08/03/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023]
Abstract
Understanding the earliest immune responses following HIV infection is critical to inform future vaccines and therapeutics. Here, we review recent prospective human studies in at-risk populations that have provided insight into immune responses during acute infection, including additional relevant data from non-human primate (NHP) studies. We discuss the timing, nature, and function of the diverse immune responses induced, the onset of immune dysfunction, and the effects of early anti-retroviral therapy administration. Treatment at onset of viremia mitigates peripheral T and B cell dysfunction, limits seroconversion, and enhances cellular antiviral immunity despite persistence of infection in lymphoid tissues. We highlight pertinent areas for future investigation, and how application of high-throughput technologies, alongside targeted NHP studies, may elucidate immune response features to target in novel preventions and cures.
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Affiliation(s)
- Samuel W Kazer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA; HIV Pathogenesis Programme, Nelson R. Mandela School of Medicine, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Alex K Shalek
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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32
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Kaneko N, Boucau J, Kuo HH, Perugino C, Mahajan VS, Farmer JR, Liu H, Diefenbach TJ, Piechocka-Trocha A, Lefteri K, Waring MT, Premo KR, Walker BD, Li JZ, Gaiha G, Yu XG, Lichterfeld M, Padera RF, Pillai S. Expansion of Cytotoxic CD4+ T cells in the lungs in severe COVID-19. medRxiv 2021. [PMID: 33791730 DOI: 10.1101/2021.03.23.21253885] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The contributions of T cells infiltrating the lungs to SARS-CoV-2 clearance and disease progression are poorly understood. Although studies of CD8+ T cells in bronchoalveolar lavage and blood have suggested that these cells are exhausted in severe COVID-19, CD4+ T cells have not been systematically interrogated within the lung parenchyma. We establish here that cytotoxic CD4+ T cells (CD4+CTLs) are prominently expanded in the COVID-19 lung infiltrate. CD4+CTL numbers in the lung increase with disease severity and progression is accompanied by widespread HLA-DR expression on lung epithelial and endothelial cells, increased apoptosis of epithelial cells and tissue remodeling. Based on quantitative evidence for re-activation in the lung milieu, CD4+ CTLs are as likely to drive viral clearance as CD8+ T cells and may also be contributors to lung inflammation and eventually to fibrosis in severe COVID-19. In Brief In severe COVID-19 cytotoxic CD4+ T cells accumulate in draining lymph nodes and in the lungs during the resolving phase of the disease. Re-activated cytotoxic CD4+ T cells and cytotoxic CD8+ T cells are present in roughly equivalent numbers in the lungs at this stage and these cells likely collaborate to eliminate virally infected cells and potentially induce fibrosis. A large fraction of epithelial and endothelial cells in the lung express HLA class II in COVID-19 and there is temporal convergence between CD4+CTL accumulation and apoptosis in the lung. Highlights In severe COVID-19, activated CD4+ CTLs accumulate in the lungs late in diseaseThese cells likely participate in SARS-CoV-2 clearance, collaborating with CD8+ T cells many of which exhibit an exhausted phenotypeT cells likely contribute to the late exacerbation of inflammationCD4+CTLs have been linked to fibrosis in many disorders and could also be responsible for the eventual induction of fibrosis in a subset of COVID-19 patients. Summary The contributions of T cells infiltrating the lungs to SARS-CoV-2 clearance and disease progression are poorly understood. Although studies of CD8+ T cells in bronchoalveolar lavage and blood have suggested that these cells are exhausted in severe COVID-19, CD4+ T cells have not been systematically interrogated within the lung parenchyma. We establish here that cytotoxic CD4+ T cells (CD4+CTLs) are prominently expanded in the COVID-19 lung infiltrate. CD4+CTL numbers in the lung increase with disease severity and progression is accompanied by widespread HLA-DR expression on lung epithelial and endothelial cells, increased apoptosis of epithelial cells and tissue remodeling. Based on quantitative evidence for re-activation in the lung milieu, CD4+ CTLs are as likely to drive viral clearance as CD8+ T cells and may also be contributors to lung inflammation and eventually to fibrosis in severe COVID-19.
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33
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Affiliation(s)
- Bruce D Walker
- From the Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA
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34
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Clayton KL, Mylvaganam G, Villasmil-Ocando A, Stuart H, Maus MV, Rashidian M, Ploegh HL, Walker BD. HIV-infected macrophages resist efficient NK cell-mediated killing while preserving inflammatory cytokine responses. Cell Host Microbe 2021; 29:435-447.e9. [PMID: 33571449 DOI: 10.1016/j.chom.2021.01.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 06/17/2020] [Revised: 10/19/2020] [Accepted: 01/12/2021] [Indexed: 12/30/2022]
Abstract
Natural killer (NK) cells are innate cytolytic effectors that target HIV-infected CD4+ T cells. In conjunction with antibodies recognizing the HIV envelope, NK cells also eliminate HIV-infected targets through antibody-dependent cellular cytotoxicity (ADCC). However, how these NK cell functions impact infected macrophages is less understood. We show that HIV-infected macrophages resist NK cell-mediated killing. Compared with HIV-infected CD4+ T cells, initial innate NK cell interactions with HIV-infected macrophages skew the response toward cytokine production, rather than release of cytolytic contents, causing inefficient elimination of infected macrophages. Studies with chimeric antigen receptor (CAR) T cells demonstrate that the viral envelope is equally accessible on CD4+ T cells and macrophages. Nonetheless, ADCC against macrophages is muted compared with ADCC against CD4+ T cells. Thus, HIV-infected macrophages employ mechanisms to evade immediate cytolytic NK cell function while preserving inflammatory cytokine responses. These findings emphasize the importance of eliminating infected macrophages for HIV cure efforts.
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Affiliation(s)
- Kiera L Clayton
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Geetha Mylvaganam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | | | - Heather Stuart
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Mohammad Rashidian
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Boston Children's Hospital, Boston, MA 02115, USA
| | - Hidde L Ploegh
- Boston Children's Hospital, Boston, MA 02115, USA; Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Massachusetts General Hospital, Boston, MA 02114, USA; Department of Immunology, Harvard Medical School, Boston, MA 02115, USA; Institute of Medical Engineering and Sciences and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA.
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35
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Garcia-Bates TM, Palma ML, Anderko RR, Hsu DC, Ananworanich J, Korber BT, Gaiha GD, Phanuphak N, Thomas R, Tovanabutra S, Walker BD, Mellors JW, Piazza PA, Kroon E, Riddler SA, Michael NL, Rinaldo CR, Mailliard RB. Dendritic cells focus CTL responses toward highly conserved and topologically important HIV-1 epitopes. EBioMedicine 2021; 63:103175. [PMID: 33450518 PMCID: PMC7811131 DOI: 10.1016/j.ebiom.2020.103175] [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: 09/13/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 11/05/2022] Open
Abstract
Background During early HIV-1 infection, immunodominant T cell responses to highly variable epitopes lead to the establishment of immune escape virus variants. Here we assessed a type 1-polarized monocyte-derived dendritic cell (MDC1)-based approach to selectively elicit cytotoxic T lymphocyte (CTL) responses against highly conserved and topologically important HIV-1 epitopes in HIV-1-infected individuals from the Thailand RV254/SEARCH 010 cohort who initiated antiretroviral therapy (ART) during early infection (Fiebig stages I-IV). Methods Autologous MDC1 were used as antigen presenting cells to induce in vitro CTL responses against HIV-1 Gag, Pol, Env, and Nef as determined by flow cytometry and ELISpot assay. Ultra-conserved or topologically important antigens were respectively identified using the Epigraph tool and a structure-based network analysis approach and compared to overlapping peptides spanning the Gag proteome. Findings MDC1 presenting either the overlapping Gag, Epigraph, or Network 14–21mer peptide pools consistently activated and expanded HIV-1-specific T cells to epitopes identified at the 9–13mer peptide level. Interestingly, some CTL responses occurred outside known or expected HLA associations, providing evidence of new HLA-associated CTL epitopes. Comparative analyses demonstrated more sequence conservation among Epigraph antigens but a higher magnitude of CTL responses to Network and Gag peptide groups. Importantly, CTL responses against topologically constrained Gag epitopes contained in both the Network and Gag peptide pools were selectively enhanced in the Network pool-initiated cultures. Interpretation Our study supports the use of MDC1 as a therapeutic strategy to induce and focus CTL responses toward putative fitness-constrained regions of HIV-1 to prevent immune escape and control HIV-1 infection. Funding A full list of the funding sources is detailed in the Acknowledgment section of the manuscript.
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Affiliation(s)
- Tatiana M Garcia-Bates
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, United States
| | - Mariana L Palma
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, United States
| | - Renee R Anderko
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, United States
| | - Denise C Hsu
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States; Center for Infectious Diseases Research, Walter Reed Army Institute of Research Silver Spring, MD, United States; SEARCH, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Jintanat Ananworanich
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States; Center for Infectious Diseases Research, Walter Reed Army Institute of Research Silver Spring, MD, United States; SEARCH, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand; Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam, and Amsterdam Institute for Global Health and Development, Amsterdam, The Netherlands
| | - Bette T Korber
- Los Alamos National Laboratory, Los Alamos, NM, New Mexico Consortium, Los Alamos, NM, United States
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States; Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, United States
| | | | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States; Center for Infectious Diseases Research, Walter Reed Army Institute of Research Silver Spring, MD, United States
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States; Center for Infectious Diseases Research, Walter Reed Army Institute of Research Silver Spring, MD, United States
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States; Gastrointestinal Unit, Massachusetts General Hospital, Boston, MA, United States; The Broad Institute of MIT and Harvard, Cambridge, MA, United States; Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - John W Mellors
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, United States
| | - Paolo A Piazza
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, United States
| | - Eugene Kroon
- SEARCH, The Thai Red Cross AIDS Research Centre, Bangkok, Thailand
| | - Sharon A Riddler
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States; Center for Infectious Diseases Research, Walter Reed Army Institute of Research Silver Spring, MD, United States
| | - Charles R Rinaldo
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, United States; Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Robbie B Mailliard
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, Graduate School of Public Health, Pittsburgh, PA, United States.
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Galvan-Pena S, Leon J, Chowdhary K, Michelson DA, Vijaykumar B, Yang L, Magnuson A, Manickas-Hill Z, Piechocka-Trocha A, Worrall DP, Hall KE, Ghebremichael M, Walker BD, Li JZ, Yu XG, Mathis D, Benoist C. Profound Treg perturbations correlate with COVID-19 severity. bioRxiv 2020. [PMID: 33330871 DOI: 10.1101/2020.12.11.416180] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The hallmark of severe COVID-19 disease has been an uncontrolled inflammatory response, resulting from poorly understood immunological dysfunction. We explored the hypothesis that perturbations in FoxP3+ T regulatory cells (Treg), key enforcers of immune homeostasis, contribute to COVID-19 pathology. Cytometric and transcriptomic profiling revealed a distinct Treg phenotype in severe COVID-19 patients, with an increase in both Treg proportions and intracellular levels of the lineage-defining transcription factor FoxP3, which correlated with poor outcomes. Accordingly, these Tregs over-expressed a range of suppressive effectors, but also pro-inflammatory molecules like IL32. Most strikingly, they acquired similarity to tumor-infiltrating Tregs, known to suppress local anti-tumor responses. These traits were most marked in acute patients with severe disease, but persisted somewhat in convalescent patients. These results suggest that Tregs may play nefarious roles in COVID-19, via suppressing anti-viral T cell responses during the severe phase of the disease, and/or via a direct pro-inflammatory role.
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Choi B, Choudhary MC, Regan J, Sparks JA, Padera RF, Qiu X, Solomon IH, Kuo HH, Boucau J, Bowman K, Adhikari UD, Winkler ML, Mueller AA, Hsu TYT, Desjardins M, Baden LR, Chan BT, Walker BD, Lichterfeld M, Brigl M, Kwon DS, Kanjilal S, Richardson ET, Jonsson AH, Alter G, Barczak AK, Hanage WP, Yu XG, Gaiha GD, Seaman MS, Cernadas M, Li JZ. Persistence and Evolution of SARS-CoV-2 in an Immunocompromised Host. N Engl J Med 2020; 383:2291-2293. [PMID: 33176080 PMCID: PMC7673303 DOI: 10.1056/nejmc2031364] [Citation(s) in RCA: 826] [Impact Index Per Article: 206.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Bina Choi
- Brigham and Women's Hospital, Boston, MA
| | | | | | | | | | - Xueting Qiu
- Harvard T.H. Chan School of Public Health, Boston, MA
| | | | | | - Julie Boucau
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
| | - Amy K Barczak
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
| | | | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
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Edlow AG, Li JZ, Collier ARY, Atyeo C, James KE, Boatin AA, Gray KJ, Bordt EA, Shook LL, Yonker LM, Fasano A, Diouf K, Croul N, Devane S, Yockey LJ, Lima R, Shui J, Matute JD, Lerou PH, Akinwunmi BO, Schmidt A, Feldman J, Hauser BM, Caradonna TM, De la Flor D, D’Avino P, Regan J, Corry H, Coxen K, Fajnzylber J, Pepin D, Seaman MS, Barouch DH, Walker BD, Yu XG, Kaimal AJ, Roberts DJ, Alter G. Assessment of Maternal and Neonatal SARS-CoV-2 Viral Load, Transplacental Antibody Transfer, and Placental Pathology in Pregnancies During the COVID-19 Pandemic. JAMA Netw Open 2020; 3:e2030455. [PMID: 33351086 PMCID: PMC7756241 DOI: 10.1001/jamanetworkopen.2020.30455] [Citation(s) in RCA: 252] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/28/2020] [Indexed: 12/15/2022] Open
Abstract
Importance Biological data are lacking with respect to risk of vertical transmission and mechanisms of fetoplacental protection in maternal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Objective To quantify SARS-CoV-2 viral load in maternal and neonatal biofluids, transplacental passage of anti-SARS-CoV-2 antibody, and incidence of fetoplacental infection. Design, Setting, and Participants This cohort study was conducted among pregnant women presenting for care at 3 tertiary care centers in Boston, Massachusetts. Women with reverse transcription-polymerase chain reaction (RT-PCR) results positive for SARS-CoV-2 were recruited from April 2 to June 13, 2020, and follow-up occurred through July 10, 2020. Contemporaneous participants without SARS-CoV-2 infection were enrolled as a convenience sample from pregnant women with RT-PCR results negative for SARS-CoV-2. Exposures SARS-CoV-2 infection in pregnancy, defined by nasopharyngeal swab RT-PCR. Main Outcomes and Measures The main outcomes were SARS-CoV-2 viral load in maternal plasma or respiratory fluids and umbilical cord plasma, quantification of anti-SARS-CoV-2 antibodies in maternal and cord plasma, and presence of SARS-CoV-2 RNA in the placenta. Results Among 127 pregnant women enrolled, 64 with RT-PCR results positive for SARS-CoV-2 (mean [SD] age, 31.6 [5.6] years) and 63 with RT-PCR results negative for SARS-CoV-2 (mean [SD] age, 33.9 [5.4] years) provided samples for analysis. Of women with SARS-CoV-2 infection, 23 (36%) were asymptomatic, 22 (34%) had mild disease, 7 (11%) had moderate disease, 10 (16%) had severe disease, and 2 (3%) had critical disease. In viral load analyses among 107 women, there was no detectable viremia in maternal or cord blood and no evidence of vertical transmission. Among 77 neonates tested in whom SARS-CoV-2 antibodies were quantified in cord blood, 1 had detectable immunoglobuilin M to nucleocapsid. Among 88 placentas tested, SARS-CoV-2 RNA was not detected in any. In antibody analyses among 37 women with SARS-CoV-2 infection, anti-receptor binding domain immunoglobin G was detected in 24 women (65%) and anti-nucleocapsid was detected in 26 women (70%). Mother-to-neonate transfer of anti-SARS-CoV-2 antibodies was significantly lower than transfer of anti-influenza hemagglutinin A antibodies (mean [SD] cord-to-maternal ratio: anti-receptor binding domain immunoglobin G, 0.72 [0.57]; anti-nucleocapsid, 0.74 [0.44]; anti-influenza, 1.44 [0.80]; P < .001). Nonoverlapping placental expression of SARS-CoV-2 receptors angiotensin-converting enzyme 2 and transmembrane serine protease 2 was noted. Conclusions and Relevance In this cohort study, there was no evidence of placental infection or definitive vertical transmission of SARS-CoV-2. Transplacental transfer of anti-SARS-CoV-2 antibodies was inefficient. Lack of viremia and reduced coexpression and colocalization of placental angiotensin-converting enzyme 2 and transmembrane serine protease 2 may serve as protective mechanisms against vertical transmission.
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Affiliation(s)
- Andrea G. Edlow
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston
- Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston
| | - Jonathan Z. Li
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ai-ris Y. Collier
- Department of Obstetrics, Gynecology and Reproductive Biology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts
| | - Kaitlyn E. James
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Adeline A. Boatin
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Kathryn J. Gray
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Evan A. Bordt
- Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Lydia L. Shook
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Lael M. Yonker
- Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Alessio Fasano
- Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Khady Diouf
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Natalie Croul
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Samantha Devane
- Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Laura J. Yockey
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Rosiane Lima
- Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Jessica Shui
- Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Juan D. Matute
- Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Paul H. Lerou
- Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Babatunde O. Akinwunmi
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Aaron Schmidt
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts
| | - Blake M. Hauser
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts
| | - Timothy M. Caradonna
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts
| | - Denis De la Flor
- Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Paolo D’Avino
- Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston
| | - James Regan
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Heather Corry
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Kendyll Coxen
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jesse Fajnzylber
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - David Pepin
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Anjali J. Kaimal
- Department of Obstetrics, Gynecology and Reproductive Biology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Drucilla J. Roberts
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts
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39
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Shrock E, Fujimura E, Kula T, Timms RT, Lee IH, Leng Y, Robinson ML, Sie BM, Li MZ, Chen Y, Logue J, Zuiani A, McCulloch D, Lelis FJN, Henson S, Monaco DR, Travers M, Habibi S, Clarke WA, Caturegli P, Laeyendecker O, Piechocka-Trocha A, Li JZ, Khatri A, Chu HY, Villani AC, Kays K, Goldberg MB, Hacohen N, Filbin MR, Yu XG, Walker BD, Wesemann DR, Larman HB, Lederer JA, Elledge SJ. Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity. Science 2020; 370:science.abd4250. [PMID: 32994364 PMCID: PMC7857405 DOI: 10.1126/science.abd4250] [Citation(s) in RCA: 423] [Impact Index Per Article: 105.8] [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: 06/22/2020] [Accepted: 09/25/2020] [Indexed: 12/11/2022]
Abstract
Understanding humoral responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for improving diagnostics, therapeutics, and vaccines. Deep serological profiling of 232 coronavirus disease 2019 (COVID-19) patients and 190 pre-COVID-19 era controls using VirScan revealed more than 800 epitopes in the SARS-CoV-2 proteome, including 10 epitopes likely recognized by neutralizing antibodies. Preexisting antibodies in controls recognized SARS-CoV-2 ORF1, whereas only COVID-19 patient antibodies primarily recognized spike protein and nucleoprotein. A machine learning model trained on VirScan data predicted SARS-CoV-2 exposure history with 99% sensitivity and 98% specificity; a rapid Luminex-based diagnostic was developed from the most discriminatory SARS-CoV-2 peptides. Individuals with more severe COVID-19 exhibited stronger and broader SARS-CoV-2 responses, weaker antibody responses to prior infections, and higher incidence of cytomegalovirus and herpes simplex virus 1, possibly influenced by demographic covariates. Among hospitalized patients, males produce stronger SARS-CoV-2 antibody responses than females.
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Affiliation(s)
- Ellen Shrock
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Division of Genetics, Brigham and Women’s Hospital, Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Eric Fujimura
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Division of Genetics, Brigham and Women’s Hospital, Program in Virology, Harvard Medical School, Boston, MA, USA.,Chemical Biology Program, Harvard University, Cambridge, MA, USA
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Division of Genetics, Brigham and Women’s Hospital, Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Richard T. Timms
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Division of Genetics, Brigham and Women’s Hospital, Program in Virology, Harvard Medical School, Boston, MA, USA
| | - I-Hsiu Lee
- Center for Systems Biology, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yumei Leng
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Division of Genetics, Brigham and Women’s Hospital, Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Matthew L. Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brandon M. Sie
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Division of Genetics, Brigham and Women’s Hospital, Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Mamie Z. Li
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Division of Genetics, Brigham and Women’s Hospital, Program in Virology, Harvard Medical School, Boston, MA, USA
| | - Yuezhou Chen
- Division of Allergy and Immunology and Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Jennifer Logue
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Adam Zuiani
- Division of Allergy and Immunology and Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Denise McCulloch
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Felipe J. N. Lelis
- Division of Allergy and Immunology and Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Stephanie Henson
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Daniel R. Monaco
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Meghan Travers
- Division of Allergy and Immunology and Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - Shaghayegh Habibi
- Division of Allergy and Immunology and Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - William A. Clarke
- Division of Clinical Chemistry, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Patrizio Caturegli
- Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Oliver Laeyendecker
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Division of Intramural Research, NIAID, NIH, Baltimore, MD, USA
| | - Alicja Piechocka-Trocha
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.,Howard Hughes Medical Institute, Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Z. Li
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.,Infectious Disease Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ashok Khatri
- Endocrine Unit and Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Alexandra-Chloé Villani
- Massachusetts General Hospital Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Kyle Kays
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Marcia B. Goldberg
- Center for Bacterial Pathogenesis, Division of Infectious Diseases, Department of Medicine and Microbiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nir Hacohen
- Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Michael R. Filbin
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Xu G. Yu
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.,Infectious Disease Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA.,Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Bruce D. Walker
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.,Howard Hughes Medical Institute, Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.,Centre for the AIDS Programme of Research in South Africa, Congella, South Africa
| | - Duane R. Wesemann
- Division of Allergy and Immunology and Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA
| | - H. Benjamin Larman
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - James A. Lederer
- Department of Surgery, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephen J. Elledge
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Division of Genetics, Brigham and Women’s Hospital, Program in Virology, Harvard Medical School, Boston, MA, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.,Corresponding author.
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40
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Fajnzylber J, Regan J, Coxen K, Corry H, Wong C, Rosenthal A, Worrall D, Giguel F, Piechocka-Trocha A, Atyeo C, Fischinger S, Chan A, Flaherty KT, Hall K, Dougan M, Ryan ET, Gillespie E, Chishti R, Li Y, Jilg N, Hanidziar D, Baron RM, Baden L, Tsibris AM, Armstrong KA, Kuritzkes DR, Alter G, Walker BD, Yu X, Li JZ. SARS-CoV-2 viral load is associated with increased disease severity and mortality. Nat Commun 2020; 11:5493. [PMID: 33127906 PMCID: PMC7603483 DOI: 10.1038/s41467-020-19057-5] [Citation(s) in RCA: 609] [Impact Index Per Article: 152.3] [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: 07/15/2020] [Accepted: 09/22/2020] [Indexed: 01/08/2023] Open
Abstract
The relationship between SARS-CoV-2 viral load and risk of disease progression remains largely undefined in coronavirus disease 2019 (COVID-19). Here, we quantify SARS-CoV-2 viral load from participants with a diverse range of COVID-19 disease severity, including those requiring hospitalization, outpatients with mild disease, and individuals with resolved infection. We detected SARS-CoV-2 plasma RNA in 27% of hospitalized participants, and 13% of outpatients diagnosed with COVID-19. Amongst the participants hospitalized with COVID-19, we report that a higher prevalence of detectable SARS-CoV-2 plasma viral load is associated with worse respiratory disease severity, lower absolute lymphocyte counts, and increased markers of inflammation, including C-reactive protein and IL-6. SARS-CoV-2 viral loads, especially plasma viremia, are associated with increased risk of mortality. Our data show that SARS-CoV-2 viral loads may aid in the risk stratification of patients with COVID-19, and therefore its role in disease pathogenesis should be further explored.
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Affiliation(s)
- Jesse Fajnzylber
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - James Regan
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kendyll Coxen
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Heather Corry
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Colline Wong
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Daniel Worrall
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, MA, USA
| | - Francoise Giguel
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, MA, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, MA, USA
| | - Andrew Chan
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Keith T Flaherty
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kathryn Hall
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael Dougan
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Edward T Ryan
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Rida Chishti
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yijia Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nikolaus Jilg
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dusan Hanidziar
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rebecca M Baron
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lindsey Baden
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Athe M Tsibris
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Xu Yu
- Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, MA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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41
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Joung J, Ladha A, Saito M, Kim NG, Woolley AE, Segel M, Barretto RPJ, Ranu A, Macrae RK, Faure G, Ioannidi EI, Krajeski RN, Bruneau R, Huang MLW, Yu XG, Li JZ, Walker BD, Hung DT, Greninger AL, Jerome KR, Gootenberg JS, Abudayyeh OO, Zhang F. Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing. N Engl J Med 2020; 383:1492-1494. [PMID: 32937062 PMCID: PMC7510942 DOI: 10.1056/nejmc2026172] [Citation(s) in RCA: 411] [Impact Index Per Article: 102.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Julia Joung
- Massachusetts Institute of Technology, Cambridge, MA
| | - Alim Ladha
- Massachusetts Institute of Technology, Cambridge, MA
| | - Makoto Saito
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | | | | | | | | | | | | | | | | | | | - Xu G Yu
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | | | | | | | | | | | | | | | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA
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42
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Jin SW, Alsahafi N, Kuang XT, Swann SA, Toyoda M, Göttlinger H, Walker BD, Ueno T, Finzi A, Brumme ZL, Brockman MA. Natural HIV-1 Nef Polymorphisms Impair SERINC5 Downregulation Activity. Cell Rep 2020; 29:1449-1457.e5. [PMID: 31693887 PMCID: PMC6925589 DOI: 10.1016/j.celrep.2019.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 05/01/2018] [Revised: 07/26/2019] [Accepted: 10/01/2019] [Indexed: 11/30/2022] Open
Abstract
HIV-1 Nef enhances virion infectivity by counteracting host restriction factor SERINC5; however, the impact of natural Nef polymorphisms on this function is largely unknown. We characterize SERINC5 downregulation activity of 91 primary HIV-1 subtype B nef alleles, including isolates from 45 elite controllers and 46 chronic progressors. Controller-derived Nef clones display lower ability to downregulate SERINC5 (median 80% activity) compared with progressor-derived clones (median 96% activity) (p = 0.0005). We identify 18 Nef polymorphisms associated with differential function, including two CTL escape mutations that contribute to lower SERINC5 downregulation: K94E, driven by HLA-B∗08, and H116N, driven by the protective allele HLA-B∗57. HIV-1 strains encoding Nef K94E and/or H116N display lower infectivity and replication capacity in the presence of SERINC5. Our results demonstrate that natural polymorphisms in HIV-1 Nef can impair its ability to internalize SERINC5, indicating that variation in this recently described function may contribute to differences in viral pathogenesis.
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Affiliation(s)
- Steven W Jin
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Nirmin Alsahafi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Xiaomei T Kuang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Shayda A Swann
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Mako Toyoda
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Heinrich Göttlinger
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada; Department of Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC, Canada
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Mark A Brockman
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.
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43
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Painter MM, Zimmerman GE, Merlino MS, Robertson AW, Terry VH, Ren X, McLeod MR, Gomez-Rodriguez L, Garcia KA, Leonard JA, Leopold KE, Neevel AJ, Lubow J, Olson E, Piechocka-Trocha A, Collins DR, Tripathi A, Raghavan M, Walker BD, Hurley JH, Sherman DH, Collins KL. Concanamycin A counteracts HIV-1 Nef to enhance immune clearance of infected primary cells by cytotoxic T lymphocytes. Proc Natl Acad Sci U S A 2020; 117:23835-23846. [PMID: 32900948 PMCID: PMC7519347 DOI: 10.1073/pnas.2008615117] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nef is an HIV-encoded accessory protein that enhances pathogenicity by down-regulating major histocompatibility class I (MHC-I) expression to evade killing by cytotoxic T lymphocytes (CTLs). A potent Nef inhibitor that restores MHC-I is needed to promote immune-mediated clearance of HIV-infected cells. We discovered that the plecomacrolide family of natural products restored MHC-I to the surface of Nef-expressing primary cells with variable potency. Concanamycin A (CMA) counteracted Nef at subnanomolar concentrations that did not interfere with lysosomal acidification or degradation and were nontoxic in primary cell cultures. CMA specifically reversed Nef-mediated down-regulation of MHC-I, but not CD4, and cells treated with CMA showed reduced formation of the Nef:MHC-I:AP-1 complex required for MHC-I down-regulation. CMA restored expression of diverse allotypes of MHC-I in Nef-expressing cells and inhibited Nef alleles from divergent clades of HIV and simian immunodeficiency virus, including from primary patient isolates. Lastly, we found that restoration of MHC-I in HIV-infected cells was accompanied by enhanced CTL-mediated clearance of infected cells comparable to genetic deletion of Nef. Thus, we propose CMA as a lead compound for therapeutic inhibition of Nef to enhance immune-mediated clearance of HIV-infected cells.
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Affiliation(s)
- Mark M Painter
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109
| | | | - Madeline S Merlino
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Andrew W Robertson
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan Ann Arbor, MI 48109
| | - Valeri H Terry
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Xuefeng Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Megan R McLeod
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Lyanne Gomez-Rodriguez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Kirsten A Garcia
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Jolie A Leonard
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Kay E Leopold
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Andrew J Neevel
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Jay Lubow
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Eli Olson
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - David R Collins
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Kathleen L Collins
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109
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44
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Jiang C, Lian X, Gao C, Sun X, Einkauf KB, Chevalier JM, Chen SMY, Hua S, Rhee B, Chang K, Blackmer JE, Osborn M, Peluso MJ, Hoh R, Somsouk M, Milush J, Bertagnolli LN, Sweet SE, Varriale JA, Burbelo PD, Chun TW, Laird GM, Serrao E, Engelman AN, Carrington M, Siliciano RF, Siliciano JM, Deeks SG, Walker BD, Lichterfeld M, Yu XG. Distinct viral reservoirs in individuals with spontaneous control of HIV-1. Nature 2020; 585:261-267. [PMID: 32848246 PMCID: PMC7837306 DOI: 10.1038/s41586-020-2651-8] [Citation(s) in RCA: 211] [Impact Index Per Article: 52.8] [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: 10/02/2019] [Accepted: 07/15/2020] [Indexed: 02/01/2023]
Abstract
Sustained, drug-free control of HIV-1 replication is naturally achieved in less than 0.5% of infected individuals (here termed 'elite controllers'), despite the presence of a replication-competent viral reservoir1. Inducing such an ability to spontaneously maintain undetectable plasma viraemia is a major objective of HIV-1 cure research, but the characteristics of proviral reservoirs in elite controllers remain to be determined. Here, using next-generation sequencing of near-full-length single HIV-1 genomes and corresponding chromosomal integration sites, we show that the proviral reservoirs of elite controllers frequently consist of oligoclonal to near-monoclonal clusters of intact proviral sequences. In contrast to individuals treated with long-term antiretroviral therapy, intact proviral sequences from elite controllers were integrated at highly distinct sites in the human genome and were preferentially located in centromeric satellite DNA or in Krüppel-associated box domain-containing zinc finger genes on chromosome 19, both of which are associated with heterochromatin features. Moreover, the integration sites of intact proviral sequences from elite controllers showed an increased distance to transcriptional start sites and accessible chromatin of the host genome and were enriched in repressive chromatin marks. These data suggest that a distinct configuration of the proviral reservoir represents a structural correlate of natural viral control, and that the quality, rather than the quantity, of viral reservoirs can be an important distinguishing feature for a functional cure of HIV-1 infection. Moreover, in one elite controller, we were unable to detect intact proviral sequences despite analysing more than 1.5 billion peripheral blood mononuclear cells, which raises the possibility that a sterilizing cure of HIV-1 infection, which has previously been observed only following allogeneic haematopoietic stem cell transplantation2,3, may be feasible in rare instances.
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Affiliation(s)
- Chenyang Jiang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Kevin B Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Joshua M Chevalier
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Stephane Hua
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Ben Rhee
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Kaylee Chang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew Osborn
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Michael J Peluso
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Ma Somsouk
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Jeffrey Milush
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Lynn N Bertagnolli
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah E Sweet
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joseph A Varriale
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter D Burbelo
- Dental Clinical Research Core, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Tae-Wook Chun
- National Institute of Allergies and Infectious Diseases, Bethesda, MD, USA
| | | | - Erik Serrao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Janet M Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Steven G Deeks
- Department of Medicine, University of California at San Francisco, San Francisco, CA, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
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45
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Kaneko N, Kuo HH, Boucau J, Farmer JR, Allard-Chamard H, Mahajan VS, Piechocka-Trocha A, Lefteri K, Osborn M, Bals J, Bartsch YC, Bonheur N, Caradonna TM, Chevalier J, Chowdhury F, Diefenbach TJ, Einkauf K, Fallon J, Feldman J, Finn KK, Garcia-Broncano P, Hartana CA, Hauser BM, Jiang C, Kaplonek P, Karpell M, Koscher EC, Lian X, Liu H, Liu J, Ly NL, Michell AR, Rassadkina Y, Seiger K, Sessa L, Shin S, Singh N, Sun W, Sun X, Ticheli HJ, Waring MT, Zhu AL, Alter G, Li JZ, Lingwood D, Schmidt AG, Lichterfeld M, Walker BD, Yu XG, Padera RF, Pillai S. Loss of Bcl-6-Expressing T Follicular Helper Cells and Germinal Centers in COVID-19. Cell 2020; 183:143-157.e13. [PMID: 32877699 PMCID: PMC7437499 DOI: 10.1016/j.cell.2020.08.025] [Citation(s) in RCA: 498] [Impact Index Per Article: 124.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/24/2020] [Accepted: 08/14/2020] [Indexed: 01/08/2023]
Abstract
Humoral responses in coronavirus disease 2019 (COVID-19) are often of limited durability, as seen with other human coronavirus epidemics. To address the underlying etiology, we examined post mortem thoracic lymph nodes and spleens in acute SARS-CoV-2 infection and observed the absence of germinal centers and a striking reduction in Bcl-6+ germinal center B cells but preservation of AID+ B cells. Absence of germinal centers correlated with an early specific block in Bcl-6+ TFH cell differentiation together with an increase in T-bet+ TH1 cells and aberrant extra-follicular TNF-α accumulation. Parallel peripheral blood studies revealed loss of transitional and follicular B cells in severe disease and accumulation of SARS-CoV-2-specific "disease-related" B cell populations. These data identify defective Bcl-6+ TFH cell generation and dysregulated humoral immune induction early in COVID-19 disease, providing a mechanistic explanation for the limited durability of antibody responses in coronavirus infections, and suggest that achieving herd immunity through natural infection may be difficult.
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Affiliation(s)
- Naoki Kaneko
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hsiao-Hsuan Kuo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jocelyn R Farmer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hugues Allard-Chamard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Rheumatology, Faculté de Médecine et des Sciences de la Santé de l'Université de Sherbrooke et Centre de Recherche Clinique Étienne-Le Bel, Sherbrooke, QC J1K 2R1, Canada
| | - Vinay S Mahajan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Kristina Lefteri
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Matthew Osborn
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Julia Bals
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Yannic C Bartsch
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Nathalie Bonheur
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Josh Chevalier
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Fatema Chowdhury
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Kevin Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jon Fallon
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Kelsey K Finn
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | | | - Blake M Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Chenyang Jiang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Paulina Kaplonek
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Marshall Karpell
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Eric C Koscher
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hang Liu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jinqing Liu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ngoc L Ly
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashlin R Michell
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Kyra Seiger
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Libera Sessa
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Sally Shin
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Nishant Singh
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Weiwei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hannah J Ticheli
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Michael T Waring
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Alex L Zhu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jonathan Z Li
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology and Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Robert F Padera
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Shiv Pillai
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
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46
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Kaneko N, Kuo HH, Boucau J, Farmer JR, Allard-Chamard H, Mahajan VS, Piechocka-Trocha A, Lefteri K, Osborn M, Bals J, Bartsch YC, Bonheur N, Caradonna TM, Chevalier J, Chowdhury F, Diefenbach TJ, Einkauf K, Fallon J, Feldman J, Finn KK, Garcia-Broncano P, Hartana CA, Hauser BM, Jiang C, Kaplonek P, Karpell M, Koscher EC, Lian X, Liu H, Liu J, Ly NL, Michell AR, Rassadkina Y, Seiger K, Sessa L, Shin S, Singh N, Sun W, Sun X, Ticheli HJ, Waring MT, Zhu AL, Li J, Lingwood D, Schmidt AG, Lichterfeld M, Walker BD, Yu X, Padera RF, Pillai S. The Loss of Bcl-6 Expressing T Follicular Helper Cells and the Absence of Germinal Centers in COVID-19. ACTA ACUST UNITED AC 2020:3652322. [PMID: 32742244 DOI: 10.2139/ssrn.3652322] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 07/22/2020] [Indexed: 01/08/2023]
Abstract
Humoral responses in COVID-19 disease are often of limited durability, as seen with other human coronavirus epidemics. To address the underlying etiology, we examined postmortem thoracic lymph nodes and spleens in acute SARS-CoV-2 infection and observed the absence of germinal centers, a striking reduction in Bcl-6+ germinal center B cells but preservation of AID+ B cells. Absence of germinal centers correlated with an early specific block in Bcl-6+TFH cell differentiation together with an increase in T-bet+TH1 cells and aberrant extra-follicular TNF-a accumulation. Parallel peripheral blood studies revealed loss of transitional and follicular B cells in severe disease and accumulation of SARS-CoV-2-specific "disease-related" B cell populations. These data identify defective Bcl-6+TFH cell generation and dysregulated humoral immune induction early in COVID-19 disease, providing a mechanistic explanation for the limited durability of antibody responses in coronavirus infections and suggest that achieving herd immunity through natural infection may be difficult. Funding: This work was supported by NIH U19 AI110495 to SP, NIH R01 AI146779 to AGS, NIH R01AI137057 and DP2DA042422 to DL, BMH was supported by NIGMS T32 GM007753, TMC was supported by T32 AI007245. Funding for these studies from the Massachusetts Consortium of Pathogen Readiness, the Mark and Lisa Schwartz Foundation and Enid Schwartz is also acknowledged. Conflict of Interest: None. Ethical Approval: This study was performed with the approval of the Institutional Review Boards at the Massachusetts General Hospital and the Brigham and Women's Hospital.
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Affiliation(s)
- Naoki Kaneko
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hsiao-Hsuan Kuo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Julie Boucau
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jocelyn R Farmer
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hugues Allard-Chamard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Division of Rheumatology, Faculté de médecine et des sciences de la santé de l' Université de Sherbrooke et Centre de Recherche Clinique Étienne-Le Bel, Sherbrooke, Québec, J1K 2R1, Canada
| | - Vinay S Mahajan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Chevy Chase MD, 20815
| | - Kristina Lefteri
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Matt Osborn
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Julia Bals
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Yannic C Bartsch
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Nathalie Bonheur
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Josh Chevalier
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Fatema Chowdhury
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Kevin Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jon Fallon
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Kelsey K Finn
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | | | - Blake M Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Chenyang Jiang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Paulina Kaplonek
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Marshall Karpell
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Eric C Koscher
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hang Liu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jinqing Liu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ngoc L Ly
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ashlin R Michell
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Kyra Seiger
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Libera Sessa
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Sally Shin
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Nishant Singh
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Weiwei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Xiaoming Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Hannah J Ticheli
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Michael T Waring
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Chevy Chase MD, 20815
| | - Alex L Zhu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jonathan Li
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Department of Microbiology, Harvard Medical School, Boston, MA 02115
| | - Matthias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Chevy Chase MD, 20815.,Department of Biology and Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Xu Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Robert F Padera
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Shiv Pillai
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
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47
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Ndhlovu ZM, Kazer SW, Nkosi T, Ogunshola F, Muema DM, Anmole G, Swann SA, Moodley A, Dong K, Reddy T, Brockman MA, Shalek AK, Ndung'u T, Walker BD. Augmentation of HIV-specific T cell function by immediate treatment of hyperacute HIV-1 infection. Sci Transl Med 2020; 11:11/493/eaau0528. [PMID: 31118290 DOI: 10.1126/scitranslmed.aau0528] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/31/2018] [Accepted: 03/28/2019] [Indexed: 12/13/2022]
Abstract
Sustained viremia after acute HIV infection is associated with profound CD4+ T cell loss and exhaustion of HIV-specific CD8+ T cell responses. To determine the impact of combination antiretroviral therapy (cART) on these processes, we examined the evolution of immune responses in acutely infected individuals initiating treatment before peak viremia. Immediate treatment of Fiebig stages I and II infection led to a rapid decline in viral load and diminished magnitude of HIV-specific (tetramer+) CD8+ T cell responses compared to untreated donors. There was a strong positive correlation between cumulative viral antigen exposure before full cART-induced suppression and immune responses measured by MHC class I tetramers, IFN-γ ELISPOT, and CD8+ T cell activation. HIV-specific CD8+ T responses of early treated individuals were characterized by increased CD127 and BCL-2 expression, greater in vitro IFN-γ secretion, and enhanced differentiation into effector memory (Tem) cells. Transcriptional analysis of tetramer+ CD8+ T cells from treated persons revealed reduced expression of genes associated with activation and apoptosis, with concurrent up-regulation of prosurvival genes including BCL-2, AXL, and SRC Early treatment also resulted in robust HIV-specific CD4+ T cell responses compared to untreated HIV-infected individuals. Our data show that limiting acute viremia results in enhanced functionality of HIV-specific CD4+ and CD8+ T cells, preserving key antiviral properties of these cells.
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Affiliation(s)
- Zaza M Ndhlovu
- Africa Health Research Institute, 4036 Durban, South Africa. .,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Samuel W Kazer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA 02139, USA.,Department of Chemistry and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Thandeka Nkosi
- Africa Health Research Institute, 4036 Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Funsho Ogunshola
- Africa Health Research Institute, 4036 Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Daniel M Muema
- Africa Health Research Institute, 4036 Durban, South Africa
| | - Gursev Anmole
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Shayda A Swann
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Amber Moodley
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Krista Dong
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Tarylee Reddy
- South Africa Medical Research Council, 4091 Durban, South Africa
| | - Mark A Brockman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.,Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Alex K Shalek
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.,Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA 02139, USA.,Department of Chemistry and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Thumbi Ndung'u
- Africa Health Research Institute, 4036 Durban, South Africa.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4013 Durban, South Africa
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,HIV Pathogenesis Programme, Doris Duke Medical Research Institute, University of KwaZulu-Natal, 4013 Durban, South Africa.,Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
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48
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Monel B, McKeon A, Lamothe-Molina P, Jani P, Boucau J, Pacheco Y, Jones RB, Le Gall S, Walker BD. HIV Controllers Exhibit Effective CD8 + T Cell Recognition of HIV-1-Infected Non-activated CD4 + T Cells. Cell Rep 2020; 27:142-153.e4. [PMID: 30943397 PMCID: PMC6449512 DOI: 10.1016/j.celrep.2019.03.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 07/27/2018] [Revised: 11/25/2018] [Accepted: 03/05/2019] [Indexed: 02/07/2023] Open
Abstract
Even with sustained antiretroviral therapy, resting CD4+ T cells remain a persistent reservoir of HIV infection, representing a critical barrier to curing HIV. Here, we demonstrate that CD8+ T cells recognize infected, non-activated CD4+ T cells in the absence of de novo protein production, as measured by immune synapse formation, degranulation, cytokine production, and killing of infected cells. Immune recognition is induced by HLA-I presentation of peptides derived from incoming viral particles, and recognition occurred either following cell-free virus infection or following cell-to-cell spread. CD8+ T cells from HIV controllers mediate more effective immune recognition than CD8+ T cells from progressors. These results indicate that non-activated HIV-infected CD4+ T cells can be targeted by CD8+ T cells directly after HIV entry, before reverse transcription, and thus before the establishment of latency, and suggest a mechanism whereby the immune response may reduce the size of the HIV reservoir.
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Affiliation(s)
- Blandine Monel
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Annmarie McKeon
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Pedro Lamothe-Molina
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Priya Jani
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Julie Boucau
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Yovana Pacheco
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA; Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - R Brad Jones
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA; Division of Infectious Diseases, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sylvie Le Gall
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Bruce D Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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49
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Joung J, Ladha A, Saito M, Segel M, Bruneau R, Huang MLW, Kim NG, Yu X, Li J, Walker BD, Greninger AL, Jerome KR, Gootenberg JS, Abudayyeh OO, Zhang F. Point-of-care testing for COVID-19 using SHERLOCK diagnostics. medRxiv 2020:2020.05.04.20091231. [PMID: 32511521 PMCID: PMC7273289 DOI: 10.1101/2020.05.04.20091231] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The recent outbreak of the novel coronavirus SARS-CoV-2, which causes COVID-19, can be diagnosed using RT-qPCR, but inadequate access to reagents and equipment has slowed disease detection and impeded efforts to mitigate viral spread. Alternative approaches based on combinations of isothermal amplification and CRISPR-mediated detection, such as the SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKing) technique, offer reduced dependence on RT-qPCR equipment, but previously reported methods required multiple fluid handling steps, complicating their deployment outside clinical labs. Here we developed a simple test chemistry called STOP (SHERLOCK Testing in One Pot) for detecting SARS-CoV-2 in one hour that is suitable for point-of-care use. This simplified test, STOPCovid, provides sensitivity comparable to RT-qPCR-based SARS-CoV-2 tests and has a limit of detection of 100 copies of viral genome input in saliva or nasopharyngeal swabs per reaction. Using lateral flow readout, the test returns result in 70 minutes, and using fluorescence readout, the test returns result in 40 minutes. Moreover, we validated STOPCovid using nasopharyngeal swabs from COVID-19 patients and were able to correctly diagnose 12 positive and 5 negative patients out of 3 replicates. We envision that implementation of STOPCovid will significantly aid "test-trace-isolate" efforts, especially in low-resource settings, which will be critical for long-term public health safety and effective reopening of the society.
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Affiliation(s)
- Julia Joung
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT
- Department of Biological Engineering
| | - Alim Ladha
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT
- Department of Biological Engineering
| | - Makoto Saito
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT
- Department of Biological Engineering
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael Segel
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT
- Department of Biological Engineering
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Nam-Gyun Kim
- University of Washington, Seattle, WA 98102, USA
| | - Xu Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Massachusetts General Hospital, Boston, MA 02114, USA
- Massachusetts Consortium for Pathogen Readiness, Boston, MA 20115
| | - Jonathan Li
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Brigham and Women's Hospital, Boston, MA 02115, USA
- Massachusetts Consortium for Pathogen Readiness, Boston, MA 20115
| | - Bruce D Walker
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Massachusetts Consortium for Pathogen Readiness, Boston, MA 20115
| | - Alexander L Greninger
- University of Washington, Seattle, WA 98102, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Keith R Jerome
- University of Washington, Seattle, WA 98102, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT
- Massachusetts Consortium for Pathogen Readiness, Boston, MA 20115
| | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT
- Massachusetts Consortium for Pathogen Readiness, Boston, MA 20115
| | - Feng Zhang
- Howard Hughes Medical Institute, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research at MIT
- Department of Biological Engineering
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Massachusetts Consortium for Pathogen Readiness, Boston, MA 20115
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50
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Kazer SW, Aicher TP, Muema DM, Miao VN, Ordovas-Montanes J, Ziegler CGK, Moodley A, Dong KL, Ndhlovu ZM, Ndung’u T, Walker BD, Shalek AK. Integrated single-cell analysis of multicellular immune dynamics during hyper-acute HIV infection. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.248.4] [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: 01/02/2023]
Abstract
Abstract
Development of effective vaccines and therapeutics is facilitated by understanding the earliest immune responses to infection. Here, we apply single-cell RNA-sequencing (scRNA-seq) and a novel gene module discovery-based framework to longitudinally profile peripheral multicellular immune responses in untreated hyper-acute HIV infection.
We profiled >59,000 single cells from four individuals across multiple acute infection timepoints (including pre-infection), utilizing scRNA-seq data to identify transient immune responses with cell subset resolution. Onset of viremia induced interferon stimulated gene (ISG) responses integrated across multiple cell types, wherein monocytes notably contributed to the cytokine milieu. Otherwise obscured in bulk analyses, we describe a second set of responses following ISG upregulation that align in time: pro-inflammatory T cell differentiation, prolonged monocyte MHC-II upregulation, and persistent NK cytolytic killing. Leveraging our temporal, cell-type resolved data, we nominate putative cell-cell signaling networks and their key cytokines during infection. Two participants who later develop viremic control associated with elevated frequencies of proliferating cytotoxic cells, inclusive of a previously unappreciated NK cell subset, immediately following HIV detection.
Our study reveals both cooperative and cell subset specific immune responses during untreated hyper-acute HIV infection with temporal resolution, nominating monocytes, NK cells, and pro-inflammatory signaling as perturbation targets for future vaccine studies. Moreover, our gene module discovery framework can be readily applied to other longitudinal studies in humans and other model organisms.
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Affiliation(s)
- Samuel W Kazer
- 1Ragon Institute of MGH, MIT, and Harvard
- 2Massachusetts Institute of Technology
- 3Broad Inst. of MIT and Harvard
| | - Toby P Aicher
- 1Ragon Institute of MGH, MIT, and Harvard
- 4NYU Medical Center
| | | | - Vincent N Miao
- 1Ragon Institute of MGH, MIT, and Harvard
- 6Harvard-MIT Health Sciences and Technology
| | | | - Carly G K Ziegler
- 1Ragon Institute of MGH, MIT, and Harvard
- 6Harvard-MIT Health Sciences and Technology
| | | | - Krista L Dong
- 1Ragon Institute of MGH, MIT, and Harvard
- 8University of KwaZulu-Natal, South Africa
| | - Zaza M Ndhlovu
- 1Ragon Institute of MGH, MIT, and Harvard
- 5Africa Health Research Institute, South Africa
- 8University of KwaZulu-Natal, South Africa
- 9Howard Hughes Medical Institute
| | - Thumbi Ndung’u
- 1Ragon Institute of MGH, MIT, and Harvard
- 5Africa Health Research Institute, South Africa
- 8University of KwaZulu-Natal, South Africa
- 10Division of Infection and Immunity, University College London, London, WC1E 6BT, United Kingdom, United Kingdom
- 11Max Planck Institute for Infection Biology, Germany
| | - Bruce D Walker
- 1Ragon Institute of MGH, MIT, and Harvard
- 8University of KwaZulu-Natal, South Africa
- 9Howard Hughes Medical Institute
| | - Alex K Shalek
- 1Ragon Institute of MGH, MIT, and Harvard
- 2Massachusetts Institute of Technology
- 3Broad Inst. of MIT and Harvard
- 6Harvard-MIT Health Sciences and Technology
- 12Koch Institute for Integrative Cancer Research at MIT
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