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Koofhethile CK, Gao C, Chang C, Lian X, Shapiro R, Yu XG, Lichterfeld M, Kanki PJ. The HIV-2 proviral landscape is dominated by defective proviruses. AIDS 2024; 38:309-316. [PMID: 37916471 PMCID: PMC10842655 DOI: 10.1097/qad.0000000000003776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Compared with HIV-1 infection, HIV-2 infection is associated with a slower progression to AIDS. Understanding the persistence of HIV-2 infection might inform the mechanisms responsible for differences in the pathogenicity of HIV-2 versus HIV-1. METHODS In this study, we analyzed the genetic composition of the proviral reservoir in archived blood samples collected from 13 untreated HIV-2-infected adults from Senegal. We used single-genome, near-full-length individual proviral sequencing (FLIP-Seq) to assess the relative frequency of intact and defective proviruses. RESULTS Ten out of 13 (77%) study participants demonstrated virologic suppression (<90 HIV RNA copies/ml) while the remaining 3 (23%) had detectable HIV RNA. We obtained 363 proviral sequences from peripheral blood mononuclear cells (PBMCs) from the 13 study participants. Within these sequences, 342 (94%) defective proviruses were detected. Twenty-one (6%) intact proviruses were detected from three study participants, with one study participant displaying a large clone consisting of 16 genome-intact sequences. CONCLUSION This data suggests that similar to HIV-1 infection, the proviral landscape of HIV-2 is dominated by defective proviruses.
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Affiliation(s)
- Catherine K. Koofhethile
- Harvard T.H. Chan School of Public Health, Boston
- Ragon Institute of MGH, MIT and Harvard, Cambridge
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge
| | | | | | | | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
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2
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Armani-Tourret M, Gao C, Hartana CA, Sun W, Carrere L, Vela L, Hochroth A, Bellefroid M, Sbrolla A, Shea K, Flynn T, Roseto I, Rassadkina Y, Lee C, Giguel F, Malhotra R, Bushman FD, Gandhi RT, Yu XG, Kuritzkes DR, Lichterfeld M. Selection of epigenetically privileged HIV-1 proviruses during treatment with panobinostat and interferon-α2a. Cell 2024; 187:1238-1254.e14. [PMID: 38367616 PMCID: PMC10903630 DOI: 10.1016/j.cell.2024.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 11/26/2023] [Accepted: 01/24/2024] [Indexed: 02/19/2024]
Abstract
CD4+ T cells with latent HIV-1 infection persist despite treatment with antiretroviral agents and represent the main barrier to a cure of HIV-1 infection. Pharmacological disruption of viral latency may expose HIV-1-infected cells to host immune activity, but the clinical efficacy of latency-reversing agents for reducing HIV-1 persistence remains to be proven. Here, we show in a randomized-controlled human clinical trial that the histone deacetylase inhibitor panobinostat, when administered in combination with pegylated interferon-α2a, induces a structural transformation of the HIV-1 reservoir cell pool, characterized by a disproportionate overrepresentation of HIV-1 proviruses integrated in ZNF genes and in chromatin regions with reduced H3K27ac marks, the molecular target sites for panobinostat. By contrast, proviruses near H3K27ac marks were actively selected against, likely due to increased susceptibility to panobinostat. These data suggest that latency-reversing treatment can increase the immunological vulnerability of HIV-1 reservoir cells and accelerate the selection of epigenetically privileged HIV-1 proviruses.
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Affiliation(s)
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ciputra Adijaya Hartana
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - WeiWei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Leah Carrere
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Liliana Vela
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | | | - Amy Sbrolla
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Katrina Shea
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Theresa Flynn
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Isabelle Roseto
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Carole Lee
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Francoise Giguel
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rajeev Malhotra
- Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rajesh T Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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3
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Gasca-Capote C, Lian X, Gao C, Roseto IC, Jiménez-León MR, Gladkov G, Camacho-Sojo MI, Pérez-Gómez A, Gallego I, Lopez-Cortes LE, Bachiller S, Vitalle J, Rafii-El-Idrissi Benhnia M, Ostos FJ, Collado-Romacho AR, Santos J, Palacios R, Gomez-Ayerbe C, Muñoz-Medina L, Ruiz-Sancho A, Frias M, Rivero-Juarez A, Roca-Oporto C, Hidalgo-Tenorio C, Rull A, Olalla J, Lopez-Ruz MA, Vidal F, Viladés C, Mastrangelo A, Cavassini M, Espinosa N, Perreau M, Peraire J, Rivero A, López-Cortes LF, Lichterfeld M, Yu XG, Ruiz-Mateos E. The HIV-1 reservoir landscape in persistent elite controllers and transient elite controllers. J Clin Invest 2024; 134:e174215. [PMID: 38376918 PMCID: PMC11014653 DOI: 10.1172/jci174215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 02/13/2024] [Indexed: 02/21/2024] Open
Abstract
BACKGROUNDPersistent controllers (PCs) maintain antiretroviral-free HIV-1 control indefinitely over time, while transient controllers (TCs) eventually lose virological control. It is essential to characterize the quality of the HIV reservoir in terms of these phenotypes in order to identify the factors that lead to HIV progression and to open new avenues toward an HIV cure.METHODSThe characterization of HIV-1 reservoir from peripheral blood mononuclear cells was performed using next-generation sequencing techniques, such as full-length individual and matched integration site proviral sequencing (FLIP-Seq; MIP-Seq).RESULTSPCs and TCs, before losing virological control, presented significantly lower total, intact, and defective proviruses compared with those of participants on antiretroviral therapy (ART). No differences were found in total and defective proviruses between PCs and TCs. However, intact provirus levels were lower in PCs compared with TCs; indeed the intact/defective HIV-DNA ratio was significantly higher in TCs. Clonally expanded intact proviruses were found only in PCs and located in centromeric satellite DNA or zinc-finger genes, both associated with heterochromatin features. In contrast, sampled intact proviruses were located in permissive genic euchromatic positions in TCs.CONCLUSIONSThese results suggest the need for, and can give guidance to, the design of future research to identify a distinct proviral landscape that may be associated with the persistent control of HIV-1 without ART.FUNDINGInstituto de Salud Carlos III (FI17/00186, FI19/00083, MV20/00057, PI18/01532, PI19/01127 and PI22/01796), Gilead Fellowships (GLD22/00147). NIH grants AI155171, AI116228, AI078799, HL134539, DA047034, MH134823, amfAR ARCHE and the Bill and Melinda Gates Foundation.
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Affiliation(s)
- Carmen Gasca-Capote
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Isabelle C. Roseto
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - María Reyes Jiménez-León
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Gregory Gladkov
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - María Inés Camacho-Sojo
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Alberto Pérez-Gómez
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Isabel Gallego
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Luis E. Lopez-Cortes
- Clinical Unit of Infectious Diseases and Microbiology, Virgen Macarena University Hospital, Seville, Spain
- Department of Medicine and Microbiology, School of Medicine and
- IBiS, Virgen Macarena University Hospital, CSIC, University of Seville, Seville, Spain
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Sara Bachiller
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
- Department of Medical Biochemistry, Molecular Biology, and Immunology, School of Medicine, University of Seville, Seville, Spain
| | - Joana Vitalle
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Mohamed Rafii-El-Idrissi Benhnia
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
- Department of Medical Biochemistry, Molecular Biology, and Immunology, School of Medicine, University of Seville, Seville, Spain
| | - Francisco J. Ostos
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
- Department of Medical Biochemistry, Molecular Biology, and Immunology, School of Medicine, University of Seville, Seville, Spain
| | | | - Jesús Santos
- Infectious Diseases, Microbiology and Preventive Medicine Unit, Virgen de la Victoria University Hospital, Malaga, Spain
| | - Rosario Palacios
- Infectious Diseases, Microbiology and Preventive Medicine Unit, Virgen de la Victoria University Hospital, Malaga, Spain
| | - Cristina Gomez-Ayerbe
- Infectious Diseases, Microbiology and Preventive Medicine Unit, Virgen de la Victoria University Hospital, Malaga, Spain
| | - Leopoldo Muñoz-Medina
- Unit of Infectious Diseases, San Cecilio University Hospital, Biohealth Research Institute, IBS-Granada, Granada, Spain
| | - Andrés Ruiz-Sancho
- Unit of Infectious Diseases, San Cecilio University Hospital, Biohealth Research Institute, IBS-Granada, Granada, Spain
| | - Mario Frias
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Service of Infectious Diseases, Reina Sofía University Hospital, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba University, Cordoba, Spain
| | - Antonio Rivero-Juarez
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Service of Infectious Diseases, Reina Sofía University Hospital, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba University, Cordoba, Spain
| | - Cristina Roca-Oporto
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Carmen Hidalgo-Tenorio
- Unit of Infectious Diseases, Virgen de las Nieves University Hospital, Biohealth Research Institute, IBS-Granada, Granada, Spain
| | - Anna Rull
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Joan XXIII University Hospital of Tarragona, IISPV, University of Rovira i Virgili, Tarragona, Spain
| | - Julian Olalla
- Internal Medicine Department, Costa Del Sol Hospital, Marbella, Spain
| | - Miguel A. Lopez-Ruz
- Unit of Infectious Diseases, Virgen de las Nieves University Hospital, Biohealth Research Institute, IBS-Granada, Granada, Spain
| | - Francesc Vidal
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Joan XXIII University Hospital of Tarragona, IISPV, University of Rovira i Virgili, Tarragona, Spain
| | - Consuelo Viladés
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Joan XXIII University Hospital of Tarragona, IISPV, University of Rovira i Virgili, Tarragona, Spain
| | | | - Matthias Cavassini
- Service of Infectious Diseases, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Nuria Espinosa
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Matthieu Perreau
- Service of Immunology and Allergy, Lausanne University Hospital and
| | - Joaquin Peraire
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Joan XXIII University Hospital of Tarragona, IISPV, University of Rovira i Virgili, Tarragona, Spain
| | - Antonio Rivero
- CIBERINFEC, Institute of Health Carlos III (ISCIII), Madrid, Spain
- Service of Infectious Diseases, Reina Sofía University Hospital, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Córdoba University, Cordoba, Spain
| | - Luis F. López-Cortes
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, 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
| | - Ezequiel Ruiz-Mateos
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocio University Hospital, Spanish National Research Council (CSIC), University of Seville, Clinical Unit of Infectious Diseases, Microbiology and Parasitology, Seville, Spain
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4
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Armani-Tourret M, Bone B, Tan TS, Sun W, Bellefroid M, Struyve T, Louella M, Yu XG, Lichterfeld M. Immune targeting of HIV-1 reservoir cells: a path to elimination strategies and cure. Nat Rev Microbiol 2024:10.1038/s41579-024-01010-8. [PMID: 38337034 DOI: 10.1038/s41579-024-01010-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Successful approaches for eradication or cure of HIV-1 infection are likely to include immunological mechanisms, but remarkably little is known about how human immune responses can recognize and interact with the few HIV-1-infected cells that harbour genome-intact viral DNA, persist long term despite antiretroviral therapy and represent the main barrier to a cure. For a long time regarded as being completely shielded from host immune responses due to viral latency, these cells do, on closer examination with single-cell analytic techniques, display discrete footprints of immune selection, implying that human immune responses may be able to effectively engage and target at least some of these cells. The failure to eliminate rebound-competent virally infected cells in the majority of persons likely reflects the evolution of a highly selected pool of reservoir cells that are effectively camouflaged from immune recognition or rely on sophisticated approaches for resisting immune-mediated killing. Understanding the fine-tuned interplay between host immune responses and viral reservoir cells will help to design improved interventions that exploit the immunological vulnerabilities of HIV-1 reservoir cells.
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Affiliation(s)
- Marie Armani-Tourret
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Benjamin Bone
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Toong Seng Tan
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Weiwei Sun
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Maxime Bellefroid
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Tine Struyve
- HIV Cure Research Center, Ghent University, Ghent, Belgium
| | - Michael Louella
- Community Advisory Board, Delaney AIDS Research Enterprise (DARE), San Francisco, CA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Xu G Yu
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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5
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Oh DS, Kim E, Lu G, Normand R, Shook LL, Lyall A, Jasset O, Demidkin S, Gilbert E, Kim J, Akinwunmi B, Tantivit J, Tirard A, Arnold BY, Slowikowski K, Goldberg MB, Filbin MR, Hacohen N, Nguyen LH, Chan AT, Yu XG, Li JZ, Yonker L, Fasano A, Perlis RH, Pasternak O, Gray KJ, Choi GB, Drew DA, Sen P, Villani AC, Edlow AG, Huh JR. SARS-CoV-2 infection elucidates unique features of pregnancy-specific immunity. medRxiv 2024:2024.02.05.24301794. [PMID: 38370801 PMCID: PMC10871456 DOI: 10.1101/2024.02.05.24301794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Pregnancy is a risk factor for increased severity of SARS-CoV-2 and other respiratory infections. The mechanisms underlying this risk have not been well-established, partly due to a limited understanding of how pregnancy shapes immune responses. To gain insight into the role of pregnancy in modulating immune responses at steady state and upon perturbation, we collected peripheral blood mononuclear cells (PBMC), plasma, and stool from 226 women, including 152 pregnant individuals (n = 96 with SARS-CoV-2 infection and n = 56 healthy controls) and 74 non-pregnant women (n = 55 with SARS-CoV-2 and n = 19 healthy controls). We found that SARS-CoV-2 infection was associated with altered T cell responses in pregnant compared to non-pregnant women. Differences included a lower percentage of memory T cells, a distinct clonal expansion of CD4-expressing CD8 + T cells, and the enhanced expression of T cell exhaustion markers, such as programmed cell death-1 (PD-1) and T cell immunoglobulin and mucin domain-3 (Tim-3), in pregnant women. We identified additional evidence of immune dysfunction in severely and critically ill pregnant women, including a lack of expected elevation in regulatory T cell (Treg) levels, diminished interferon responses, and profound suppression of monocyte function. Consistent with earlier data, we found maternal obesity was also associated with altered immune responses to SARS-CoV-2 infection, including enhanced production of inflammatory cytokines by T cells. Certain gut bacterial species were altered in pregnancy and upon SARS-CoV-2 infection in pregnant individuals compared to non-pregnant women. Shifts in cytokine and chemokine levels were also identified in the sera of pregnant individuals, most notably a robust increase of interleukin-27 (IL-27), a cytokine known to drive T cell exhaustion, in the pregnant uninfected control group compared to all non-pregnant groups. IL-27 levels were also significantly higher in uninfected pregnant controls compared to pregnant SARS-CoV-2-infected individuals. Using two different preclinical mouse models of inflammation-induced fetal demise and respiratory influenza viral infection, we found that enhanced IL-27 protects developing fetuses from maternal inflammation but renders adult female mice vulnerable to viral infection. These combined findings from human and murine studies reveal nuanced pregnancy-associated immune responses, suggesting mechanisms underlying the increased susceptibility of pregnant individuals to viral respiratory infections.
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Hartana CA, Lancien M, Gao C, Rassadkina Y, Lichterfeld M, Yu XG. IL-15-dependent immune crosstalk between natural killer cells and dendritic cells in HIV-1 elite controllers. Cell Rep 2023; 42:113530. [PMID: 38048223 PMCID: PMC10765318 DOI: 10.1016/j.celrep.2023.113530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 10/04/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
As the principal effector cell population of the innate immune system, natural killer (NK) cells may make critical contributions to natural, immune-mediated control of HIV-1 replication. Using genome-wide assessments of activating and inhibitory chromatin features, we demonstrate here that cytotoxic NK (cNK) cells from elite controllers (ECs) display elevated activating histone modifications at the interleukin 2 (IL-2)/IL-15 receptor β chain and the BCL2 gene loci. These histone changes translate into increased responsiveness of cNK cells to paracrine IL-15 secretion, which coincides with higher levels of IL-15 transcription by myeloid dendritic cells in ECs. The distinct immune crosstalk between these innate immune cell populations results in improved IL-15-dependent cNK cell survival and cytotoxicity, paired with a metabolic profile biased toward IL-15-mediated glycolytic activities. Together, these results suggest that cNK cells from ECs display a programmed IL-15 response signature and support the emerging role of innate immune pathways in natural, drug-free control of HIV-1.
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Affiliation(s)
| | - Melanie Lancien
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Ce Gao
- Ragon Institute of MGH, MIT, and Harvard, 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; Broad Institute of MIT and Harvard, Cambridge, MA 02142, 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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7
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Sun W, Rassadkina Y, Gao C, Collens SI, Lian X, Solomon IH, Mukerji SS, Yu XG, Lichterfeld M. Persistence of intact HIV-1 proviruses in the brain during antiretroviral therapy. eLife 2023; 12:RP89837. [PMID: 37938115 PMCID: PMC10631759 DOI: 10.7554/elife.89837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
HIV-1 reservoir cells that circulate in peripheral blood during suppressive antiretroviral therapy (ART) have been well characterized, but little is known about the dissemination of HIV-1-infected cells across multiple anatomical tissues, especially the CNS. Here, we performed single-genome, near full-length HIV-1 next-generation sequencing to evaluate the proviral landscape in distinct anatomical compartments, including multiple CNS tissues, from 3 ART-treated participants at autopsy. While lymph nodes and, to a lesser extent, gastrointestinal and genitourinary tissues represented tissue hotspots for the persistence of intact proviruses, we also observed intact proviruses in CNS tissue sections, particularly in the basal ganglia. Multi-compartment dissemination of clonal intact and defective proviral sequences occurred across multiple anatomical tissues, including the CNS, and evidence for the clonal proliferation of HIV-1-infected cells was found in the basal ganglia, in the frontal lobe, in the thalamus and in periventricular white matter. Deep analysis of HIV-1 reservoirs in distinct tissues will be informative for advancing HIV-1 cure strategies.
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Affiliation(s)
- Weiwei Sun
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | | | - Ce Gao
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | | | - Xiaodong Lian
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
| | - Isaac H Solomon
- Department of Pathology, Brigham and Women’s HospitalBostonUnited States
| | - Shibani S Mukerji
- Department of Neurology, Massachusetts General HospitalBostonUnited States
| | - Xu G Yu
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Infectious Disease Division, Brigham and Women’s HospitalBostonUnited States
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and HarvardCambridgeUnited States
- Infectious Disease Division, Brigham and Women’s HospitalBostonUnited States
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8
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Sun W, Rassadkina Y, Gao C, Collens SI, Lian X, Solomon IH, Mukerji S, Yu XG, Lichterfeld M. Persistence of intact HIV-1 proviruses in the brain during antiretroviral therapy. bioRxiv 2023:2023.06.26.546135. [PMID: 37425847 PMCID: PMC10327102 DOI: 10.1101/2023.06.26.546135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
HIV-1 reservoir cells that circulate in peripheral blood during suppressive antiretroviral therapy (ART) have been well characterized, but little is known about the dissemination of HIV-1-infected cells across multiple anatomical tissues, especially the central nervous system (CNS). Here, we performed single-genome, near full-length HIV-1 next-generation sequencing to evaluate the proviral landscape in distinct anatomical compartments, including multiple CNS tissues, from 3 ART-treated participants at autopsy. While lymph nodes and, to a lesser extent, gastrointestinal and genitourinary tissues represented tissue hotspots for the persistence of intact proviruses, we also observed intact proviruses in CNS tissue sections, particularly in the basal ganglia. Multi-compartment dissemination of clonal intact and defective proviral sequences occurred across multiple anatomical tissues, including the CNS, and evidence for the clonal proliferation of HIV-1-infected cells was found in the basal ganglia, in the frontal lobe, in the thalamus and in periventricular white matter. Deep analysis of HIV-1 reservoirs in distinct tissues will be informative for advancing HIV-1 cure strategies.
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Affiliation(s)
- Weiwei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
| | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
| | | | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Shibani Mukerji
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA
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9
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Hartana CA, Broncano PG, Maswabi K, Ajibola G, Moyo S, Mohammed T, Maphorisa C, Makhema J, Powis KM, Lockman S, Burbelo PD, Gao C, Yu XG, Kuritzkes DR, Shapiro R, Lichterfeld M. Immune Modulation of HIV-1 Reservoir Size in Early-Treated Neonates. J Infect Dis 2023; 228:281-286. [PMID: 37201510 PMCID: PMC10420392 DOI: 10.1093/infdis/jiad173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/20/2023] Open
Abstract
Immune mechanisms that modulate human immunodeficiency virus-1 (HIV-1) reservoir size in neonates are poorly understood. Using samples from neonates who initiated antiretroviral therapy shortly after birth, we demonstrate that interleukin-8-secreting CD4 T cells, which are selectively expanded in early infancy, are more resistant to HIV-1 infection and inversely correlated with the frequency of intact proviruses at birth. Moreover, newborns with HIV-1 infection displayed a distinct B-cell profile at birth, with reduction of memory B cells and expansion of plasmablasts and transitional B cells; however, B-cell immune perturbations were unrelated to HIV-1 reservoir size and normalized after initiation of antiretroviral therapy. Clinical Trials Registration. NCT02369406.
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Affiliation(s)
- Ciputra Adijaya Hartana
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Pilar Garcia Broncano
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Kenneth Maswabi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Kathleen M Powis
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine and Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Shahin Lockman
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard Medical School, Boston, Massachusetts, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Ce Gao
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Xu G Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Mathias Lichterfeld
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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10
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Bruno PM, Timms RT, Abdelfattah NS, Leng Y, Lelis FJN, Wesemann DR, Yu XG, Elledge SJ. High-throughput, targeted MHC class I immunopeptidomics using a functional genetics screening platform. Nat Biotechnol 2023; 41:980-992. [PMID: 36593401 PMCID: PMC10314971 DOI: 10.1038/s41587-022-01566-x] [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: 11/01/2021] [Accepted: 10/13/2022] [Indexed: 01/03/2023]
Abstract
Identification of CD8+ T cell epitopes is critical for the development of immunotherapeutics. Existing methods for major histocompatibility complex class I (MHC class I) ligand discovery are time intensive, specialized and unable to interrogate specific proteins on a large scale. Here, we present EpiScan, which uses surface MHC class I levels as a readout for whether a genetically encoded peptide is an MHC class I ligand. Predetermined starting pools composed of >100,000 peptides can be designed using oligonucleotide synthesis, permitting large-scale MHC class I screening. We exploit this programmability of EpiScan to uncover an unappreciated role for cysteine that increases the number of predicted ligands by 9-21%, reveal affinity hierarchies by analysis of biased anchor peptide libraries and screen viral proteomes for MHC class I ligands. Using these data, we generate and iteratively refine peptide binding predictions to create EpiScan Predictor. EpiScan Predictor performs comparably to other state-of-the-art MHC class I peptide binding prediction algorithms without suffering from underrepresentation of cysteine-containing peptides. Thus, targeted immunopeptidomics using EpiScan will accelerate CD8+ T cell epitope discovery toward the goal of individual-specific immunotherapeutics.
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Affiliation(s)
- Peter M Bruno
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Richard T Timms
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Nouran S Abdelfattah
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Yumei Leng
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Felipe J N Lelis
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Duane R Wesemann
- Department of Medicine, Division of Allergy and Immunology, Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, 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
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School and Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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11
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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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12
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Swank Z, Senussi Y, Manickas-Hill Z, Yu XG, Li JZ, Alter G, Walt DR. Reply to Alaedini and Wormser. Clin Infect Dis 2023; 76:1342-1343. [PMID: 36385394 DOI: 10.1093/cid/ciac896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Zoe Swank
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Yasmeen Senussi
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | | | - Xu G Yu
- Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jonathan Z Li
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - David R Walt
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
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13
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Yue H, Nowak RP, Overwijn D, Payne NC, Fischinger S, Atyeo C, Lam EC, St. Denis K, Brais LK, Konishi Y, Sklavenitis-Pistofidis R, Baden LR, Nilles EJ, Karlson EW, Yu XG, Li JZ, Woolley AE, Ghobrial IM, Meyerhardt JA, Balazs AB, Alter G, Mazitschek R, Fischer ES. Diagnostic TR-FRET assays for detection of antibodies in patient samples. Cell Rep Methods 2023; 3:100421. [PMID: 37056371 PMCID: PMC10088089 DOI: 10.1016/j.crmeth.2023.100421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/15/2022] [Accepted: 02/14/2023] [Indexed: 02/22/2023]
Abstract
Serological assays are important diagnostic tools for surveying exposure to the pathogen, monitoring immune response post vaccination, and managing spread of the infectious agent among the population. Current serological laboratory assays are often limited because they require the use of specialized laboratory technology and/or work with a limited number of sample types. Here, we evaluate an alternative by developing time-resolved Förster resonance energy transfer (TR-FRET) homogeneous assays that exhibited exceptional versatility, scalability, and sensitivity and outperformed or matched currently used strategies in terms of sensitivity, specificity, and precision. We validated the performance of the assays measuring total immunoglobulin G (IgG) levels; antibodies against severe acute respiratory syndrome coronavirus (SARS-CoV) or Middle Eastern respiratory syndrome (MERS)-CoV spike (S) protein; and SARS-CoV-2 S and nucleocapsid (N) proteins and applied it to several large sample sets and real-world applications. We further established a TR-FRET-based ACE2-S competition assay to assess the neutralization propensity of the antibodies. Overall, these TR-FRET-based serological assays can be rapidly extended to other antigens and are compatible with commonly used plate readers.
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Affiliation(s)
- Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Radosław P. Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Daan Overwijn
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - N. Connor Payne
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Center for Systems Biology, Massachusetts General Hospital (MGH), Boston, MA 02114, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Evan C. Lam
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Kerri St. Denis
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Lauren K. Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yoshinobu Konishi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Romanos Sklavenitis-Pistofidis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lindsey R. Baden
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Eric J. Nilles
- Department of Emergency Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | | | - Xu G. Yu
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Jonathan Z. Li
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ann E. Woolley
- Division of Infectious Diseases, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Irene M. Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Alejandro B. Balazs
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Galit Alter
- Ragon Institute of MGH, Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA 02139, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital (MGH), Boston, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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14
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Etemad B, Sun X, Li Y, Melberg M, Moisi D, Gottlieb R, Ahmed H, Aga E, Bosch RJ, Acosta EP, Yuki Y, Martin MP, Carrington M, Gandhi RT, Jacobson JM, Volberding P, Connick E, Mitsuyasu R, Frank I, Saag M, Eron JJ, Skiest D, Margolis DM, Havlir D, Schooley RT, Lederman MM, Yu XG, Li JZ. HIV post-treatment controllers have distinct immunological and virological features. Proc Natl Acad Sci U S A 2023; 120:e2218960120. [PMID: 36877848 PMCID: PMC10089217 DOI: 10.1073/pnas.2218960120] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/06/2023] [Indexed: 03/08/2023] Open
Abstract
HIV post-treatment controllers (PTCs) are rare individuals who maintain low levels of viremia after stopping antiretroviral therapy (ART). Understanding the mechanisms of HIV post-treatment control will inform development of strategies aiming at achieving HIV functional cure. In this study, we evaluated 22 PTCs from 8 AIDS Clinical Trials Group (ACTG) analytical treatment interruption (ATI) studies who maintained viral loads ≤400 copies/mL for ≥24 wk. There were no significant differences in demographics or frequency of protective and susceptible human leukocyte antigen (HLA) alleles between PTCs and post-treatment noncontrollers (NCs, n = 37). Unlike NCs, PTCs demonstrated a stable HIV reservoir measured by cell-associated RNA (CA-RNA) and intact proviral DNA assay (IPDA) during analytical treatment interruption (ATI). Immunologically, PTCs demonstrated significantly lower CD4+ and CD8+ T cell activation, lower CD4+ T cell exhaustion, and more robust Gag-specific CD4+ T cell responses and natural killer (NK) cell responses. Sparse partial least squares discriminant analysis (sPLS-DA) identified a set of features enriched in PTCs, including a higher CD4+ T cell% and CD4+/CD8+ ratio, more functional NK cells, and a lower CD4+ T cell exhaustion level. These results provide insights into the key viral reservoir features and immunological profiles for HIV PTCs and have implications for future studies evaluating interventions to achieve an HIV functional cure.
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Affiliation(s)
- Behzad Etemad
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02139
| | - Xiaoming Sun
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA02139
| | - Yijia Li
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02139
| | - Meghan Melberg
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02139
| | - Daniela Moisi
- School of Medicine, Case Western Reserve University, Cleveland, OH44106
| | - Rachel Gottlieb
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02139
| | - Hayat Ahmed
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02139
| | - Evgenia Aga
- Harvard T. H. Chan School of Public Health, Boston, MA02115
| | | | - Edward P. Acosta
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL35233
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD21702
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20814
| | - Maureen P. Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD21702
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20814
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA02139
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD21702
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD20814
| | - Rajesh T. Gandhi
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA02114
| | | | - Paul Volberding
- School of Medicine, University of California San Francisco, San Francisco, CA94143
| | | | - Ronald Mitsuyasu
- School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Ian Frank
- School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Michael Saag
- School of Medicine, University of Alabama at Birmingham, Birmingham, AL35233
| | - Joseph J. Eron
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Daniel Skiest
- Department of Medicine, University of Massachusetts Chan Medical School - Baystate, Springfield, MA01199
| | - David M. Margolis
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Diane Havlir
- School of Medicine, University of California San Francisco, San Francisco, CA94143
| | - Robert T. Schooley
- Department of Medicine, University of California San Diego, San Diego, CA92103
| | | | - Xu G. Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA02139
| | - Jonathan Z. Li
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA02139
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15
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Swank Z, Senussi Y, Manickas-Hill Z, Yu XG, Li JZ, Alter G, Walt DR. Persistent Circulating Severe Acute Respiratory Syndrome Coronavirus 2 Spike Is Associated With Post-acute Coronavirus Disease 2019 Sequelae. Clin Infect Dis 2023; 76:e487-e490. [PMID: 36052466 PMCID: PMC10169416 DOI: 10.1093/cid/ciac722] [Citation(s) in RCA: 147] [Impact Index Per Article: 147.0] [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: 07/05/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 02/02/2023] Open
Abstract
The diagnosis of postacute sequelae of coronavirus disease 2019 (PASC) poses an ongoing medical challenge. To identify biomarkers associated with PASC we analyzed plasma samples collected from PASC and coronavirus disease 2019 patients to quantify viral antigens and inflammatory markers. We detect severe acute respiratory syndrome coronavirus 2 spike predominantly in PASC patients up to 12 months after diagnosis.
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Affiliation(s)
- Zoe Swank
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - Yasmeen Senussi
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | | | - Xu G Yu
- Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jonathan Z Li
- Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - David R Walt
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
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16
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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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17
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Koofhethile CK, Rinaldi S, Rassadkina Y, Dinh VB, Gao C, Pallikkuth S, Garcia-Broncano P, de Armas LR, Pahwa R, Cotugno N, Vaz P, Lain MG, Palma P, Yu XG, Shapiro R, Pahwa S, Lichterfeld M. HIV-1 reservoir evolution in infants infected with clade C from Mozambique. Int J Infect Dis 2023; 127:129-136. [PMID: 36476348 PMCID: PMC9892347 DOI: 10.1016/j.ijid.2022.11.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 09/08/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The persistence of HIV-1-infected cells during antiretroviral therapy is well documented but may be modulated by early initiation of antiretroviral therapy in infants. METHODS Here, we longitudinally analyzed the proviral landscape in nine infants with vertical HIV-1 infection from Mozambique over a median period of 24 months, using single-genome, near full-length, next-generation proviral sequencing. RESULTS We observed a rapid decline in the frequency of intact proviruses, leading to a disproportional under-representation of intact HIV-1 sequences within the total number of HIV-1 DNA sequences after 12-24 months of therapy. In addition, proviral integration site profiling in one infant demonstrated clonal expansion of infected cells harboring intact proviruses and indicated that viral rebound was associated with an integration site profile dominated by intact proviruses integrated into genic and accessible chromatin locations. CONCLUSION Together, these results permit rare insight into the evolution of the HIV-1 reservoir in infants infected with HIV-1 and suggest that the rapid decline of intact proviruses, relative to defective proviruses, may be attributed to a higher vulnerability of genome-intact proviruses to antiviral immunity. Technologies to analyze combinations of intact proviral sequences and corresponding integration sites permit a high-resolution analysis of HIV-1 reservoir cells after early antiretroviral treatment initiation in infants.
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Affiliation(s)
- Catherine K Koofhethile
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA; Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | | | | | - Nicola Cotugno
- Academic Department of Pediatrics, Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Paula Vaz
- Fundação Ariel Glaser contra o SIDA Pediátrico, Maputo, Mozambique
| | | | - Paolo Palma
- Academic Department of Pediatrics, Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy; Chair of Pediatrics, Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Roger Shapiro
- Harvard TH Chan School of Public Health, Boston, 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.
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18
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Lian X, Seiger KW, Parsons EM, Gao C, Sun W, Gladkov GT, Roseto IC, Einkauf KB, Osborn MR, Chevalier JM, Jiang C, Blackmer J, Carrington M, Rosenberg ES, Lederman MM, McMahon DK, Bosch RJ, Jacobson JM, Gandhi RT, Peluso MJ, Chun TW, Deeks SG, Yu XG, Lichterfeld M. Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy. Cell Host Microbe 2023; 31:83-96.e5. [PMID: 36596305 PMCID: PMC9839361 DOI: 10.1016/j.chom.2022.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [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: 07/07/2022] [Revised: 10/08/2022] [Accepted: 11/30/2022] [Indexed: 01/03/2023]
Abstract
HIV-1 establishes a life-long reservoir of virally infected cells which cannot be eliminated by antiretroviral therapy (ART). Here, we demonstrate a markedly altered viral reservoir profile of long-term ART-treated individuals, characterized by large clones of intact proviruses preferentially integrated in heterochromatin locations, most prominently in centromeric satellite/micro-satellite DNA. Longitudinal evaluations suggested that this specific reservoir configuration results from selection processes that promote the persistence of intact proviruses in repressive chromatin positions, while proviruses in permissive chromosomal locations are more likely to be eliminated. A bias toward chromosomal integration sites in heterochromatin locations was also observed for intact proviruses in study participants who maintained viral control after discontinuation of antiretroviral therapy. Together, these results raise the possibility that antiviral selection mechanisms during long-term ART may induce an HIV-1 reservoir structure with features of deep latency and, possibly, more limited abilities to drive rebound viremia upon treatment interruptions.
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Affiliation(s)
- Xiaodong Lian
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Kyra W Seiger
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Elizabeth M Parsons
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ce Gao
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Weiwei Sun
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Gregory T Gladkov
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Kevin B Einkauf
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Matthew R Osborn
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Joshua M Chevalier
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Chenyang Jiang
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Jane Blackmer
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; 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, Frederick, MD 21701, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Eric S Rosenberg
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Ronald J Bosch
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Rajesh T Gandhi
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Xu G Yu
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA 02115, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
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19
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Martin-Gayo E, Gao C, Calvet-Mirabent M, Ouyang Z, Lichterfeld M, Yu XG. Cooperation between cGAS and RIG-I sensing pathways enables improved innate recognition of HIV-1 by myeloid dendritic cells in elite controllers. Front Immunol 2022; 13:1017164. [PMID: 36569826 PMCID: PMC9768436 DOI: 10.3389/fimmu.2022.1017164] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
Introduction Spontaneous control of HIV-1 replication in the absence of anti-retroviral therapy (ART) naturally occurs in a small proportion of HIV-1-infected individuals known as elite controllers (EC), likely as a result of improved innate and adaptive immune mechanisms. Previous studies suggest that enhanced cytosolic immune recognition of HIV-1 reverse transcripts in conventional dendritic cells (mDC) from EC enables effective induction of antiviral effector T cell responses. However, the specific molecular circuits responsible for such improved innate recognition of HIV-1 in mDC from these individuals remain unknown. Results and methods Here, we identified a subpopulation of EC whose mDC displayed higher baseline abilities to respond to intracellular HIV-1 dsDNA stimulation. A computational analysis of transcriptional signatures from such high responder EC, combined with functional studies, suggested cytosolic recognition of HIV-1 dsDNA by cGAS, combined with sensing of viral mRNA by RIG-I after polymerase III-mediated HIV-1 DNA transcription. Discussion Together, our work identifies collaborative networks of innate sensing pathways that enhance cell-intrinsic abilities of mDC to induce antiviral innate responses against HIV-1; these observations might be useful for the therapeutic induction of effective antiviral immune responses.
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Affiliation(s)
- Enrique Martin-Gayo
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Massachusetts General Hospital, Cambridge, MA, United States,Universidad Autónoma de Madrid, Immunology Unit, Hospital Universitario de la Princesa, Madrid, Spain,*Correspondence: Enrique Martin-Gayo, ; Xu G. Yu,
| | - Ce Gao
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Massachusetts General Hospital, Cambridge, MA, United States,Infectious Disease Divisions, Brigham and Women’s Hospital and Massachusetts General Hospital, Boston, MA, United States
| | - Marta Calvet-Mirabent
- Universidad Autónoma de Madrid, Immunology Unit, Hospital Universitario de la Princesa, Madrid, Spain
| | - Zhengyu Ouyang
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Massachusetts General Hospital, Cambridge, MA, United States,Infectious Disease Divisions, Brigham and Women’s Hospital and Massachusetts General Hospital, Boston, MA, United States
| | - Mathias Lichterfeld
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Massachusetts General Hospital, Cambridge, MA, United States,Infectious Disease Divisions, Brigham and Women’s Hospital and Massachusetts General Hospital, Boston, MA, United States
| | - Xu G. Yu
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Massachusetts General Hospital, Cambridge, MA, United States,Infectious Disease Divisions, Brigham and Women’s Hospital and Massachusetts General Hospital, Boston, MA, United States,*Correspondence: Enrique Martin-Gayo, ; Xu G. Yu,
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20
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Sun X, Gao C, Zhao K, Yang Y, Rassadkina Y, Fajnzylber J, Regan J, Li JZ, Lichterfeld M, Yu XG. Immune-profiling of SARS-CoV-2 viremic patients reveals dysregulated innate immune responses. Front Immunol 2022; 13:984553. [DOI: 10.3389/fimmu.2022.984553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/01/2022] [Indexed: 11/10/2022] Open
Abstract
SARS-CoV-2 plasma viremia has been associated with severe disease and death in COVID-19. However, the effects of viremia on immune responses in blood cells remain unclear. The current study comprehensively examined transcriptional signatures of PBMCs involving T cells, B cells, NK cells, monocytes, myeloid dendritic cells (mDCs), and plasmacytoid dendritic cells (pDCs) respectively, from three different groups including individuals with moderate (nM), or severe disease with (vS) or without (nS) detectable plasma viral load. Whole transcriptome analysis demonstrated that all seven immune cell subsets were associated with disease severity regardless of cell type. Supervised clustering analysis demonstrated that mDCs and pDCs gene signatures could distinguish disease severity. Notably, transcriptional signatures of the vS group were enriched in pathways related to DNA repair, E2F targets, and G2M checkpoints; in contrast, transcriptional signatures of the nM group were enriched in interferon responses. Moreover, we observed an impaired induction of interferon responses accompanied by imbalanced cell-intrinsic immune sensing and an excessive inflammatory response in patients with severe disease (nS and vS). In sum, our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in seven major immune cells in COVID-19 patients.
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21
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Lichterfeld M, Gao C, Yu XG. An ordeal that does not heal: understanding barriers to a cure for HIV-1 infection. Trends Immunol 2022; 43:608-616. [PMID: 35905706 PMCID: PMC9346997 DOI: 10.1016/j.it.2022.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 12/23/2022]
Abstract
With more than 38 million people living with HIV-1 (PLWH) worldwide, developing a cure for HIV-1 remains a major global health priority. Lifelong persistence of HIV-1 is frequently attributed to a pool of stable, transcriptionally silent HIV-1 proviruses, which are unaffected by currently available antiretroviral therapy (ART) or host immune activity. In this opinion article, we propose a more dynamic interpretation of HIV-1 reservoir cell biology and argue that HIV-1 proviruses frequently display residual viral transcriptional activity, making them vulnerable to longitudinal immune-mediated selection processes. Such mechanisms may, over extended periods of ART, induce an attenuated viral reservoir profile characterized by intact proviruses preferentially integrated into heterochromatin locations. We suggest that intensifying and accelerating naturally occurring selection mechanisms might represent a promising strategy for finding a potential cure for HIV-1 infection.
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Affiliation(s)
- 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.
| | - 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
| | - 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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22
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Nelson RW, Chen Y, Venezia OL, Majerus RM, Shin DS, Carrington MN, Yu XG, Wesemann DR, Moon JJ, Luster AD. SARS-CoV-2 epitope-specific CD4 + memory T cell responses across COVID-19 disease severity and antibody durability. Sci Immunol 2022; 7:eabl9464. [PMID: 35857584 PMCID: PMC9097883 DOI: 10.1126/sciimmunol.abl9464] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 04/15/2022] [Indexed: 01/14/2023]
Abstract
CD4+ T cells are central to long-term immunity against viruses through the functions of T helper 1 (TH1) and T follicular helper (TFH) cell subsets. To better understand the role of these subsets in coronavirus disease 2019 (COVID-19) immunity, we conducted a longitudinal study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific CD4+ T cell and antibody responses in convalescent individuals who seroconverted during the first wave of the pandemic in Boston, MA, USA, across a range of COVID-19 disease severities. Analyses of spike (S) and nucleocapsid (N) epitope-specific CD4+ T cells using peptide and major histocompatibility complex class II (pMHCII) tetramers demonstrated expanded populations of T cells recognizing the different SARS-CoV-2 epitopes in most individuals compared with prepandemic controls. Individuals who experienced a milder disease course not requiring hospitalization had a greater percentage of circulating TFH (cTFH) and TH1 cells among SARS-CoV-2-specific cells. Analysis of SARS-CoV-2-specific CD4+ T cells responses in a subset of individuals with sustained anti-S antibody responses after viral clearance also revealed an increased proportion of memory cTFH cells. Our findings indicate that efficient early disease control also predicts favorable long-term adaptive immunity.
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Affiliation(s)
- Ryan W. Nelson
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Yuezhou Chen
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
| | - Olivia L. Venezia
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
| | | | - Daniel S. Shin
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - MGH COVID-19 Collection & Processing Team†
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School; Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Queens University of Charlotte, Charlotte, NC, USA
- Ragon Institute of MGH, MIT and Harvard; Cambridge, MA, 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, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Mary N. Carrington
- Ragon Institute of MGH, MIT and Harvard; Cambridge, MA, 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, USA
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard; Cambridge, MA, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
| | - Duane R. Wesemann
- Department of Medicine, Division of Allergy and Clinical Immunology, Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard; Cambridge, MA, USA
| | - James J. Moon
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Andrew D. Luster
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
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23
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Hartana CA, Garcia-Broncano P, Rassadkina Y, Lian X, Jiang C, Einkauf KB, Maswabi K, Ajibola G, Moyo S, Mohammed T, Maphorisa C, Makhema J, Yuki Y, Martin M, Bennett K, Jean-Philippe P, Viard M, Hughes MD, Powis KM, Carrington M, Lockman S, Gao C, Yu XG, Kuritzkes DR, Shapiro R, Lichterfeld M. Immune correlates of HIV-1 reservoir cell decline in early-treated infants. Cell Rep 2022; 40:111126. [PMID: 35858580 PMCID: PMC9314543 DOI: 10.1016/j.celrep.2022.111126] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/13/2022] [Accepted: 06/30/2022] [Indexed: 11/03/2022] Open
Abstract
Initiation of antiretroviral therapy (ART) in infected neonates within hours after birth limits viral reservoir seeding but does not prevent long-term HIV-1 persistence. Here, we report parallel assessments of HIV-1 reservoir cells and innate antiviral immune responses in a unique cohort of 37 infected neonates from Botswana who started ART extremely early, frequently within hours after birth. Decline of genome-intact HIV-1 proviruses occurs rapidly after initiation of ART and is associated with an increase in natural killer (NK) cell populations expressing the cytotoxicity marker CD57 and with a decrease in NK cell subsets expressing the inhibitory marker NKG2A. Immune perturbations in innate lymphoid cells, myeloid dendritic cells, and monocytes detected at birth normalize after rapid institution of antiretroviral therapy but do not notably influence HIV-1 reservoir cell dynamics. These results suggest that HIV-1 reservoir cell seeding and evolution in early-treated neonates is markedly influenced by antiviral NK cell immune responses.
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Affiliation(s)
- Ciputra Adijaya Hartana
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Pilar Garcia-Broncano
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Chenyang Jiang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kevin B Einkauf
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Kenneth Maswabi
- Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Gbolahan Ajibola
- Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Terence Mohammed
- Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Joseph Makhema
- Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 20892, USA; 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 20892, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kara Bennett
- Bennett Statistical Consulting, Inc., Ballston Lake, NY 12019, USA
| | | | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 20892, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael D Hughes
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kathleen M Powis
- Harvard Medical School, Boston, MA 02115, USA; Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Medicine and Pediatrics, Massachusetts General Hospital, Boston, MA 02114, 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 20892, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shahin Lockman
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Roger Shapiro
- Harvard Medical School, Boston, MA 02115, USA; Botswana - Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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24
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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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25
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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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26
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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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27
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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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28
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Raines NH, Cheung MD, Wilson LS, Edberg JC, Erdmann NB, Schmaier AA, Berryhill TF, Manickas-Hill Z, Li JZ, Yu XG, Agarwal A, Barnes S, Parikh SM. Nicotinamide Adenine Dinucleotide Biosynthetic Impairment and Urinary Metabolomic Alterations Observed in Hospitalized Adults With COVID-19-Related Acute Kidney Injury. Kidney Int Rep 2021; 6:3002-3013. [PMID: 34541422 PMCID: PMC8439094 DOI: 10.1016/j.ekir.2021.09.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/03/2021] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION Acute kidney injury (AKI) is common in COVID-19 and associated with increased morbidity and mortality. We investigated alterations in the urine metabolome to test the hypothesis that impaired nicotinamide adenine dinucleotide (NAD+) biosynthesis and other deficiencies in energy metabolism in the kidney, previously characterized in ischemic, toxic, and inflammatory etiologies of AKI, will be present in COVID-19-associated AKI. METHODS This is a case-control study among the following 2 independent populations of adults hospitalized with COVID-19: a critically ill population in Boston, Massachusetts, and a general population in Birmingham, Alabama. The cases had AKI stages 2 or 3 by Kidney Disease Improving Global Outcomes (KDIGO) criteria; the controls had no AKI. Metabolites were measured by liquid chromatography-mass spectrometry. RESULTS A total of 14 cases and 14 controls were included from Boston and 8 cases and 10 controls from Birmingham. Increased urinary quinolinate-to-tryptophan ratio (Q/T), found with impaired NAD+ biosynthesis, was present in the cases at each location and pooled across locations (median [interquartile range]: 1.34 [0.59-2.96] in cases, 0.31 [0.13-1.63] in controls, P = 0.0013). Altered energy metabolism and purine metabolism contributed to a distinct urinary metabolomic signature that differentiated patients with and without AKI (supervised random forest class error: 2 of 28 in Boston, 0 of 18 in Birmingham). CONCLUSION Urinary metabolites spanning multiple biochemical pathways differentiate AKI versus non-AKI in patients hospitalized with COVID-19 and suggest a conserved impairment in NAD+ biosynthesis, which may present a novel therapeutic target to mitigate COVID-19-associated AKI.
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Affiliation(s)
- Nathan H. Raines
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew D. Cheung
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Landon S. Wilson
- Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jeffrey C. Edberg
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nathaniel B. Erdmann
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alec A. Schmaier
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Taylor F. Berryhill
- Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Zachary Manickas-Hill
- Ragon Institute of the Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard University, Massachusetts General Hospital, Cambridge, Massachusetts, USA
| | - Jonathan Z. Li
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Xu G. Yu
- Ragon Institute of the Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard University, Massachusetts General Hospital, Cambridge, Massachusetts, USA
| | - Anupam Agarwal
- Division of Nephrology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Stephen Barnes
- Targeted Metabolomics and Proteomics Laboratory, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Samir M. Parikh
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
- Division of Nephrology, Department of Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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29
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Schmaier AA, Pajares Hurtado GM, Manickas-Hill ZJ, Sack KD, Chen SM, Bhambhani V, Quadir J, Nath AK, Collier ARY, Ngo D, Barouch DH, Shapiro NI, Gerszten RE, Yu XG, Peters KG, Flaumenhaft R, Parikh SM. Tie2 activation protects against prothrombotic endothelial dysfunction in COVID-19. JCI Insight 2021; 6:e151527. [PMID: 34506304 PMCID: PMC8564889 DOI: 10.1172/jci.insight.151527] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/09/2021] [Indexed: 12/27/2022] Open
Abstract
Endothelial dysfunction accompanies the microvascular thrombosis commonly observed in severe COVID-19. Constitutively, the endothelial surface is anticoagulant, a property maintained at least in part via signaling through the Tie2 receptor. During inflammation, the Tie2 antagonist angiopoietin-2 (Angpt-2) is released from endothelial cells and inhibits Tie2, promoting a prothrombotic phenotypic shift. We sought to assess whether severe COVID-19 is associated with procoagulant endothelial dysfunction and alterations in the Tie2/angiopoietin axis. Primary HUVECs treated with plasma from patients with severe COVID-19 upregulated the expression of thromboinflammatory genes, inhibited the expression of antithrombotic genes, and promoted coagulation on the endothelial surface. Pharmacologic activation of Tie2 with the small molecule AKB-9778 reversed the prothrombotic state induced by COVID-19 plasma in primary endothelial cells. Lung autopsies from patients with COVID-19 demonstrated a prothrombotic endothelial signature. Assessment of circulating endothelial markers in a cohort of 98 patients with mild, moderate, or severe COVID-19 revealed endothelial dysfunction indicative of a prothrombotic state. Angpt-2 concentrations rose with increasing disease severity, and the highest levels were associated with worse survival. These data highlight the disruption of Tie2/angiopoietin signaling and procoagulant changes in endothelial cells in severe COVID-19. Our findings provide rationale for current trials of Tie2-activating therapy with AKB-9778 in COVID-19.
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Affiliation(s)
- Alec A. Schmaier
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Kelsey D. Sack
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
- Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Siyu M. Chen
- Cardiovascular Research Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Victoria Bhambhani
- Cardiovascular Research Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Juweria Quadir
- Cardiovascular Research Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Anjali K. Nath
- Cardiovascular Research Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | | | - Debby Ngo
- Division of Pulmonary, Critical Care and Sleep Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Dan H. Barouch
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Center for Virology and Vaccine Research, and
| | - Nathan I. Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Robert E. Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Infectious Diseases Division, Brigham and Women’s Hospital and Harvard Medical School, Massachusetts, Boston USA
| | - MGH COVID-19 Collection and Processing Team
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- The MGH COVID-19 Collection and Processing Team is detailed in Supplemental Acknowledgments
| | | | | | - Samir M. Parikh
- Division of Nephrology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
- Division of Nephrology, University of Texas Southwestern, Dallas, Texas, USA
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30
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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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31
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Abstract
PURPOSE OF REVIEW HIV-1 elite controllers encompass small populations of people infected with HIV-1 who can spontaneously control plasma viral loads below the limit of detection, in the absence of antiretroviral treatment. Antiviral immune responses are likely to contribute to such an impressive HIV-1 disease outcome. In this review, we discuss recent novel findings regarding antiviral innate and adaptive immune responses in elite controllers. RECENT FINDINGS Elite controllers maintain a pool of infected cells in which intact HIV-1 proviruses are more frequently integrated into noncoding regions of the host genome, likely conferring a state of deep latency. This atypical viral reservoir configuration is best explained by potent antiviral immune responses that can successfully eliminate virally infected cells in which proviruses are integrated into permissive chromatin. However, identifying the specific type and nature of this immune selection pressure represents a formidable challenge. Recent studies continue to support the role of HIV-1-specific CD8+ T cells as the main driver of elite immune control of HIV-1, however, increasing evidence suggests that their role is complemented by a fine-tuned interplay with innate immune cell subsets. Therefore, the combination of different immune effector mechanisms may shape antiviral immunity in elite controllers. SUMMARY Understanding the complex immune mechanisms responsible for natural, drug-free HIV-1 control represents a premier avenue to find and develop interventions for a cure of HIV-1 infection. Future single-cell assays designed to uncover the full genetic, epigenetic, transcriptional and functional complexity of antiviral immune responses in elite controllers may allow us to define correlates of antiviral immune protection in greater detail.
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Affiliation(s)
| | - Xu G. Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA; 02139, USA
- Infectious Disease Division, Brigham and Women’s Hospital, Boston, MA, USA
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32
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Kim MH, Salloum S, Wang JY, Lai Ping W, Regan J, Lefteri K, Manickas-Hill Z, Gao C, Li JZ, Sadreyev RI, Yu XG, Chung RT. Type I, II, and III Interferon Signatures Correspond to Coronavirus Disease 2019 Severity. J Infect Dis 2021; 224:777-782. [PMID: 34467988 PMCID: PMC8244575 DOI: 10.1093/infdis/jiab288] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/21/2021] [Indexed: 01/19/2023] Open
Abstract
We analyzed plasma levels of interferons (IFNs) and cytokines, and expression of IFN-stimulated genes in peripheral blood mononuclear cells in patients with coronavirus disease 2019 of varying disease severity. Patients hospitalized with mild disease exhibited transient type I IFN responses, while intensive care unit patients had prolonged type I IFN responses. Type II IFN responses were compromised in intensive care unit patients. Type III IFN responses were induced in the early phase of infection, even in convalescent patients. These results highlight the importance of early type I and III IFN responses in controlling coronavirus disease 2019 progression.
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Affiliation(s)
- Myung-Ho Kim
- Gastrointestinal Unit, Massachusetts General Hospital,
Boston, MA, USA
| | - Shadi Salloum
- Gastrointestinal Unit, Massachusetts General Hospital,
Boston, MA, USA
| | - Jeffrey Y Wang
- Gastrointestinal Unit, Massachusetts General Hospital,
Boston, MA, USA
| | - Wong Lai Ping
- Department of Molecular Biology, Massachusetts General
Hospital, Boston, MA, USA
| | - James Regan
- Department of Infectious Diseases, Brigham and Women's
Hospital, Boston, MA, USA
| | | | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard,
Cambridge, MA, USA
| | | | - Jonathan Z Li
- Department of Infectious Diseases, Brigham and Women's
Hospital and Harvard Medical School, Boston, MA, USA
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General
Hospital and Harvard Medical School, Boston, MA, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard,
Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital,
Boston, MA, USA
| | - Raymond T Chung
- Gastrointestinal Unit, Massachusetts General Hospital,
Boston, MA, USA
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33
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Regan J, Flynn JP, Rosenthal A, Jordan H, Li Y, Chishti R, Giguel F, Corry H, Coxen K, Fajnzylber J, Gillespie E, Kuritzkes DR, Hacohen N, Goldberg MB, Filbin MR, Yu XG, Baden L, Ribeiro RM, Perelson AS, Conway JM, Li JZ. Viral Load Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospitalized Individuals With Coronavirus Disease 2019. Open Forum Infect Dis 2021; 8:ofab153. [PMID: 34430669 PMCID: PMC8083268 DOI: 10.1093/ofid/ofab153] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 03/11/2021] [Accepted: 03/23/2021] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kinetics remain understudied, including the impact of remdesivir. In hospitalized individuals, peak sputum viral load occurred in week 2 of symptoms, whereas viremia peaked within 1 week of symptom-onset, suggesting early systemic seeding of SARS-CoV-2. Remdesivir treatment was associated with faster viral decay.
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Affiliation(s)
- James Regan
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - James P Flynn
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Alexandra Rosenthal
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hannah Jordan
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yijia Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rida Chishti
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Francoise Giguel
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heather Corry
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kendyll Coxen
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jesse Fajnzylber
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Elizabeth Gillespie
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel R Kuritzkes
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nir Hacohen
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Marcia B Goldberg
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael R Filbin
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Xu G Yu
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Harvard Medical School, Cambridge, Massachusetts, USA
| | - Lindsey Baden
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ruy M Ribeiro
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Alan S Perelson
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.,New Mexico Consortium, Los Alamos, New Mexico, USA
| | - Jessica M Conway
- Department of Mathematics and Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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34
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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 B, Yu XG, Yonker LM, Luban J. Innate lymphoid cells and disease tolerance in SARS-CoV-2 infection. medRxiv 2021. [PMID: 33469605 PMCID: PMC7814851 DOI: 10.1101/2021.01.14.21249839] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
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. This 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, and the percentage of amphiregulin-producing ILCs was higher in females than in males. 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 accounts for increased COVID-19 severity with age and in males.
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Affiliation(s)
- Noah J Silverstein
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Medical Scientist Training Program, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Yetao Wang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115
| | - Zachary Manickas-Hill
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Claudia Carbone
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ann Dauphin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Brittany P Boribong
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center, Boston, MA, USA.,Massachusetts General Hospital, Department of Pediatrics, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Maggie Loiselle
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center, Boston, MA, USA
| | - Jameson Davis
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center, Boston, MA, USA
| | - Maureen M Leonard
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center, Boston, MA, USA.,Massachusetts General Hospital, Department of Pediatrics, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Leticia Kuri-Cervantes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Nuala J Meyer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michael R Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan Z Li
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115.,Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Bruce Walker
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115.,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
| | - Xu G Yu
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Lael M Yonker
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center, Boston, MA, USA.,Massachusetts General Hospital, Department of Pediatrics, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA
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35
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Harb H, Benamar M, Lai PS, Contini P, Griffith JW, Crestani E, Schmitz-Abe K, Chen Q, Fong J, Marri L, Filaci G, Del Zotto G, Pishesha N, Kolifrath S, Broggi A, Ghosh S, Gelmez MY, Oktelik FB, Cetin EA, Kiykim A, Kose M, Wang Z, Cui Y, Yu XG, Li JZ, Berra L, Stephen-Victor E, Charbonnier LM, Zanoni I, Ploegh H, Deniz G, De Palma R, Chatila TA. Notch4 signaling limits regulatory T-cell-mediated tissue repair and promotes severe lung inflammation in viral infections. Immunity 2021; 54:1186-1199.e7. [PMID: 33915108 PMCID: PMC8080416 DOI: 10.1016/j.immuni.2021.04.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [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: 10/21/2020] [Revised: 02/02/2021] [Accepted: 04/02/2021] [Indexed: 12/12/2022]
Abstract
A cardinal feature of COVID-19 is lung inflammation and respiratory failure. In a prospective multi-country cohort of COVID-19 patients, we found that increased Notch4 expression on circulating regulatory T (Treg) cells was associated with disease severity, predicted mortality, and declined upon recovery. Deletion of Notch4 in Treg cells or therapy with anti-Notch4 antibodies in conventional and humanized mice normalized the dysregulated innate immunity and rescued disease morbidity and mortality induced by a synthetic analog of viral RNA or by influenza H1N1 virus. Mechanistically, Notch4 suppressed the induction by interleukin-18 of amphiregulin, a cytokine necessary for tissue repair. Protection by Notch4 inhibition was recapitulated by therapy with Amphiregulin and, reciprocally, abrogated by its antagonism. Amphiregulin declined in COVID-19 subjects as a function of disease severity and Notch4 expression. Thus, Notch4 expression on Treg cells dynamically restrains amphiregulin-dependent tissue repair to promote severe lung inflammation, with therapeutic implications for COVID-19 and related infections.
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MESH Headings
- Amphiregulin/pharmacology
- Animals
- Biomarkers
- Cytokines/metabolism
- Disease Models, Animal
- Disease Susceptibility
- Host-Pathogen Interactions/immunology
- Humans
- Immunity, Cellular
- Immunohistochemistry
- Immunomodulation/drug effects
- Inflammation Mediators/metabolism
- Influenza A virus/physiology
- Lung/immunology
- Lung/metabolism
- Lung/pathology
- Lung/virology
- Mice
- Mice, Transgenic
- Pneumonia, Viral/etiology
- Pneumonia, Viral/metabolism
- Pneumonia, Viral/pathology
- Receptor, Notch4/antagonists & inhibitors
- Receptor, Notch4/genetics
- Receptor, Notch4/metabolism
- Severity of Illness Index
- Signal Transduction
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
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Affiliation(s)
- Hani Harb
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Mehdi Benamar
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Peggy S Lai
- Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Paola Contini
- Deptartment of Internal Medicine, University of Genoa, Genoa, Italy; Unit of Clinical Immunology and Translational Medicine, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Jason W Griffith
- Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Elena Crestani
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Klaus Schmitz-Abe
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Qian Chen
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Jason Fong
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Luca Marri
- Unit of Clinical Immunology and Translational Medicine, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Gilberto Filaci
- Biotherapy Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Genny Del Zotto
- Department of Research and Diagnostics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Novalia Pishesha
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Stephen Kolifrath
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Achille Broggi
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Sreya Ghosh
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Metin Yusuf Gelmez
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine (Aziz Sancar DETAE), Istanbul University, Istanbul, Turkey
| | - Fatma Betul Oktelik
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine (Aziz Sancar DETAE), Istanbul University, Istanbul, Turkey
| | - Esin Aktas Cetin
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine (Aziz Sancar DETAE), Istanbul University, Istanbul, Turkey
| | - Ayca Kiykim
- Division of Pediatric Allergy and Immunology, Faculty of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - Murat Kose
- Department of Internal Medicine, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Ziwei Wang
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Ye Cui
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Xu G Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard Medical School, Boston, MA, USA
| | - Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lorenzo Berra
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Emmanuel Stephen-Victor
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Louis-Marie Charbonnier
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Ivan Zanoni
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Hidde Ploegh
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Gunnur Deniz
- Department of Immunology, Aziz Sancar Institute of Experimental Medicine (Aziz Sancar DETAE), Istanbul University, Istanbul, Turkey
| | - Raffaele De Palma
- Deptartment of Internal Medicine, University of Genoa, Genoa, Italy; Unit of Clinical Immunology and Translational Medicine, IRCCS Ospedale Policlinico San Martino, Genoa, Italy; CNR-Institute of Biomolecular Chemistry (IBC), Via Campi Flegrei 34, 80078 Pozzuoli, Napoli, Italy
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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Schmaier AA, Hurtado GP, Manickas-Hill ZJ, Sack KD, Chen SM, Bhambhani V, Quadir J, Nath AK, Collier ARY, Ngo D, Barouch DH, Gerszten RE, Yu XG, Peters K, Flaumenhaft R, Parikh SM. Tie2 activation protects against prothrombotic endothelial dysfunction in COVID-19. medRxiv 2021. [PMID: 34031665 DOI: 10.1101/2021.05.13.21257070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Profound endothelial dysfunction accompanies the microvascular thrombosis commonly observed in severe COVID-19. In the quiescent state, the endothelial surface is anticoagulant, a property maintained at least in part via constitutive signaling through the Tie2 receptor. During inflammation, the Tie2 antagonist angiopoietin-2 (Angpt-2) is released from activated endothelial cells and inhibits Tie2, promoting a prothrombotic phenotypic shift. We sought to assess whether severe COVID-19 is associated with procoagulant dysfunction of the endothelium and alterations in the Tie2-angiopoietin axis. Primary human endothelial cells treated with plasma from patients with severe COVID-19 upregulated the expression of thromboinflammatory genes, inhibited expression of antithrombotic genes, and promoted coagulation on the endothelial surface. Pharmacologic activation of Tie2 with the small molecule AKB-9778 reversed the prothrombotic state induced by COVID-19 plasma in primary endothelial cells. On lung autopsy specimens from COVID-19 patients, we found a prothrombotic endothelial signature as evidenced by increased von Willebrand Factor and loss of anticoagulant proteins. Assessment of circulating endothelial markers in a cohort of 98 patients with mild, moderate, or severe COVID-19 revealed profound endothelial dysfunction indicative of a prothrombotic state. Angpt-2 concentrations rose with increasing disease severity and highest levels were associated with worse survival. These data highlight the disruption of Tie2-angiopoietin signaling and procoagulant changes in endothelial cells in severe COVID-19. Moreover, our findings provide novel rationale for current trials of Tie2 activating therapy with AKB-9778 in severe COVID-19 disease.
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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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Siddiqi HK, Weber B, Zhou G, Regan J, Fajnzylber J, Coxen K, Corry H, Yu XG, DiCarli M, Li JZ, Bhatt DL. Increased Prevalence of Myocardial Injury in Patients with SARS-CoV-2 Viremia. Am J Med 2021; 134:542-546. [PMID: 33181107 PMCID: PMC7654293 DOI: 10.1016/j.amjmed.2020.09.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Patients with coronavirus disease 2019 (COVID-19) have a high prevalence of detectable troponin and myocardial injury. In addition, a subset of patients with COVID-19 has detectable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral loads. The objective of this study was to understand the relationship among SARS-CoV-2 viremia, detectable troponin, and myocardial injury in hospitalized patients with COVID-19. METHODS SARS-CoV-2 plasma viral load was measured in plasma samples drawn from patients hospitalized for COVID-19 at 2 academic medical centers. Baseline characteristics and clinically obtained high-sensitivity cardiac troponin T (hs-cTnT) values were abstracted from the medical record. The main outcome was detectable hs-cTnT (≥6 ng/mL) and myocardial injury (hs-cTnT ≥14 ng/mL; >99th percentile for assay). RESULTS A total of 70 hospitalized patients with COVID-19 were included in this study, with 39% females and median age 58 ± 17 years; 21 patients (30%) were found to have detectable SARS-CoV-2 viral load and were classified in the viremia group. Patients with viremia were significantly older than those without viremia. All of the patients with viremia (100%) had detectable troponin during hospitalization compared with 59% of patients without viremia (P = 0.0003). Myocardial injury was seen in 76% of patients with viremia and 38% of those patients without viremia (P = 0.004). CONCLUSIONS Hospitalized patients with COVID-19 with SARS-CoV-2 viremia have a significantly higher prevalence of detectable troponin and myocardial injury during their hospitalization compared with patients who did not. This first report of the relationship among SARS-CoV-2 viremia, detectable troponin, and myocardial injury in patients with COVID-19 points to additional mechanistic pathways that require deeper study to understand the complex interplay among these unique findings, cardiovascular outcomes, and mortality in COVID-19.
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Affiliation(s)
- Hasan K Siddiqi
- Heart and Vascular Center, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Brittany Weber
- Heart and Vascular Center, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Cardiovascular Imaging Program, Departments of Medicine and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Guohai Zhou
- Center for Clinical Investigation, Brigham and Women's Hospital, Boston, Mass
| | - James Regan
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Jesse Fajnzylber
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Kendyll Coxen
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Heather Corry
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Xu G Yu
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Massachusetts General Hospital, Harvard Medical School, Boston, Mass; Ragon Institute of MGH, MIT and Harvard University, Boston, Mass
| | - Marcelo DiCarli
- Heart and Vascular Center, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass; Cardiovascular Imaging Program, Departments of Medicine and Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Jonathan Z Li
- Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Deepak L Bhatt
- Heart and Vascular Center, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass.
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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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40
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Jilg N, Garcia-Broncano P, Peluso M, Segal FP, Bosch RJ, Roberts-Toler C, Chen SMY, Van Dam CN, Keefer MC, Kuritzkes DR, Landay AL, Deeks S, Yu XG, Sax PE, Li JZ. Maintenance of Viral Suppression in Human Immunodeficiency Virus Controllers Despite Waning T-Cell Responses During Antiretroviral Therapy. J Infect Dis 2021; 222:1837-1842. [PMID: 32496516 DOI: 10.1093/infdis/jiaa294] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 05/28/2020] [Indexed: 12/18/2022] Open
Abstract
AIDS Clinical Trials Group study A5308 found reduced T-cell activation and exhaustion in human immunodeficiency virus (HIV) controllers start antiretroviral therapy (ART). We further assessed HIV-specific T-cell responses and post-ART viral loads. Before ART, the 31% of participants with persistently undetectable viremia had more robust HIV-specific T-cell responses. During ART, significant decreases were observed in a broad range of T-cell responses. Eight controllers in A5308 and the Study of the Consequences of the Protease Inhibitor Era (SCOPE) cohort showed no viremia above the level of quantification in the first 12 weeks after ART discontinuation. ART significantly reduced HIV-specific T-cell responses in HIV controllers but did not adversely affect controller status after ART discontinuation.
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Affiliation(s)
- Nikolaus Jilg
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Michael Peluso
- University of California, San Francisco, California, USA
| | - Florencia P Segal
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ronald J Bosch
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Samantha M Y Chen
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Michael C Keefer
- University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Daniel R Kuritzkes
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Alan L Landay
- Rush University Medical Center, Chicago, Illinois, USA
| | - Steven Deeks
- University of California, San Francisco, California, USA
| | - Xu G Yu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Paul E Sax
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Kim MH, Salloum S, Wang JY, Wong LP, Regan J, Lefteri K, Manickas-Hill Z, Li JZ, Sadreyev RI, Yu XG, Chung RT. Type I, II, and III interferon signatures correspond to COVID-19 disease severity. medRxiv 2021. [PMID: 33758894 DOI: 10.1101/2021.03.10.21253317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We analyzed the plasma levels of interferons and cytokines, and the expression of interferon-stimulated genes in peripheral blood mononuclear cells in COVID-19 patients with different disease severity. Mild patients exhibited transient type I interferon responses, while ICU patients had prolonged type I interferon responses with hyper-inflammation mediated by interferon regulatory factor 1. Type II interferon responses were compromised in ICU patients. Type III interferon responses were induced in the early phase of SARS-CoV-2 infection, even in convalescent patients. These results highlight the importance of type I and III interferon responses during the early phase of infection in controlling COVID-19 progression.
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Li Y, Regan J, Fajnzylber J, Coxen K, Corry H, Wong C, Rosenthal A, Atyeo C, Fischinger S, Gillespie E, Chishti R, Baden L, Yu XG, Alter G, Kim A, Li JZ. Liver Fibrosis Index FIB-4 Is Associated With Mortality in COVID-19. Hepatol Commun 2021; 5:434-445. [PMID: 34553511 PMCID: PMC7753559 DOI: 10.1002/hep4.1650] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/27/2020] [Accepted: 11/01/2020] [Indexed: 12/11/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is associated with adverse outcomes, including need for invasive mechanical ventilation and death in people with risk factors. Liver enzyme elevation is commonly seen in this group, but its clinical significance remains elusive. In this study, we calculated the Fibrosis-4 (FIB-4) score for a cohort of hospitalized patients with COVID-19 and assessed its association with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA, inflammatory cytokine levels, and clinical outcome. A total of 202 hospitalized participants who tested positive for SARS-CoV-2 by nasopharyngeal sampling were included in this analysis. FIB-4 was calculated for each participant using the alanine aminotransferase, aspartate aminotransferase, age, and platelet count. We evaluated the association between FIB-4 and mortality using both multivariate logistic regression and Cox proportional hazards model. Correlations between FIB-4 and SARS-CoV-2 RNA and cytokine levels were evaluated using the Spearman test. Among the 202 participants, 22 died. The median FIB-4 in participants who survived and died were 1.91 and 3.98 (P < 0.001 by Mann-Whitney U test), respectively. Each one-unit increment in FIB-4 was associated with an increased odds of death (odds ratio, 1.79; 95% confidence interval, 1.36, 2.35; P < 0.001) after adjusting for baseline characteristics including sex, body mass index, hypertension, diabetes, and history of liver diseases. During hospitalization, FIB-4 peaked and then normalized in the survival group but failed to normalize in the death group. FIB-4 was positively correlated with the level of SARS-CoV-2 viral load and monocyte-associated cytokines, especially interleukin-6 and interferon gamma-induced protein 10. Conclusion: FIB-4 is associated with mortality in COVID-19, independent of underlying conditions including liver diseases. FIB-4 may be a simple and inexpensive approach to risk-stratify individuals with COVID-19.
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Affiliation(s)
- Yijia Li
- Division of Infectious DiseasesBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | - James Regan
- Division of Infectious DiseasesBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | - Jesse Fajnzylber
- Division of Infectious DiseasesBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | - Kendyll Coxen
- Division of Infectious DiseasesBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | - Heather Corry
- Division of Infectious DiseasesBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | - Colline Wong
- Division of Infectious DiseasesBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | - Alexandra Rosenthal
- Division of Infectious DiseasesBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | - Caroline Atyeo
- Ragon Institute of MGHMIT and HarvardHarvard Medical SchoolCambridgeMAUSA
| | | | - Elizabeth Gillespie
- Division of Infectious DiseasesBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | - Rida Chishti
- Division of Infectious DiseasesBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | - Lindsey Baden
- Division of Infectious DiseasesBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
| | - Xu G Yu
- Ragon Institute of MGHMIT and HarvardHarvard Medical SchoolCambridgeMAUSA
| | - Galit Alter
- Ragon Institute of MGHMIT and HarvardHarvard Medical SchoolCambridgeMAUSA
- Division of Infectious DiseasesMassachusetts General HospitalHarvard Medical SchoolBostonMAUSA
| | - Arthur Kim
- Division of Infectious DiseasesMassachusetts General HospitalHarvard Medical SchoolBostonMAUSA
| | - Jonathan Z Li
- Division of Infectious DiseasesBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA
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Shokr A, Pacheco LGC, Thirumalaraju P, Kanakasabapathy MK, Gandhi J, Kartik D, Silva FSR, Erdogmus E, Kandula H, Luo S, Yu XG, Chung RT, Li JZ, Kuritzkes DR, Shafiee H. Mobile Health (mHealth) Viral Diagnostics Enabled with Adaptive Adversarial Learning. ACS Nano 2021; 15:665-673. [PMID: 33226787 PMCID: PMC8299938 DOI: 10.1021/acsnano.0c06807] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Deep-learning (DL)-based image processing has potential to revolutionize the use of smartphones in mobile health (mHealth) diagnostics of infectious diseases. However, the high variability in cellphone image data acquisition and the common need for large amounts of specialist-annotated images for traditional DL model training may preclude generalizability of smartphone-based diagnostics. Here, we employed adversarial neural networks with conditioning to develop an easily reconfigurable virus diagnostic platform that leverages a dataset of smartphone-taken microfluidic chip photos to rapidly generate image classifiers for different target pathogens on-demand. Adversarial learning was also used to augment this real image dataset by generating 16,000 realistic synthetic microchip images, through style generative adversarial networks (StyleGAN). We used this platform, termed smartphone-based pathogen detection resource multiplier using adversarial networks (SPyDERMAN), to accurately detect different intact viruses in clinical samples and to detect viral nucleic acids through integration with CRISPR diagnostics. We evaluated the performance of the system in detecting five different virus targets using 179 patient samples. The generalizability of the system was confirmed by rapid reconfiguration to detect SARS-CoV-2 antigens in nasal swab samples (n = 62) with 100% accuracy. Overall, the SPyDERMAN system may contribute to epidemic preparedness strategies by providing a platform for smartphone-based diagnostics that can be adapted to a given emerging viral agent within days of work.
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Affiliation(s)
- Ahmed Shokr
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Luis G C Pacheco
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
- Department of Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA 40110-100, Brazil
| | - Prudhvi Thirumalaraju
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Manoj Kumar Kanakasabapathy
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Jahnavi Gandhi
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Deeksha Kartik
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Filipe S R Silva
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
- Department of Biotechnology, Institute of Health Sciences, Federal University of Bahia, Salvador, BA 40110-100, Brazil
| | - Eda Erdogmus
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Hemanth Kandula
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Shenglin Luo
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
| | - Xu G Yu
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, Massachusetts 02129, United States
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Raymond T Chung
- Liver Center, Gastrointestinal Division, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Hadi Shafiee
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02139, United States
- Harvard Medical School, Boston, Massachusetts 02115, United States
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44
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Li JZ, Segal FP, Bosch RJ, Lalama CM, Roberts-Toler C, Delagreverie H, Getz R, Garcia-Broncano P, Kinslow J, Tressler R, Van Dam CN, Keefer M, Carrington M, Lichterfeld M, Kuritzkes D, Yu XG, Landay A, Sax PE. Antiretroviral Therapy Reduces T-cell Activation and Immune Exhaustion Markers in Human Immunodeficiency Virus Controllers. Clin Infect Dis 2021; 70:1636-1642. [PMID: 31131858 DOI: 10.1093/cid/ciz442] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/24/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Despite low plasma human immunodeficiency virus (HIV) RNA, HIV controllers have evidence of viral replication and elevated inflammation. We assessed the effect of antiretroviral therapy (ART) on HIV suppression, immune activation, and quality of life (QoL). METHODS A5308 was a prospective, open-label study of rilpivirine/emtricitabine/tenofovir disoproxil fumarate in ART-naive HIV controllers (N = 35), defined as having HIV RNA <500 copies/mL for ≥12 months. The primary outcome measured change in %CD38+HLA-DR+ CD8+ T cells. Residual plasma viremia was measured using the integrase single-copy assay. QoL was measured using the EQ-5D questionnaire. Outcomes were evaluated using repeated measures general estimating equations models. RESULTS Before ART, HIV controllers with undetectable residual viremia <0.6 HIV-1 RNA copies/mL had higher CD4+ counts and lower levels of T-cell activation than those with detectable residual viremia. ART use was effective in further increasing the proportion of individuals with undetectable residual viremia (pre-ART vs after 24-48 weeks of ART: 19% vs 94%, P < .001). Significant declines were observed in the %CD38+HLA-DR+CD8+ T cells at 24-48 (-4.0%, P = .001) and 72-96 (-7.2%, P < .001) weeks after ART initiation. ART use resulted in decreases of several cellular markers of immune exhaustion and in a modest but significant improvement in self-reported QoL. There were no significant changes in CD4+ counts or HIV DNA. CONCLUSIONS ART in HIV controllers reduces T-cell activation and improves markers of immune exhaustion. These results support the possible clinical benefits of ART in this population.
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Affiliation(s)
- Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Florencia P Segal
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ronald J Bosch
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Christina M Lalama
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Carla Roberts-Toler
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Heloise Delagreverie
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.,Service de Microbiologie, Universite Paris Diderot, Paris, France
| | - Rachel Getz
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Jennifer Kinslow
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois
| | - Randall Tressler
- Division of AIDS, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Cornelius N Van Dam
- Regional Center for Infectious Disease, Cone Health, Greensboro, North Carolina
| | - Michael Keefer
- Division of Infectious Diseases, University of Rochester School of Medicine and Dentistry, New York
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Cambridge.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Mathias Lichterfeld
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Xu G Yu
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, Cambridge
| | - Alan Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois
| | - Paul E Sax
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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45
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Yonker LM, Neilan AM, Bartsch Y, Patel AB, Regan J, Arya P, Gootkind E, Park G, Hardcastle M, St John A, Appleman L, Chiu ML, Fialkowski A, De La Flor D, Lima R, Bordt EA, Yockey LJ, D'Avino P, Fischinger S, Shui JE, Lerou PH, Bonventre JV, Yu XG, Ryan ET, Bassett IV, Irimia D, Edlow AG, Alter G, Li JZ, Fasano A. Reply. J Pediatr 2021; 228:317-319. [PMID: 32971143 PMCID: PMC7505093 DOI: 10.1016/j.jpeds.2020.09.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 11/20/2022]
Affiliation(s)
- Lael M Yonker
- Mucosal Immunology and Biology Research Center, Department of Pediatrics
| | - Anne M Neilan
- Department of Pediatrics and Department of Internal Medicine, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | - Yannic Bartsch
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Harvard Medical School, Cambridge; Harvard Medical School, Boston, Massachusetts
| | - Ankit B Patel
- Department of Medicine, Renal Division, Brigham and Women's Hospital; Harvard Medical School, Boston, Massachusetts
| | - James Regan
- Department of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts
| | - Puneeta Arya
- Department of Pediatrics, Massachusetts General Hospital Harvard Medical School, Boston, Massachusetts
| | - Elizabeth Gootkind
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Grace Park
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Margot Hardcastle
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Anita St John
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Lori Appleman
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Michelle L Chiu
- Department of Pediatrics, Massachusetts General Hospital Harvard Medical School, Boston, Massachusetts
| | | | - Denis De La Flor
- Mucosal Immunology and Biology Research Center, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Rosiane Lima
- Mucosal Immunology and Biology Research Center, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Evan A Bordt
- Department of Pediatrics, Massachusetts General Hospital Harvard Medical School, Boston, Massachusetts
| | - Laura J Yockey
- Department of Internal Medicine, Vincent Center for Reproductive Biology
| | - Paolo D'Avino
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Stephanie Fischinger
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Harvard Medical School, Cambridge, Massachusetts
| | - Jessica E Shui
- Department of Pediatrics, Massachusetts General Hospital
| | - Paul H Lerou
- Department of Pediatrics, Massachusetts General Hospital
| | - Joseph V Bonventre
- Department of Medicine, Renal Division, Brigham and Women's Hospital; Harvard Medical School, Boston, Massachusetts
| | - Xu G Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Harvard Medical School, Cambridge, Massachusetts; Department of Infectious Diseases, Brigham and Women's Hospital; Harvard Medical School, Boston, Massachusetts
| | - Edward T Ryan
- Department of Pediatrics and Department of Internal Medicine, Massachusetts General Hospital; Harvard Medical School; Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | | | - Daniel Irimia
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | - Andrea G Edlow
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Vincent Center for Reproductive Biology
| | | | - Jonathan Z Li
- Department of Infectious Diseases, Brigham and Women's Hospital
| | - Alessio Fasano
- Mucosal Immunology and Biology Research Center, Department of Pediatrics, Massachusetts General Hospital Harvard Medical School, Boston, Massachusetts
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46
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Yonker LM, Neilan AM, Bartsch Y, Patel AB, Regan J, Arya P, Gootkind E, Park G, Hardcastle M, St John A, Appleman L, Chiu ML, Fialkowski A, De la Flor D, Lima R, Bordt EA, Yockey LJ, D'Avino P, Fischinger S, Shui JE, Lerou PH, Bonventre JV, Yu XG, Ryan ET, Bassett IV, Irimia D, Edlow AG, Alter G, Li JZ, Fasano A. Reply. J Pediatr 2021; 228:320-323. [PMID: 32956696 PMCID: PMC7500434 DOI: 10.1016/j.jpeds.2020.09.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 09/16/2020] [Indexed: 11/12/2022]
Affiliation(s)
- Lael M Yonker
- Mucosal Immunology and Biology Research Center; Department of Pediatrics, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | - Anne M Neilan
- Department of Pediatrics; Department of Internal Medicine, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | - Yannic Bartsch
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard Medical School, Cambridge, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - Ankit B Patel
- Renal Division, Department of Medicine, Brigham and Women's Hospital; Harvard Medical School, Boston, Massachusetts
| | - James Regan
- Department of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts
| | - Puneeta Arya
- Department of Pediatrics, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | - Elizabeth Gootkind
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Grace Park
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Margot Hardcastle
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Anita St John
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Lori Appleman
- Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Michelle L Chiu
- Department of Pediatrics, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | | | - Denis De la Flor
- Mucosal Immunology and Biology Research Center; Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Rosiane Lima
- Mucosal Immunology and Biology Research Center; Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts
| | - Evan A Bordt
- Department of Pediatrics, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | - Laura J Yockey
- Department of Internal Medicine; Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA
| | - Paolo D'Avino
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, Massachusetts
| | - Stephanie Fischinger
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard Medical School, Cambridge, Massachusetts
| | - Jessica E Shui
- Department of Pediatrics, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | - Paul H Lerou
- Department of Pediatrics, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | - Joseph V Bonventre
- Renal Division, Department of Medicine, Brigham and Women's Hospital; Harvard Medical School, Boston, Massachusetts
| | - Xu G Yu
- Ragon Institute of Massachusetts General Hospital, MIT and Harvard Medical School, Cambridge, Massachusetts; Department of Infectious Diseases, Brigham and Women's Hospital; Harvard Medical School, Boston, Massachusetts
| | - Edward T Ryan
- Department of Pediatrics; Department of Internal Medicine, Massachusetts General Hospital; Harvard Medical School; Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Ingrid V Bassett
- Department of Internal Medicine, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | - Daniel Irimia
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | - Andrea G Edlow
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology; Vincent Center for Reproductive Biology, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | - Galit Alter
- Vincent Center for Reproductive Biology, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
| | - Jonathan Z Li
- Department of Infectious Diseases, Brigham and Women's Hospital; Harvard Medical School, Boston, Massachusetts
| | - Alessio Fasano
- Mucosal Immunology and Biology Research Center; Department of Pediatrics, Massachusetts General Hospital; Harvard Medical School, Boston, Massachusetts
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47
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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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49
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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: 248] [Impact Index Per Article: 62.0] [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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50
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Yonker LM, Neilan AM, Bartsch Y, Patel AB, Regan J, Arya P, Gootkind E, Park G, Hardcastle M, St John A, Appleman L, Chiu ML, Fialkowski A, De la Flor D, Lima R, Bordt EA, Yockey LJ, D'Avino P, Fischinger S, Shui JE, Lerou PH, Bonventre JV, Yu XG, Ryan ET, Bassett IV, Irimia D, Edlow AG, Alter G, Li JZ, Fasano A. Pediatric Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Clinical Presentation, Infectivity, and Immune Responses. J Pediatr 2020; 227:45-52.e5. [PMID: 32827525 PMCID: PMC7438214 DOI: 10.1016/j.jpeds.2020.08.037] [Citation(s) in RCA: 224] [Impact Index Per Article: 56.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 01/08/2023]
Abstract
OBJECTIVES As schools plan for re-opening, understanding the potential role children play in the coronavirus infectious disease 2019 (COVID-19) pandemic and the factors that drive severe illness in children is critical. STUDY DESIGN Children ages 0-22 years with suspected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection presenting to urgent care clinics or being hospitalized for confirmed/suspected SARS-CoV-2 infection or multisystem inflammatory syndrome in children (MIS-C) at Massachusetts General Hospital were offered enrollment in the Massachusetts General Hospital Pediatric COVID-19 Biorepository. Enrolled children provided nasopharyngeal, oropharyngeal, and/or blood specimens. SARS-CoV-2 viral load, ACE2 RNA levels, and serology for SARS-CoV-2 were quantified. RESULTS A total of 192 children (mean age, 10.2 ± 7.0 years) were enrolled. Forty-nine children (26%) were diagnosed with acute SARS-CoV-2 infection; an additional 18 children (9%) met the criteria for MIS-C. Only 25 children (51%) with acute SARS-CoV-2 infection presented with fever; symptoms of SARS-CoV-2 infection, if present, were nonspecific. Nasopharyngeal viral load was highest in children in the first 2 days of symptoms, significantly higher than hospitalized adults with severe disease (P = .002). Age did not impact viral load, but younger children had lower angiotensin-converting enzyme 2 expression (P = .004). Immunoglobulin M (IgM) and Immunoglobulin G (IgG) to the receptor binding domain of the SARS-CoV-2 spike protein were increased in severe MIS-C (P < .001), with dysregulated humoral responses observed. CONCLUSIONS This study reveals that children may be a potential source of contagion in the SARS-CoV-2 pandemic despite having milder disease or a lack of symptoms; immune dysregulation is implicated in severe postinfectious MIS-C.
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Key Words
- ace2, angiotensin-converting enzyme
- covid-19, coronavirus disease-19
- ipo8, importin-8
- irb, institutional review board
- mgh, massachusetts general hospital
- mis-c, multisystem inflammatory syndrome in children
- nt-probnb, n-terminal pro b-type natriuretic peptide
- rbd, receptor binding domain
- rsv, respiratory syncytial virus
- sars-cov-2, severe acute respiratory syndrome coronavirus 2
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Affiliation(s)
- Lael M Yonker
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA.
| | - Anne M Neilan
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA; Department of Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Yannic Bartsch
- Harvard Medical School, Boston, MA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Harvard Medical School, Cambridge, MA
| | - Ankit B Patel
- Harvard Medical School, Boston, MA; Brigham and Women's Hospital, Department of Medicine, Renal Division, Boston, MA
| | - James Regan
- Department of Infectious Diseases, Brigham and Women's Hospital, Boston, MA
| | - Puneeta Arya
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | | | - Grace Park
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Margot Hardcastle
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Anita St John
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Lori Appleman
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Michelle L Chiu
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | | | - Denis De la Flor
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Rosiane Lima
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA
| | - Evan A Bordt
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Laura J Yockey
- Department of Internal Medicine, Massachusetts General Hospital, Boston, MA; Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA
| | - Paolo D'Avino
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA
| | - Stephanie Fischinger
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Harvard Medical School, Cambridge, MA
| | - Jessica E Shui
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Paul H Lerou
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Joseph V Bonventre
- Harvard Medical School, Boston, MA; Brigham and Women's Hospital, Department of Medicine, Renal Division, Boston, MA
| | - Xu G Yu
- Harvard Medical School, Boston, MA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Harvard Medical School, Cambridge, MA; Department of Infectious Diseases, Brigham and Women's Hospital, Boston, MA
| | - Edward T Ryan
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA; Department of Internal Medicine, Massachusetts General Hospital, Boston, MA; Harvard T.H. Chan School of Public Health, Boston, MA
| | - Ingrid V Bassett
- Harvard Medical School, Boston, MA; Department of Internal Medicine, Massachusetts General Hospital, Boston, MA
| | - Daniel Irimia
- Harvard Medical School, Boston, MA; Center for Engineering in Medicine, Department of Surgery, Boston, MA
| | - Andrea G Edlow
- Harvard Medical School, Boston, MA; Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, MA; Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Massachusetts General Hospital Boston, Boston, MA
| | - Galit Alter
- Harvard Medical School, Boston, MA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Harvard Medical School, Cambridge, MA
| | - Jonathan Z Li
- Harvard Medical School, Boston, MA; Department of Infectious Diseases, Brigham and Women's Hospital, Boston, MA
| | - Alessio Fasano
- Mucosal Immunology and Biology Research Center, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA; Harvard Medical School, Boston, MA
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