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Blest HTW, Redmond A, Avissar J, Barker J, Bridgeman A, Fowler G, Chauveau L, Hertzog J, Vendrell I, Fischer R, Iversen MB, Jing L, Koelle DM, Paludan SR, Kessler BM, Crump CM, Rehwinkel J. HSV-1 employs UL56 to antagonize expression and function of cGAMP channels. Cell Rep 2024; 43:114122. [PMID: 38652659 DOI: 10.1016/j.celrep.2024.114122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/21/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024] Open
Abstract
DNA sensing is important for antiviral immunity. The DNA sensor cGAS synthesizes 2'3'-cyclic GMP-AMP (cGAMP), a second messenger that activates STING, which induces innate immunity. cGAMP not only activates STING in the cell where it is produced but cGAMP also transfers to other cells. Transporters, channels, and pores (including SLC19A1, SLC46A2, P2X7, ABCC1, and volume-regulated anion channels (VRACs)) release cGAMP into the extracellular space and/or import cGAMP. We report that infection with multiple human viruses depletes some of these cGAMP conduits. This includes herpes simplex virus 1 (HSV-1) that targets SLC46A2, P2X7, and the VRAC subunits LRRC8A and LRRC8C for degradation. The HSV-1 protein UL56 is necessary and sufficient for these effects that are mediated at least partially by proteasomal turnover. UL56 thereby inhibits cGAMP uptake via VRAC, SLC46A2, and P2X7. Taken together, HSV-1 antagonizes intercellular cGAMP transfer. We propose that this limits innate immunity by reducing cell-to-cell communication via the immunotransmitter cGAMP.
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Affiliation(s)
- Henry T W Blest
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Alexander Redmond
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Jed Avissar
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Jake Barker
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, UK
| | - Anne Bridgeman
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Gerissa Fowler
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Lise Chauveau
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Jonny Hertzog
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marie B Iversen
- Department of Biomedicine, Aarhus University, Aarhus Aarhus C, Denmark
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Benaroya Research Institute, Seattle, WA 98101, USA
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, Aarhus Aarhus C, Denmark
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Colin M Crump
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, UK
| | - Jan Rehwinkel
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK.
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2
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Ouwendijk WJD, Roychoudhury P, Cunningham AL, Jerome KR, Koelle DM, Kinchington PR, Mohr I, Wilson AC, Verjans GGMGM, Depledge DP. Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice. J Virol 2024; 98:e0185823. [PMID: 38445887 PMCID: PMC11019907 DOI: 10.1128/jvi.01858-23] [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: 11/28/2023] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
Most individuals are latently infected with herpes simplex virus type 1 (HSV-1), and it is well-established that HSV-1 establishes latency in sensory neurons of peripheral ganglia. However, it was recently proposed that latent HSV-1 is also present in immune cells recovered from the ganglia of experimentally infected mice. Here, we reanalyzed the single-cell RNA sequencing (scRNA-Seq) data that formed the basis for that conclusion. Unexpectedly, off-target priming in 3' scRNA-Seq experiments enabled the detection of non-polyadenylated HSV-1 latency-associated transcript (LAT) intronic RNAs. However, LAT reads were near-exclusively detected in mixed populations of cells undergoing cell death. Specific loss of HSV-1 LAT and neuronal transcripts during quality control filtering indicated widespread destruction of neurons, supporting the presence of contaminating cell-free RNA in other cells following tissue processing. In conclusion, the reported detection of latent HSV-1 in non-neuronal cells is best explained using compromised scRNA-Seq datasets.IMPORTANCEMost people are infected with herpes simplex virus type 1 (HSV-1) during their life. Once infected, the virus generally remains in a latent (silent) state, hiding within the neurons of peripheral ganglia. Periodic reactivation (reawakening) of the virus may cause fresh diseases such as cold sores. A recent study using single-cell RNA sequencing (scRNA-Seq) proposed that HSV-1 can also establish latency in the immune cells of mice, challenging existing dogma. We reanalyzed the data from that study and identified several flaws in the methodologies and analyses performed that invalidate the published conclusions. Specifically, we showed that the methodologies used resulted in widespread destruction of neurons which resulted in the presence of contaminants that confound the data analysis. We thus conclude that there remains little to no evidence for HSV-1 latency in immune cells.
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Affiliation(s)
- Werner J. D. Ouwendijk
- HerpesLabNL, Department of Viroscience, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - David M. Koelle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Translational Research, Benaroya Research Institute, Seattle, Washington, USA
| | - Paul R. Kinchington
- Department of Ophthalmology and of Molecular Microbiology and Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
| | | | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York, New York, USA
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF) partner site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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3
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Reid TB, Godornes C, Campbell VL, Laing KJ, Tantalo LC, Gomez A, Pholsena TN, Lieberman NAP, Krause TM, Cegielski VI, Culver LA, Nguyen N, Tong DQ, Hawley KL, Greninger AL, Giacani L, Cameron CE, Dombrowski JC, Wald A, Koelle DM. Treponema pallidum periplasmic and membrane proteins are recognized by circulating and skin CD4+ T cells. bioRxiv 2024:2024.02.27.581790. [PMID: 38464313 PMCID: PMC10925203 DOI: 10.1101/2024.02.27.581790] [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: 03/12/2024]
Abstract
Background Histologic and serologic studies suggest the induction of local and systemic Treponema pallidum ( Tp )-specific CD4+ T cell responses to Tp infection. We hypothesized that Tp -specific CD4+ T cells are detectable in blood and in the skin rash of secondary syphilis and persist in both compartments after treatment. Methods PBMC collected from 67 participants were screened by IFNγ ELISPOT response to Tp sonicate. Tp -reactive T cell lines from blood and skin were probed for responses to 88 recombinant Tp antigens. Peptide epitopes and HLA class II restriction were defined for selected antigens. Results We detected CD4+ T cell responses to Tp sonicate ex vivo. Using Tp -reactive T cell lines we observed recognition of 14 discrete proteins, 13 of which localize to bacterial membranes or the periplasmic space. After therapy, Tp -specific T cells persisted for at least 6 months in skin and 10 years in blood. Conclusions Tp infection elicits an antigen-specific CD4+ T cell response in blood and skin. Tp -specific CD4+ T cells persist as memory in both compartments long after curative therapy. The Tp antigenic targets we identified may be high priority vaccine candidates.
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4
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Pulliam T, Jani S, Jing L, Ryu H, Jojic A, Shasha C, Zhang J, Kulikauskas R, Church C, Garnett-Benson C, Gooley T, Chapuis A, Paulson K, Smith KN, Pardoll DM, Newell EW, Koelle DM, Topalian SL, Nghiem P. Circulating cancer-specific CD8 T cell frequency is associated with response to PD-1 blockade in Merkel cell carcinoma. Cell Rep Med 2024; 5:101412. [PMID: 38340723 PMCID: PMC10897614 DOI: 10.1016/j.xcrm.2024.101412] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/01/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Understanding cancer immunobiology has been hampered by difficulty identifying cancer-specific T cells. Merkel cell polyomavirus (MCPyV) causes most Merkel cell carcinomas (MCCs). All patients with virus-driven MCC express MCPyV oncoproteins, facilitating identification of virus (cancer)-specific T cells. We studied MCPyV-specific T cells from 27 patients with MCC using MCPyV peptide-HLA-I multimers, 26-color flow cytometry, single-cell transcriptomics, and T cell receptor (TCR) sequencing. In a prospective clinical trial, higher circulating MCPyV-specific CD8 T cell frequency before anti-PD-1 treatment was strongly associated with 2-year recurrence-free survival (75% if detectable, 0% if undetectable, p = 0.0018; ClinicalTrial.gov: NCT02488759). Intratumorally, such T cells were typically present, but their frequency did not significantly associate with response. Circulating MCPyV-specific CD8 T cells had increased stem/memory and decreased exhaustion signatures relative to their intratumoral counterparts. These results suggest that cancer-specific CD8 T cells in the blood may play a role in anti-PD-1 responses. Thus, strategies that augment their number or mobilize them into tumors could improve outcomes.
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Affiliation(s)
- Thomas Pulliam
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Saumya Jani
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Heeju Ryu
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ana Jojic
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Carolyn Shasha
- Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jiajia Zhang
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Rima Kulikauskas
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Candice Church
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | | | - Ted Gooley
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Aude Chapuis
- Department of Medicine, University of Washington, Seattle, WA 98109, USA; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kelly Paulson
- Paul G. Allen Research Center, Providence-Swedish Cancer Institute, Seattle, WA 98104, USA; Elson S. Floyd College of Medicine, Washington State University, Spokane, WA 99202, USA
| | - Kellie N Smith
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21827, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Evan W Newell
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA; Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - David M Koelle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA; Vaccine and Infectious Disease Department, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98109, USA; Benaroya Research Institute, Seattle, WA 98101, USA
| | - Suzanne L Topalian
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21287, USA; Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Paul Nghiem
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA 98109, USA.
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5
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Ryu H, Bi TM, Pulliam TH, Sarkar K, Church CD, Kumar N, Mayer-Blackwell K, Jani S, Ramchurren N, Hansen UK, Hadrup SR, Fling SP, Koelle DM, Nghiem P, Newell EW. Merkel cell polyomavirus-specific and CD39 +CLA + CD8 T cells as blood-based predictive biomarkers for PD-1 blockade in Merkel cell carcinoma. Cell Rep Med 2024; 5:101390. [PMID: 38340724 PMCID: PMC10897544 DOI: 10.1016/j.xcrm.2023.101390] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/29/2023] [Accepted: 12/21/2023] [Indexed: 02/12/2024]
Abstract
Merkel cell carcinoma is a skin cancer often driven by Merkel cell polyomavirus (MCPyV) with high rates of response to anti-PD-1 therapy despite low mutational burden. MCPyV-specific CD8 T cells are implicated in anti-PD-1-associated immune responses and provide a means to directly study tumor-specific T cell responses to treatment. Using mass cytometry and combinatorial tetramer staining, we find that baseline frequencies of blood MCPyV-specific cells correlated with response and survival. Frequencies of these cells decrease markedly during response to therapy. Phenotypes of MCPyV-specific CD8 T cells have distinct expression patterns of CD39, cutaneous lymphocyte-associated antigen (CLA), and CD103. Correspondingly, overall bulk CD39+CLA+ CD8 T cell frequencies in blood correlate with MCPyV-specific cell frequencies and similarly predicted favorable clinical outcomes. Conversely, frequencies of CD39+CD103+ CD8 T cells are associated with tumor burden and worse outcomes. These cell subsets can be useful as biomarkers and to isolate blood-derived tumor-specific T cells.
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Affiliation(s)
- Heeju Ryu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Timothy M Bi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Thomas H Pulliam
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Korok Sarkar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Candice D Church
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Nandita Kumar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - Saumya Jani
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Nirasha Ramchurren
- Cancer Immunotherapy Trails Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ulla K Hansen
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sine R Hadrup
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Steven P Fling
- Cancer Immunotherapy Trails Network, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David M Koelle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA; Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Benaroya Research Institute, Seattle, WA, USA
| | - Paul Nghiem
- Department of Medicine, Division of Dermatology, University of Washington, Seattle, WA, USA
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA; Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA.
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6
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Babu TM, Shen X, McClelland RS, Wang Z, Selke S, Wilkens C, Hauge KA, McClurkan CL, Goecker E, Laing KJ, Koelle DM, Greninger AL, Nussenzweig MC, Montefiori DC, Corey L, Wald A. Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Subvariant Neutralization Following a Primary Vaccine Series of NVX-CoV2373 and BNT162b2 Monovalent Booster Vaccine. Open Forum Infect Dis 2024; 11:ofad673. [PMID: 38379566 PMCID: PMC10878050 DOI: 10.1093/ofid/ofad673] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 02/22/2024] Open
Abstract
We evaluated the immunologic response to a novel vaccine regimen that included 2 doses of NVX-CoV2373 (Novavax) followed by 1 dose of BNT162b2 (Pfizer-BioNTech) monovalent booster vaccine. A durable neutralizing antibody response to Omicron BA.4/BA.5 and BA.1 variants was observed at month 6 after the booster, while immune escape was noted for the XBB.1.5 variant.
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Affiliation(s)
- Tara M Babu
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - R Scott McClelland
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Washington, Seattle, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
| | - Stacy Selke
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Chloe Wilkens
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Kirsten A Hauge
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Christopher L McClurkan
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Erin Goecker
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Kerry J Laing
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - David M Koelle
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Washington, Seattle, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Lawrence Corey
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Anna Wald
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
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7
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Ford ES, Li A, Laing KJ, Dong L, Diem K, Jing L, Basu K, Ott M, Tartaglia J, Gurunathan S, Reid JL, Ecsedi M, Chapuis AG, Huang ML, Magaret AS, Johnston C, Zhu J, Koelle DM, Corey L. Expansion of the HSV-2-specific T cell repertoire in skin after immunotherapeutic HSV-2 vaccine. medRxiv 2024:2022.02.04.22270210. [PMID: 38352384 PMCID: PMC10863019 DOI: 10.1101/2022.02.04.22270210] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
The skin at the site of HSV-2 reactivation is enriched for HSV-2-specific T cells. To evaluate whether an immunotherapeutic vaccine could elicit skin-based memory T cells, we studied skin biopsies and HSV-2-reactive CD4+ T cells from peripheral blood mononuclear cells (PBMCs) by T cell receptor β (TRB) sequencing before and after vaccination with a replication-incompetent whole virus HSV-2 vaccine candidate (HSV529). The representation of HSV-2-reactive CD4+ TRB sequences from PBMCs in the skin TRB repertoire increased after the first vaccine dose. We found sustained expansion after vaccination of unique, skin-based T-cell clonotypes that were not detected in HSV-2-reactive CD4+ T cells isolated from PBMCs. In one participant a switch in immunodominance occurred with the emergence of a T cell receptor (TCR) αβ pair after vaccination that was not detected in blood. This TCRαβ was shown to be HSV-2-reactive by expression of a synthetic TCR in a Jurkat-based NR4A1 reporter system. The skin in areas of HSV-2 reactivation possesses an oligoclonal TRB repertoire that is distinct from the circulation. Defining the influence of therapeutic vaccination on the HSV-2-specific TRB repertoire requires tissue-based evaluation.
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Affiliation(s)
- Emily S Ford
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Center, Seattle WA
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle WA
| | - Alvason Li
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Center, Seattle WA
| | - Kerry J Laing
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle WA
| | - Lichun Dong
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle WA
| | - Kurt Diem
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA
| | - Lichen Jing
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle WA
| | - Krithi Basu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle WA
| | - Mariliis Ott
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle WA
| | | | | | - Jack L Reid
- Clinical Research Division, Fred Hutch Cancer Center, Seattle WA
| | - Matyas Ecsedi
- Clinical Research Division, Fred Hutch Cancer Center, Seattle WA
| | - Aude G Chapuis
- Clinical Research Division, Fred Hutch Cancer Center, Seattle WA
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA
| | - Amalia S Magaret
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Center, Seattle WA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA
| | - Christine Johnston
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Center, Seattle WA
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle WA
| | - Jia Zhu
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Center, Seattle WA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA
| | - David M Koelle
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Center, Seattle WA
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle WA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA
- Department of Global Health, University of Washington, Seattle WA
- Benaroya Research Institute, Seattle WA
| | - Lawrence Corey
- Vaccine and Infectious Diseases Division, Fred Hutch Cancer Center, Seattle WA
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle WA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA
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8
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Harbecke R, Oxman MN, Selke S, Ashbaugh ME, Lan KF, Koelle DM, Wald A. Prior Herpes Simplex Virus Infection and the Risk of Herpes Zoster. J Infect Dis 2024; 229:64-72. [PMID: 37410908 PMCID: PMC10786259 DOI: 10.1093/infdis/jiad259] [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: 01/04/2023] [Revised: 06/22/2023] [Accepted: 07/10/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND The incidence of herpes zoster (HZ) has increased in the United States concurrent with decrease in herpes simplex virus (HSV) prevalence. We hypothesized that lack of HSV-elicited cross-reactive immunity to varicella-zoster virus (VZV) results in an increased risk of HZ. Using specimens from the placebo arm of the Shingles Prevention Study, we investigated whether persons who develop HZ are less likely to have prior HSV infection than persons who do not develop HZ, and whether HZ is less severe in persons with HSV than in HSV seronegative persons. METHODS We conducted a nested case-control (1:2) study comparing the seroprevalence of HSV-1 and HSV-2 in cases (persons with polymerase chain reaction-confirmed HZ) to age-, sex-, and health-matched controls (persons without HZ). RESULTS Sera from 639 study participants (213 cases and 426 controls) yielded definitive HSV antibody results and were analyzed. Overall, HSV seropositivity rate was 75%. HSV seronegativity was significantly higher in HZ cases than controls (30.5% vs 22.3%; P = .024), with a 55% higher risk of HZ in HSV seronegative than HSV seropositive participants. HSV seropositivity was associated with more severe HZ (P = .021). CONCLUSIONS Our study demonstrated that prior infection with HSV partly protects against HZ.
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Affiliation(s)
- Ruth Harbecke
- Department of Veterans Affairs San Diego Healthcare System, San Diego, California, USA
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Michael N Oxman
- Department of Veterans Affairs San Diego Healthcare System, San Diego, California, USA
- Department of Medicine, University of California San Diego, San Diego, California, USA
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Mark E Ashbaugh
- Department of Veterans Affairs San Diego Healthcare System, San Diego, California, USA
| | - Kristine F Lan
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - David M Koelle
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
| | - Anna Wald
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington School of Medicine, Seattle, Washington, USA
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9
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Ford ES, Mayer-Blackwell K, Jing L, Laing KJ, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Greninger AL, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. Repeated mRNA vaccination sequentially boosts SARS-CoV-2-specific CD8 + T cells in persons with previous COVID-19. Nat Immunol 2024; 25:166-177. [PMID: 38057617 PMCID: PMC10981451 DOI: 10.1038/s41590-023-01692-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 10/08/2022] [Accepted: 10/27/2023] [Indexed: 12/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hybrid immunity is more protective than vaccination or previous infection alone. To investigate the kinetics of spike-reactive T (TS) cells from SARS-CoV-2 infection through messenger RNA vaccination in persons with hybrid immunity, we identified the T cell receptor (TCR) sequences of thousands of index TS cells and tracked their frequency in bulk TCRβ repertoires sampled longitudinally from the peripheral blood of persons who had recovered from coronavirus disease 2019 (COVID-19). Vaccinations led to large expansions in memory TS cell clonotypes, most of which were CD8+ T cells, while also eliciting diverse TS cell clonotypes not observed before vaccination. TCR sequence similarity clustering identified public CD8+ and CD4+ TCR motifs associated with spike (S) specificity. Synthesis of longitudinal bulk ex vivo single-chain TCRβ repertoires and paired-chain TCRɑβ sequences from droplet sequencing of TS cells provides a roadmap for the rapid assessment of T cell responses to vaccines and emerging pathogens.
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Affiliation(s)
- Emily S Ford
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kerry J Laing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Anton M Sholukh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Russell St Germain
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Emily L Bossard
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Thomas H Pulliam
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Saumya Jani
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | | | - Anna Wald
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Brett Eaton
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elizabeth Eudy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Elena Postnikova
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | | | | | - Rachel M Gittelman
- Adaptive Biotechnologies, Seattle, WA, USA
- Guardant Health, Redwood City, CA, USA
| | - Matyas Ecsedi
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Takeda Oncology, Cambridge, MA, USA
| | - Elise Wilcox
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Aude G Chapuis
- Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Andrew Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA, USA.
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Translational Research, Benaroya Research Institute, Seattle, WA, USA.
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10
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Laing KJ, Ford ES, Johnson MJ, Levin MJ, Koelle DM, Weinberg A. Recruitment of naive CD4+ T cells by the recombinant zoster vaccine correlates with persistent immunity. J Clin Invest 2023; 133:e172634. [PMID: 37788096 PMCID: PMC10688978 DOI: 10.1172/jci172634] [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: 06/06/2023] [Accepted: 09/27/2023] [Indexed: 10/05/2023] Open
Abstract
Herpes zoster (HZ) is a substantial problem for people with decreased cell-mediated immunity, including older adults. The first vaccine approved for HZ prevention, the zoster vaccine live (ZVL), which provided limited and short-lived protection, has been supplanted by the superior recombinant zoster vaccine (RZV), which provides robust and durable protection. To understand the mechanisms underlying the differential immunologic characteristics of the 2 vaccines, we used T cell receptor β chain sequencing and peptide-MHC class II tetramer staining to analyze recombinant glycoprotein E-specific (gE-specific) CD4+ T cell clonotypes in RZV and ZVL recipients. Compared with ZVL, RZV expanded more gE-specific CD4+ clonotypes, with greater breadth and higher frequency of public clonotypes. RZV recruited a higher proportion of clonotypes from naive than from memory cells, while ZVL recruited equally from memory and naive compartments. Compared with memory-derived, naive-derived clonotypes were more likely to last 5 or more years after immunization. Moreover, the frequency of tetramer+ persistent clones correlated with the frequency of tetramer+ naive CD4+ prevaccination T cells. We conclude that the ability of RZV to recruit naive CD4+ T cells into the response may contribute to the durability of its effect. The abundance, breadth, and frequency of public clonotypes may further add to its protective effect.
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Affiliation(s)
- Kerry J. Laing
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Emily S. Ford
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | | | - Myron J. Levin
- Department of Pediatrics, University of Colorado School of Medicine and
- Department of Medicine, University of Colorado School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
| | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology and
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Translational Medicine, Benaroya Research Institute, Seattle, Washington, USA
| | - Adriana Weinberg
- Department of Pediatrics, University of Colorado School of Medicine and
- Department of Medicine, University of Colorado School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
- Department of Pathology, University of Colorado School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
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11
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Ujjani C, Gooley TA, Spurgeon SE, Stephens DM, Lai C, Broome CM, O’Brien S, Zhu H, Laing KJ, Winter AM, Pongas G, Greninger AL, Koelle DM, Siddiqi T, Davids MS, Rogers KA, Danilov AV, Sperling A, Tu B, Sorensen T, Launchbury K, Burrow CJ, Quezada G, Hill JA, Shadman M, Thompson PA. Diminished humoral and cellular responses to SARS-CoV-2 vaccines in patients with chronic lymphocytic leukemia. Blood Adv 2023; 7:4728-4737. [PMID: 36516082 PMCID: PMC9906469 DOI: 10.1182/bloodadvances.2022009164] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/07/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022] Open
Abstract
Previous studies have demonstrated low rates of seroconversion to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) messenger RNA (mRNA) vaccines in patients with chronic lymphocytic leukemia (CLL). In this national collaboration of 11 cancer centers in the United States, we aimed to further characterize and understand vaccine-induced immune responses, including T-cell responses, and the impact of CLL therapeutics (#NCT04852822). Eligible patients were enrolled in 2 cohorts (1) at the time of initial vaccination and (2) at the time of booster vaccination. The serologic response rates (anti-S) from 210 patients in the initial vaccination cohort and 117 in the booster vaccination cohort were 56% (95% confidence interval [CI], 50-63) and 68% (95% CI, 60-77), respectively. Compared with patients not on therapy, those receiving B-cell-directed therapy were less likely to seroconvert (odds ratio [OR], 0.27; 95% CI, 0.15-0.49). Persistence of response was observed at 6 months; anti-S titers increased with the administration of booster vaccinations. In the initial vaccination cohort, positive correlations were observed between the quantitative serologic response and CD4 T-cell response for the Wuhan variant and, to a lesser degree, for the Omicron variant (Spearman P = 0.45 Wuhan; P = 0.25 Omicron). In the booster vaccination cohort, positive correlations were observed between serologic responses and CD4 T-cell responses for both variants (P = 0.58 Wuhan; P = 0.57 Omicron) and to a lesser degree for CD8 T-cell responses (P = 0.33 Wuhan; P = 0.22 Omicron). Although no deaths from coronavirus disease 2019 (COVID-19) have been reported after booster vaccinations, patients should use caution as newer variants emerge and escape vaccine-induced immunity. This trial was registered at www.clinicaltrials.gov as #NCT04852822.
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Affiliation(s)
- Chaitra Ujjani
- Fred Hutchinson Cancer Center, Seattle, WA
- Department of Medicine, University of Washington, Seattle, WA
| | | | | | | | - Catherine Lai
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | - Catherine M. Broome
- Lombardi Comprehensive Cancer Center, Medstar Georgetown University Hospital, Washington, DC
| | - Susan O’Brien
- Chao Family Comprehensive Cancer Center, University of California-Irvine, Irvine, CA
| | - Haiying Zhu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Kerry J. Laing
- Department of Medicine, University of Washington, Seattle, WA
| | | | - Georgios Pongas
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - David M. Koelle
- Fred Hutchinson Cancer Center, Seattle, WA
- Department of Medicine, University of Washington, Seattle, WA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
- Benaroya Research Institute, Seattle, WA
| | | | | | - Kerry A. Rogers
- The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | | | | | - Brian Tu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | | | | | | | | | - Joshua A. Hill
- Fred Hutchinson Cancer Center, Seattle, WA
- Department of Medicine, University of Washington, Seattle, WA
| | - Mazyar Shadman
- Fred Hutchinson Cancer Center, Seattle, WA
- Department of Medicine, University of Washington, Seattle, WA
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12
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Buchta Rosean C, Leyder EC, Hamilton J, Carter JJ, Galloway DA, Koelle DM, Nghiem P, Heiland T. LAMP1 targeting of the large T antigen of Merkel cell polyomavirus results in potent CD4 T cell responses and tumor inhibition. Front Immunol 2023; 14:1253568. [PMID: 37711623 PMCID: PMC10499392 DOI: 10.3389/fimmu.2023.1253568] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction Most cases of Merkel cell carcinoma (MCC), a rare and highly aggressive type of neuroendocrine skin cancer, are associated with Merkel cell polyomavirus (MCPyV) infection. MCPyV integrates into the host genome, resulting in expression of oncoproteins including a truncated form of the viral large T antigen (LT) in infected cells. These oncoproteins are an attractive target for a therapeutic cancer vaccine. Methods We designed a cancer vaccine that promotes potent, antigen-specific CD4 T cell responses to MCPyV-LT. To activate antigen-specific CD4 T cells in vivo, we utilized our nucleic acid platform, UNITE™ (UNiversal Intracellular Targeted Expression), which fuses a tumor-associated antigen with lysosomal-associated membrane protein 1 (LAMP1). This lysosomal targeting technology results in enhanced antigen presentation and potent antigen-specific T cell responses. LTS220A, encoding a mutated form of MCPyV-LT that diminishes its pro-oncogenic properties, was introduced into the UNITE™ platform. Results Vaccination with LTS220A-UNITE™ DNA vaccine (ITI-3000) induced antigen-specific CD4 T cell responses and a strong humoral response that were sufficient to delay tumor growth of a B16F10 melanoma line expressing LTS220A. This effect was dependent on the CD4 T cells' ability to produce IFNγ. Moreover, ITI-3000 induced a favorable tumor microenvironment (TME), including Th1-type cytokines and significantly enhanced numbers of CD4 and CD8 T cells as well as NK and NKT cells. Additionally, ITI-3000 synergized with an α-PD-1 immune checkpoint inhibitor to further slow tumor growth and enhance survival. Conclusions These findings strongly suggest that in pre-clinical studies, DNA vaccination with ITI-3000, using the UNITE™ platform, enhances CD4 T cell responses to MCPyV-LT that result in significant anti-tumor immune responses. These data support the initiation of a first-in-human (FIH) Phase 1 open-label study to evaluate the safety, tolerability, and immunogenicity of ITI-3000 in patients with polyomavirus-positive MCC (NCT05422781).
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Affiliation(s)
| | | | | | - Joseph J. Carter
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Denise A. Galloway
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, WA, United States
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
- Department of Translational Research, Benaroya Research Institute, Seattle, WA, United States
| | - Paul Nghiem
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA, United States
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Teri Heiland
- Immunomic Therapeutics Inc., Rockville, MD, United States
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13
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Ouwendijk WJ, Roychoudhury P, Cunningham AL, Jerome KR, Koelle DM, Kinchington PR, Mohr I, Wilson AC, Verjans GM, Depledge DP. Reanalysis of single-cell RNA sequencing data does not support herpes simplex virus 1 latency in non-neuronal ganglionic cells in mice. bioRxiv 2023:2023.07.17.549345. [PMID: 37503290 PMCID: PMC10370134 DOI: 10.1101/2023.07.17.549345] [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: 07/29/2023]
Abstract
Most individuals are latently infected with herpes simplex virus type 1 (HSV-1) and it is well-established that HSV-1 establishes latency in sensory neurons of peripheral ganglia. However, it was recently proposed that latent virus is also present in immune cells recovered from ganglia in a mouse model used for studying latency. Here, we reanalyzed the single-cell RNA sequencing (scRNA-Seq) data that formed the basis for this conclusion. Unexpectedly, off-target priming in 3' scRNA-Seq experiments enabled the detection of non-polyadenylated HSV-1 latency-associated transcript (LAT) intronic RNAs. However, LAT reads were nearexclusively detected in a mixed population of cells undergoing cell death. Specific loss of HSV1 LAT and neuronal transcripts during quality control filtering indicated widespread destruction of neurons, supporting the presence of contaminating cell-free RNA in other cells following tissue processing. In conclusion, the reported detection of latent HSV-1 in non-neuronal cells is best explained by inaccuracies in the data analyses.
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Affiliation(s)
- Werner J.D. Ouwendijk
- HerpesLabNL, Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - David M. Koelle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
- Department of Global Health, University of Washington, Seattle, WA, 98195, USA
- Department of Translational Research, Benaroya Research Institute, Seattle, WA, 98101, USA
| | - Paul R. Kinchington
- Department of Ophthalmology and of Molecular Microbiology and Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
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14
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van Gent M, Ouwendijk WJD, Campbell VL, Laing KJ, Verjans GMGM, Koelle DM. Varicella-zoster virus proteome-wide T-cell screening demonstrates low prevalence of virus-specific CD8 T-cells in latently infected human trigeminal ganglia. J Neuroinflammation 2023; 20:141. [PMID: 37308917 PMCID: PMC10259006 DOI: 10.1186/s12974-023-02820-y] [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: 01/31/2023] [Accepted: 05/28/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Trigeminal ganglia (TG) neurons are an important site of lifelong latent varicella-zoster virus (VZV) infection. Although VZV-specific T-cells are considered pivotal to control virus reactivation, their protective role at the site of latency remains uncharacterized. METHODS Paired blood and TG specimens were obtained from ten latent VZV-infected adults, of which nine were co-infected with herpes simplex virus type 1 (HSV-1). Short-term TG-derived T-cell lines (TG-TCL), generated by mitogenic stimulation of TG-derived T-cells, were probed for HSV-1- and VZV-specific T-cells using flow cytometry. We also performed VZV proteome-wide screening of TG-TCL to determine the fine antigenic specificity of VZV reactive T-cells. Finally, the relationship between T-cells and latent HSV-1 and VZV infections in TG was analyzed by reverse transcription quantitative PCR (RT-qPCR) and in situ analysis for T-cell proteins and latent viral transcripts. RESULTS VZV proteome-wide analysis of ten TG-TCL identified two VZV antigens recognized by CD8 T-cells in two separate subjects. The first was an HSV-1/VZV cross-reactive CD8 T-cell epitope, whereas the second TG harbored CD8 T-cells reactive with VZV specifically and not the homologous peptide in HSV-1. In silico analysis showed that HSV-1/VZV cross reactivity of TG-derived CD8 T-cells reactive with ten previously identified HSV-1 epitopes was unlikely, suggesting that HSV-1/VZV cross-reactive T-cells are not a common feature in dually infected TG. Finally, no association was detected between T-cell infiltration and VZV latency transcript abundance in TG by RT-qPCR or in situ analyses. CONCLUSIONS The low presence of VZV- compared to HSV-1-specific CD8 T-cells in human TG suggests that VZV reactive CD8 T-cells play a limited role in maintaining VZV latency.
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Affiliation(s)
- Michiel van Gent
- HerpesLabNL, Department of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Werner J. D. Ouwendijk
- HerpesLabNL, Department of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | | | - Kerry J. Laing
- Department of Medicine, University of Washington, Seattle, WA 98195 USA
| | - Georges M. G. M. Verjans
- HerpesLabNL, Department of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195 USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA 98109 USA
- Department of Global Health, University of Washington, Seattle, WA 98195 USA
- Department of Translational Research, Benaroya Research Institute, Seattle, WA 98101 USA
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15
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Armistead B, Jiang Y, Carlson M, Ford ES, Jani S, Houck J, Wu X, Jing L, Pecor T, Kachikis A, Yeung W, Nguyen T, Coig R, Minkah N, Larsen SE, Coler RN, Koelle DM, Harrington WE. Spike-specific T cells are enriched in breastmilk following SARS-CoV-2 mRNA vaccination. Mucosal Immunol 2023; 16:39-49. [PMID: 36642379 PMCID: PMC9836998 DOI: 10.1016/j.mucimm.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/20/2022] [Accepted: 01/07/2023] [Indexed: 01/15/2023]
Abstract
Human breastmilk is rich in T cells; however, their specificity and function are largely unknown. We compared the phenotype, diversity, and antigen specificity of T cells in breastmilk and peripheral blood of lactating individuals who received SARS-CoV-2 messenger RNA (mRNA) vaccination. Relative to blood, breastmilk contained higher frequencies of T effector and central memory populations that expressed mucosal-homing markers. T cell receptor sequence overlap was limited between blood and breastmilk. Overabundant breastmilk clones were observed in all individuals, were diverse, and contained complementarity-determining regions in three sequences with known epitope specificity, including to SARS-CoV-2 spike. SARS-CoV-2 spike-specific T cell receptors were more frequent in breastmilk compared to blood and expanded in breastmilk following a 3rd mRNA vaccine dose. Our observations indicate that the lactating breast contains a distinct T cell population that can be modulated by maternal vaccination with potential implications for passive infant protection.
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Affiliation(s)
- Blair Armistead
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Yonghou Jiang
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Marc Carlson
- Research Scientific Computing, Enterprise Analytics, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Emily S Ford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Saumya Jani
- Department of Medicine, University of Washington, Seattle, Washington, USA; Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington, USA
| | - John Houck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Xia Wu
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Tiffany Pecor
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Alisa Kachikis
- Department of Obstetrics & Gynecology, University of Washington, Seattle, Washington, USA
| | - Winnie Yeung
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Tina Nguyen
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Rene Coig
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington, USA
| | - Nana Minkah
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA; Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Sasha E Larsen
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Rhea N Coler
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA; Department of Pediatrics, University of Washington, Seattle, Washington, USA; Department of Global Health, University of Washington, Seattle, Washington, USA
| | - David M Koelle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA; Department of Laboratory Medicine & Pathology, University of Washington, Seattle, Washington, USA; Department of Global Health, University of Washington, Seattle, Washington, USA; Benaroya Research Institute, Seattle, Washington, USA
| | - Whitney E Harrington
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA; Department of Pediatrics, University of Washington, Seattle, Washington, USA; Department of Global Health, University of Washington, Seattle, Washington, USA.
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16
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Gondré-Lewis TA, Jiang C, Ford ML, Koelle DM, Sette A, Shalek AK, Thomas PG. NIAID workshop on T cell technologies. Nat Immunol 2023; 24:14-18. [PMID: 36596894 PMCID: PMC10405620 DOI: 10.1038/s41590-022-01377-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
On 15–16 June 2022, the National Institute of Allergy and Infectious Diseases hosted a virtual workshop on the topic of T cell technologies to discuss assays, novel technology development, bench and clinical application of those technologies, and challenges and innovations in the field.
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Affiliation(s)
- Timothy A Gondré-Lewis
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Rockville, MD, USA.
| | - Chao Jiang
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Rockville, MD, USA.
| | - Mandy L Ford
- Division of Transplantation, Department of Surgery, Emory University, Atlanta, GA, USA
| | - David M Koelle
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Benaroya Research Institute, Seattle, WA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alex K Shalek
- Institute for Medical Engineering and Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Paul G Thomas
- Immunology Department, St. Jude Children's Research Hospital, Memphis, TN, USA
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17
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Babu TM, Scott McClelland R, Johnston C, Selke S, Singh D, Moreno J, Taub J, Pertik M, Varon D, Pholsena T, Murphy B, Drummond M, McClellan L, Braun A, Seymour M, Hauge K, McClurkan CL, Wilkens C, Goecker E, Laing KJ, Koelle DM, Greninger AL, Wald A. 1948. Evaluation of a heterologous booster vaccine regimen: Pfizer-BioNTech BNT162b2 mRNA booster vaccine following priming with Novavax NVX-CoV2373. Open Forum Infect Dis 2022. [DOI: 10.1093/ofid/ofac492.1575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Abstract
Background
In the United States, booster vaccines for persons 18 years and older were approved under Emergency Use Authorization (EUA) in September 2021. Waning immunity following SARS-CoV-2 primary vaccination series led to recommendations for booster vaccination. Emerging data suggest that providing boosters different from the primary series (heterologous vaccination) may provide a broader immune response than boosting with the same vaccine (homologous vaccination). CDC recommended the Pfizer-BioNTech BNT162b2 30-μg mRNA booster vaccine to clinical trial participants >6 months post study vaccines if not planned for boosting within the study.
Methods
We conducted an observational study of persons who received 2 doses of Novavax protein-based NVX-CoV2373 vaccine 21 days apart, in a Phase 3 clinical trial, and subsequently received a Pfizer BNT162b2 booster vaccine under EUA. Serologic assays, including the Roche anti-nucleocapsid (N) IgG and anti-Spike (S) IgG, were performed on blood collected pre-booster (D0) and on days 18 (D18) and 34 (D34) post-booster vaccine. The anti-S IgG geometric means (GMTs) were calculated over study time points. Wilcoxon signed rank test was performed to compare anti-S IgG response between D0 and D18 and D0 and D34.
Results
Of 26 participants enrolled, 16 (57%) were women; the median age was 47 years (range 29-67). Roche anti-N antibodies were negative at all visits. Time from second NVX-CoV2373 vaccine to Pfizer BNT162b2 booster was a median of 10.4 months in 54% of participants and 7 months in 46% of participants. Anti-S IgG GMTs were 222 BAU/ml D0, 24,723 BAU/ml D18, and 24,584 BAU/ml D34 (p< 0.0001 for comparisons of D0 with D18 & D34). Overall, participants tolerated the booster vaccine without significant adverse events. Cell mediated immunity and D614G pseudovirus neutralizing antibody assays are in progress. Figure 1.Anti-S IgG titers pre and post-booster vaccine
16 participants included with all 3-time study time points for comparison.
Conclusion
Two doses of NVX-CoV2373 vaccine followed by the Pfizer BNT162b2 booster vaccine resulted in ∼100-fold increase in anti-S IgG against SARS-CoV-2. No participant had evidence of prior SARS-CoV-2 infection by anti-N IgG. Two doses of NVX-CoV2373 vaccine followed by one dose of Pfizer BNT162b2 vaccine is an effective and well-tolerated regimen for boosting anti-S IgG against SARS-CoV-2.
Disclosures
Christine Johnston, MD, MPH, AbbVie: Advisor/Consultant|Gilead: Grant/Research Support|GSK: Advisor/Consultant Kerry J. Laing, PhD, Curevo Vaccine: Advisor/Consultant|MaxHealth Biotechnology: Advisor/Consultant|Sanofi Pasteur: Grant/Research Support David M. Koelle, MD, Curevo Vaccines: Advisor/Consultant|MaxHealth LLC: Advisor/Consultant|Oxford Immunotec: gift of reagents|Sanofi: Grant/Research Support|Sensei: Grant/Research Support Alexander L. Greninger, MD, PhD, Abbott: Contract Testing|Cepheid: Contract Testing|Gilead: Grant/Research Support|Gilead: Contract Testing|Hologic: Contract Testing|Merck: Grant/Research Support|Novavax: Contract Testing|Pfizer: Contract Testing Anna Wald, MD, MPH, Aicuris: Advisor/Consultant|Auritec: Advisor/Consultant|Crozet: Advisor/Consultant|DXNow: Advisor/Consultant|GSK: Grant/Research Support|Merck: Advisor/Consultant|sanofi: Grant/Research Support|VIR: Advisor/Consultant|X-Vax: Advisor/Consultant.
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Affiliation(s)
- Tara M Babu
- University of Washington , Seattle, Washington
| | | | | | - Stacy Selke
- University of Washington , Seattle, Washington
| | | | | | - Jina Taub
- University of Washington , Seattle, Washington
| | | | - Dana Varon
- University of Washington , Seattle, Washington
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Anna Wald
- University of Washington , Seattle, Washington
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18
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Johnston C, Magaret A, Son H, Stern M, Rathbun M, Renner D, Szpara M, Gunby S, Ott M, Jing L, Campbell VL, Huang ML, Selke S, Jerome KR, Koelle DM, Wald A. Viral Shedding 1 Year Following First-Episode Genital HSV-1 Infection. JAMA 2022; 328:1730-1739. [PMID: 36272098 PMCID: PMC9588168 DOI: 10.1001/jama.2022.19061] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE Herpes simplex virus type 1 (HSV-1) is the leading cause of first-episode genital herpes in many countries. OBJECTIVE To inform counseling messages regarding genital HSV-1 transmission, oral and genital viral shedding patterns among persons with first-episode genital HSV-1 infection were assessed. The trajectory of the development of HSV-specific antibody and T-cell responses was also characterized. DESIGN, SETTING, AND PARTICIPANTS Prospective cohort followed up for up to 2 years, with 82 participants followed up between 2013 and 2018. Participants were recruited from sexual health and primary care clinics in Seattle, Washington. Persons with laboratory-documented first-episode genital HSV-1 infection, without HIV infection or current pregnancy, were referred for enrollment. EXPOSURES First-episode genital HSV-1 infection. MAIN OUTCOMES AND MEASURES Genital and oral HSV-1 shedding and lesion rates at 2 months, 11 months, and up to 2 years after initial genital HSV-1 infection. Participants self-collected oral and genital swabs for HSV polymerase chain reaction testing for 30 days at 2 and 11 months and up to 2 years after diagnosis of genital HSV-1. Blood samples were collected at serial time points to assess immune responses to HSV-1. Primary HSV-1 infection was defined as absent HSV antibody at baseline or evolving antibody profile using the University of Washington HSV Western Blot. HSV-specific T-cell responses were detected using interferon γ enzyme-linked immunospot. RESULTS Among the 82 participants, the median (range) age was 26 (16-64) years, 54 (65.9%) were women, and 42 (51.2%) had primary HSV-1 infection. At 2 months, HSV-1 was detected from the genital tract in 53 participants (64.6%) and in the mouth in 24 participants (29.3%). Genital HSV-1 shedding was detected on 275 of 2264 days (12.1%) at 2 months and declined significantly to 122 of 1719 days (7.1%) at 11 months (model-predicted rate, 6.2% [95% CI, 4.3%-8.9%] at 2 months vs 3.2% [95% CI, 1.8%-5.7%] at 11 months; relative risk, 0.52 [95% CI, 0.29-0.93]). Genital lesions were rare, reported on 65 of 2497 days (2.6%) at 2 months and 72 of 1872 days (3.8%) at 11 months. Oral HSV-1 shedding was detected on 88 of 2247 days (3.9%) at 2 months. Persons with primary HSV-1 infection had a higher risk of genital shedding compared with those with nonprimary infection (model-predicted rate, 7.9% [95% CI, 5.4%-11.7%] vs 2.9% [95% CI, 1.7%-5.0%]; relative risk, 2.75 [95% CI, 1.40-5.44]). Polyfunctional HSV-specific CD4+ and CD8+ T-cell responses were maintained during the follow-up period. CONCLUSIONS AND RELEVANCE Genital HSV-1 shedding was frequent after first-episode genital HSV-1, particularly among those with primary infection, and declined rapidly during the first year after infection.
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Affiliation(s)
- Christine Johnston
- Department of Medicine, University of Washington, Seattle
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Amalia Magaret
- Department of Medicine, University of Washington, Seattle
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle
| | - Hyunju Son
- Department of Medicine, University of Washington, Seattle
| | - Michael Stern
- Department of Medicine, University of Washington, Seattle
| | - Molly Rathbun
- Departments of Biology, Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park
| | - Daniel Renner
- Departments of Biology, Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park
| | - Moriah Szpara
- Departments of Biology, Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park
| | - Sarah Gunby
- Department of Medicine, University of Washington, Seattle
| | - Mariliis Ott
- Department of Medicine, University of Washington, Seattle
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle
| | | | - Meei-li Huang
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle
| | - Stacy Selke
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle
| | - Keith R. Jerome
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - David M. Koelle
- Department of Medicine, University of Washington, Seattle
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Departments of Global Health, University of Washington, Seattle
- Benaroya Research Institute, Seattle, Washington
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Departments of Epidemiology, University of Washington, Seattle
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19
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Zohar T, Atyeo C, Wolf CR, Logue JK, Shuey K, Franko N, Choi RY, Wald A, Koelle DM, Chu HY, Lauffenburger DA, Alter G. A multifaceted high-throughput assay for probing antigen-specific antibody-mediated primary monocyte phagocytosis and downstream functions. J Immunol Methods 2022; 510:113328. [PMID: 35934070 DOI: 10.1016/j.jim.2022.113328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/13/2022] [Accepted: 08/01/2022] [Indexed: 01/18/2023]
Abstract
Monocytes are highly versatile innate immune cells responsible for pathogen clearance, innate immune coordination, and induction of adaptive immunity. Monocytes can directly and indirectly integrate pathogen-destructive instructions and contribute to disease control via pathogen uptake, presentation, or the release of cytokines. Indirect pathogen-specific instructions are conferred via Fc-receptor signaling and triggered by antibody opsonized material. Given the tremendous variation in polyclonal humoral immunity, defining the specific antibody-responses able to arm monocytes most effectively remains incompletely understood. While monocyte cell line-based assays have been used previously, cell lines may not faithfully recapitulate the full biology of monocytes. Thus, here we describe a multifaceted antigen-specific method for probing antibody-dependent primary monocyte phagocytosis (ADMP) and secondary responses. The assay not only reliably captures phagocytic uptake of immune complexes, but also detects unique changes in surface markers and cytokine secretions profiles, poorly detected by monocytic cell lines. The assay captures divergent polyclonal-monocyte recruiting activity across subjects with varying SARS-CoV-2 disease severity and also revealed biological nuances in Fc-mutant monoclonal antibody activity related to differences in Fc-receptor binding. Thus, the ADMP assay is a flexible assay able to provide key insights into the role of humoral immunity in driving monocyte phenotypic transitions and downstream functions across many diseases.
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Affiliation(s)
- Tomer Zohar
- Ragon Institute of MGH, MIT, and Harvard, MA, Cambridge, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, MA, Cambridge, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Jennifer K Logue
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Kiel Shuey
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Nicholas Franko
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Anna Wald
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA; Department of Epidemiology, University of Washington School of Medicine, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David M Koelle
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA; Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Benaroya Research Institute, Seattle, WA, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, MA, Cambridge, USA.
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20
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Ford ES, Mayer-Blackwell K, Jing L, Sholukh AM, St Germain R, Bossard EL, Xie H, Pulliam TH, Jani S, Selke S, Burrow CJ, McClurkan CL, Wald A, Holbrook MR, Eaton B, Eudy E, Murphy M, Postnikova E, Robins HS, Elyanow R, Gittelman RM, Ecsedi M, Wilcox E, Chapuis AG, Fiore-Gartland A, Koelle DM. CD8 + T cell clonotypes from prior SARS-CoV-2 infection predominate during the cellular immune response to mRNA vaccination. Res Sq 2022:rs.3.rs-2146712. [PMID: 36263073 PMCID: PMC9580387 DOI: 10.21203/rs.3.rs-2146712/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Almost three years into the SARS-CoV-2 pandemic, hybrid immunity is highly prevalent worldwide and more protective than vaccination or prior infection alone. Given emerging resistance of variant strains to neutralizing antibodies (nAb), it is likely that T cells contribute to this protection. To understand how sequential SARS-CoV-2 infection and mRNA-vectored SARS-CoV-2 spike (S) vaccines affect T cell clonotype-level expansion kinetics, we identified and cross-referenced TCR sequences from thousands of S-reactive single cells against deeply sequenced peripheral blood TCR repertoires longitudinally collected from persons during COVID-19 convalescence through booster vaccination. Successive vaccinations recalled memory T cells and elicited antigen-specific T cell clonotypes not detected after infection. Vaccine-related recruitment of novel clonotypes and the expansion of S-specific clones were most strongly observed for CD8+ T cells. Severe COVID-19 illness was associated with a more diverse CD4+ T cell response to SARS-CoV-2 both prior to and after mRNA vaccination, suggesting imprinting of CD4+ T cells by severe infection. TCR sequence similarity search algorithms revealed myriad public TCR clusters correlating with human leukocyte antigen (HLA) alleles. Selected TCRs from distinct clusters functionally recognized S in the predicted HLA context, with fine viral peptide requirements differing between TCRs. Most subjects tested had S-specific T cells in the nasal mucosa after a 3rd mRNA vaccine dose. The blood and nasal T cell responses to vaccination revealed by clonal tracking were more heterogeneous than nAb boosts. Analysis of bulk and single cell TCR sequences reveals T cell kinetics and diversity at the clonotype level, without requiring prior knowledge of T cell epitopes or HLA restriction, providing a roadmap for rapid assessment of T cell responses to emerging pathogens.
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21
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Jani S, Pulliam TH, Mayer-Blackwell K, Bradley P, Koelle DM, Nghiem P. Development of a Merkel polyomavirus-specific T cell receptor analysis tool to guide cancer immunotherapy. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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22
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Armistead B, Jiang Y, Carlson M, Ford ES, Jani S, Houck J, Wu X, Jing L, Pecor T, Kachikis A, Yeung W, Nguyen T, Minkah N, Larsen SE, Coler RN, Koelle DM, Harrington WE. Spike-specific T cells are enriched in breastmilk following SARS-CoV-2 mRNA vaccination. medRxiv 2022:2021.12.03.21267036. [PMID: 36203549 PMCID: PMC9536058 DOI: 10.1101/2021.12.03.21267036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Human breastmilk is rich in T cells; however, their specificity and function are largely unknown. We compared the phenotype, diversity, and antigen specificity of T cells in the breastmilk and peripheral blood of lactating individuals who received SARS-CoV-2 mRNA vaccination. Relative to blood, breastmilk contained higher frequencies of T effector and central memory populations that expressed mucosal-homing markers. T cell receptor (TCR) sequence overlap was limited between blood and breastmilk. Overabundan t breastmilk clones were observed in all individuals, were diverse, and contained CDR3 sequences with known epitope specificity including to SARS-CoV-2 Spike. Spike-specific TCRs were more frequent in breastmilk compared to blood and expanded in breastmilk following a third mRNA vaccine dose. Our observations indicate that the lactating breast contains a distinct T cell population that can be modulated by maternal vaccination with potential implications for infant passive protection. One-Sentence Summary The breastmilk T cell repertoire is distinct and enriched for SARS-CoV-2 Spike-specificity after maternal mRNA vaccination.
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Affiliation(s)
- Blair Armistead
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute; Seattle, WA, USA
| | - Yonghou Jiang
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute; Seattle, WA, USA
| | - Marc Carlson
- Research Scientific Computing, Enterprise Analytics, Seattle Children’s Research Institute; Seattle, WA, USA
| | - Emily S Ford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
- Department of Medicine, University of Washington; Seattle, WA, USA
| | - Saumya Jani
- Department of Medicine, University of Washington; Seattle, WA, USA
- Department of Laboratory Medicine & Pathology, University of Washington; Seattle, WA, USA
| | - John Houck
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute; Seattle, WA, USA
| | - Xia Wu
- Department of Medicine, University of Washington; Seattle, WA, USA
| | - Lichen Jing
- Department of Medicine, University of Washington; Seattle, WA, USA
| | - Tiffany Pecor
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute; Seattle, WA, USA
| | - Alisa Kachikis
- Department of Obstetrics & Gynecology, University of Washington; Seattle, WA, USA
| | - Winnie Yeung
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute; Seattle, WA, USA
| | - Tina Nguyen
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute; Seattle, WA, USA
| | - Nana Minkah
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute; Seattle, WA, USA
- Department of Pediatrics, University of Washington; Seattle, WA, USA
| | - Sasha E Larsen
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute; Seattle, WA, USA
| | - Rhea N Coler
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute; Seattle, WA, USA
- Department of Global Health, University of Washington; Seattle, WA, USA
- Department of Pediatrics, University of Washington; Seattle, WA, USA
| | - David M Koelle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
- Department of Medicine, University of Washington; Seattle, WA, USA
- Department of Laboratory Medicine & Pathology, University of Washington; Seattle, WA, USA
- Department of Global Health, University of Washington; Seattle, WA, USA
- Benaroya Research Institute; Seattle, WA, USA
| | - Whitney E Harrington
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute; Seattle, WA, USA
- Department of Global Health, University of Washington; Seattle, WA, USA
- Department of Pediatrics, University of Washington; Seattle, WA, USA
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23
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Zhang JZ, Yeh HW, Walls AC, Wicky BIM, Sprouse KR, VanBlargan LA, Treger R, Quijano-Rubio A, Pham MN, Kraft JC, Haydon IC, Yang W, DeWitt M, Bowen JE, Chow CM, Carter L, Ravichandran R, Wener MH, Stewart L, Veesler D, Diamond MS, Greninger AL, Koelle DM, Baker D. Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants. Nat Biotechnol 2022; 40:1336-1340. [PMID: 35484405 PMCID: PMC9463068 DOI: 10.1038/s41587-022-01280-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 06/03/2021] [Accepted: 03/14/2022] [Indexed: 12/14/2022]
Abstract
We designed a protein biosensor that uses thermodynamic coupling for sensitive and rapid detection of neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in serum. The biosensor is a switchable, caged luciferase-receptor-binding domain (RBD) construct that detects serum-antibody interference with the binding of virus RBD to angiotensin-converting enzyme 2 (ACE-2) as a proxy for neutralization. Our coupling approach does not require target modification and can better distinguish sample-to-sample differences in analyte binding affinity and abundance than traditional competition-based assays.
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Affiliation(s)
- Jason Z Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
| | - Hsien-Wei Yeh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Basile I M Wicky
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Rebecca Treger
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Alfredo Quijano-Rubio
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Minh N Pham
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - John C Kraft
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ian C Haydon
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Wei Yang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Michelle DeWitt
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cameron M Chow
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Mark H Wener
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David M Koelle
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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24
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Church C, Pulliam T, Longino N, Park SY, Smythe KS, Makarov V, Riaz N, Jing L, Amezquita R, Campbell JS, Gottardo R, Pierce RH, Choi J, Chan TA, Koelle DM, Nghiem P. Transcriptional and functional analyses of neoantigen-specific CD4 T cells during a profound response to anti-PD-L1 in metastatic Merkel cell carcinoma. J Immunother Cancer 2022; 10:jitc-2022-005328. [PMID: 36252564 PMCID: PMC9472219 DOI: 10.1136/jitc-2022-005328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2022] [Indexed: 11/29/2022] Open
Abstract
Background Merkel cell carcinoma (MCC) often responds to PD-1 pathway blockade, regardless of tumor-viral status (~80% of cases driven by the Merkel cell polyomavirus (MCPyV)). Prior studies have characterized tumor-specific T cell responses to MCPyV, which have typically been CD8, but little is known about the T cell response to UV-induced neoantigens. Methods A patient in her mid-50s with virus-negative (VN) MCC developed large liver metastases after a brief initial response to chemotherapy. She received anti-PD-L1 (avelumab) and had a partial response within 4 weeks. Whole exome sequencing (WES) was performed to determine potential neoantigen peptides. Characterization of peripheral blood neoantigen T cell responses was evaluated via interferon-gamma (IFNγ) ELISpot, flow cytometry and single-cell RNA sequencing. Tumor-resident T cells were characterized by multiplexed immunohistochemistry. Results WES identified 1027 tumor-specific somatic mutations, similar to the published average of 1121 for VN-MCCs. Peptide prediction with a binding cut-off of ≤100 nM resulted in 77 peptides that were synthesized for T cell assays. Although peptides were predicted based on class I HLAs, we identified circulating CD4 T cells targeting 5 of 77 neoantigens. In contrast, no neoantigen-specific CD8 T cell responses were detected. Neoantigen-specific CD4 T cells were undetectable in blood before anti-PD-L1 therapy but became readily detectible shortly after starting therapy. T cells produced robust IFNγ when stimulated by neoantigen (mutant) peptides but not by the normal (wild-type) peptides. Single cell RNAseq showed neoantigen-reactive T cells expressed the Th1-associated transcription factor (T-bet) and associated cytokines. These CD4 T cells did not significantly exhibit cytotoxicity or non-Th1 markers. Within the pretreatment tumor, resident CD4 T cells were also Th1-skewed and expressed T-bet. Conclusions We identified and characterized tumor-specific Th1-skewed CD4 T cells targeting multiple neoantigens in a patient who experienced a profound and durable partial response to anti-PD-L1 therapy. To our knowledge, this is the first report of neoantigen-specific T cell responses in MCC. Although CD4 and CD8 T cells recognizing viral tumor antigens are often detectible in virus-positive MCC, only CD4 T cells recognizing neoantigens were detected in this patient. These findings suggest that CD4 T cells can play an important role in the response to anti-PD-(L)1 therapy.
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Affiliation(s)
- Candice Church
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Thomas Pulliam
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Natalie Longino
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Song Y Park
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kimberly S Smythe
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Center for Immunotherapy and Precision Immuno-oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Nadeem Riaz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Robert Amezquita
- Biostatistics Bioinformatics and Epidemiology Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jean S Campbell
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Raphael Gottardo
- Biostatistics Bioinformatics and Epidemiology Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Lausanne University Hospital, Lausanne, Vaud, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Robert H Pierce
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jaehyuk Choi
- Department of Dermatology, Biochemistry & Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Center for Immunotherapy and Precision Immuno-oncology, Cleveland Clinic, Cleveland, Ohio, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Benaroya Research Institute, Seattle, WA, USA
| | - Paul Nghiem
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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25
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Chang A, Sholukh AM, Wieland A, Jaye DL, Carrington M, Huang ML, Xie H, Jerome KR, Roychoudhury P, Greninger AL, Koff JL, Cohen JB, Koelle DM, Corey L, Flowers CR, Ahmed R. Herpes simplex virus lymphadenitis is associated with tumor reduction in a chronic lymphocytic leukemia patient. J Clin Invest 2022; 132:161109. [PMID: 35862190 PMCID: PMC9479599 DOI: 10.1172/jci161109] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Herpes simplex virus lymphadenitis (HSVL) is an unusual presentation of HSV reactivation in chronic lymphocytic leukemia (CLL) patients characterized by systemic symptoms and no herpetic lesions. The immune responses during HSVL have not been studied. METHODS Peripheral blood and lymph node samples of a patient with HSVL were obtained. HSV-2 viral load, antibody levels, B and T cell responses, cytokine levels, and tumor burden were measured. RESULTS This patient showed HSV-2 viremia for at least 6 weeks. During this period, she had a robust HSV-specific antibody response with neutralizing and antibody-dependent cellular phagocytosis activity. Activated (HLA-DR+, CD38+) CD4+ and CD8+ T cells increased 18-fold and HSV-specific CD8+ T cells were detected in the blood at higher numbers. HSV-specific B and T cell responses in the lymph node were also detected. Markedly elevated levels of pro-inflammatory cytokines in the blood were also observed. Surprisingly, a sustained decrease in CLL tumor burden without CLL-directed therapy was observed with this and also a prior episode of HSVL. CONCLUSION HSVL should be considered as part of the differential diagnosis in CLL patients who present with signs and symptoms of aggressive lymphoma transformation. An interesting finding was the sustained tumor control after 2 episodes of HSVL in this patient. This tumor burden reduction may be due to the HSV-specific response serving as an adjuvant for activating tumor-specific or bystander T cells. Studies in additional CLL patients are needed to confirm and extend these findings. FUNDING National Institutes of Health and Winship Cancer Institute.
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Affiliation(s)
- Andres Chang
- Winship Cancer Institute of Emory University, Atlanta, United States of America
| | - Anton M Sholukh
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Andreas Wieland
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, United States of America
| | - David L Jaye
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, United States of America
| | - Mary Carrington
- Laboratory of Experimental Immunology, Frederick National Laboratory for Cancer Research, Bethesda, United States of America
| | - Meei-Li Huang
- University of Washington, Seattle, United States of America
| | - Hong Xie
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Keith R Jerome
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Pavitra Roychoudhury
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Jean L Koff
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, United States of America
| | - Jonathon B Cohen
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, United States of America
| | - David M Koelle
- Department of Global Health, University of Washington, Seattle, United States of America
| | - Lawrence Corey
- Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Christopher R Flowers
- Department of Lymphoma and Myeloma, MD Anderson Cancer Center, Houston, United States of America
| | - Rafi Ahmed
- Emory University School of Medicine, Atlanta, United States of America
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26
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Rosean CB, Karkada M, Koelle DM, Nghiem P, Heiland T. Abstract 2052: LAMP1 targeting of the large T antigen of Merkel cell polyomavirus elicits potent CD4+ T cell responses, tumor inhibition, and provides rationale for first-in-human trial. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The majority of Merkel cell carcinomas (MCC), a rare and highly aggressive type of neuroendocrine skin cancer, are associated with Merkel cell polyomavirus (MCPyV) infection. MCPyV integrates into the host genome, resulting in expression of a truncated form of the viral large T antigen (LT) in infected cells and thus making LT an attractive target for therapeutic cancer vaccines. We designed a cancer vaccine that promotes potent, antigen-specific CD4+ T cell responses to MCPγV-LT. To activate antigen-specific CD4+ T cells in vivo, we utilized our nucleic acid platform, UNITE࣪ (UNiversal Intracellular Targeted Expression), which fuses a tumor-associated antigen with lysosomal-associated membrane protein 1 (LAMP1). This lysosomal targeting technology results in enhanced antigen presentation and a balanced T cell response. LTS220A, encoding a mutated form of MCPγV-LT that diminishes its pro-oncogenic properties, was introduced into the UNITE࣪ platform. In pre-clinical studies, vaccination with LTS220A-UNITE࣪ (ITI-3000) induced antigen-specific CD4+ T cells that were sufficient to delay tumor growth, and this effect was dependent on their ability to produce IFNγ. Moreover, ITI-3000 induced a favorable tumor microenvironment (TME), including significantly enhanced numbers of CD4+ and CD8+ T cells as well as NK and NKT cells. These findings strongly suggest that in pre-clinical studies, DNA vaccination using the UNITE࣪ platform enhances CD4+ T cell responses to MCPγV-LT that result in significant anti-tumor immune responses. We are planning a first-in-human (FIH) Phase 1 open-label study to evaluate the safety, tolerability, and immunogenicity of ITI-3000 in patients with polyomavirus-positive MCC. Patients will receive up to four intramuscular vaccinations of 4mg of ITI-3000 using the PharmaJet Stratis® needle-free injection system. The primary objectives will be safety and tolerability, observing dose-limiting toxicities, serious adverse events, standard clinical assessments, and safety laboratory parameters. Immunogenicity of the vaccine will be measured by peripheral blood assessments of T cell activation using ELISpot and flow cytometry assays.
Citation Format: Claire Buchta Rosean, Mohan Karkada, David M. Koelle, Paul Nghiem, Teri Heiland. LAMP1 targeting of the large T antigen of Merkel cell polyomavirus elicits potent CD4+ T cell responses, tumor inhibition, and provides rationale for first-in-human trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2052.
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27
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Elyanow R, Snyder TM, Dalai SC, Gittelman RM, Boonyaratanakornkit J, Wald A, Selke S, Wener MH, Morishima C, Greninger AL, Gale M, Hsiang TY, Jing L, Holbrook MR, Kaplan IM, Zahid HJ, May DH, Carlson JM, Baldo L, Manley T, Robins HS, Koelle DM. T cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibodies and disease severity. JCI Insight 2022; 7:e150070. [PMID: 35439166 PMCID: PMC9220924 DOI: 10.1172/jci.insight.150070] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 05/10/2021] [Accepted: 04/15/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUNDMeasuring the immune response to SARS-CoV-2 enables assessment of past infection and protective immunity. SARS-CoV-2 infection induces humoral and T cell responses, but these responses vary with disease severity and individual characteristics.METHODSA T cell receptor (TCR) immunosequencing assay was conducted using small-volume blood samples from 302 individuals recovered from COVID-19. Correlations between the magnitude of the T cell response and neutralizing antibody (nAb) titers or indicators of disease severity were evaluated. Sensitivity of T cell testing was assessed and compared with serologic testing.RESULTSSARS-CoV-2-specific T cell responses were significantly correlated with nAb titers and clinical indicators of disease severity, including hospitalization, fever, and difficulty breathing. Despite modest declines in depth and breadth of T cell responses during convalescence, high sensitivity was observed until at least 6 months after infection, with overall sensitivity ~5% greater than serology tests for identifying prior SARS-CoV-2 infection. Improved performance of T cell testing was most apparent in recovered, nonhospitalized individuals sampled > 150 days after initial illness, suggesting greater sensitivity than serology at later time points and in individuals with less severe disease. T cell testing identified SARS-CoV-2 infection in 68% (55 of 81) of samples with undetectable nAb titers (<1:40) and in 37% (13 of 35) of samples classified as negative by 3 antibody assays.CONCLUSIONThese results support TCR-based testing as a scalable, reliable measure of past SARS-CoV-2 infection with clinical value beyond serology.TRIAL REGISTRATIONSpecimens were accrued under trial NCT04338360 accessible at clinicaltrials.gov.FUNDINGThis work was funded by Adaptive Biotechnologies, Frederick National Laboratory for Cancer Research, NIAID, Fred Hutchinson Joel Meyers Endowment, Fast Grants, and American Society for Transplantation and Cell Therapy.
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Affiliation(s)
| | | | - Sudeb C. Dalai
- Adaptive Biotechnologies, Seattle, Washington, USA
- Stanford University School of Medicine, Stanford, California, USA
| | | | - Jim Boonyaratanakornkit
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology
- Department of Laboratory Medicine and Pathology
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology
| | - Mark H. Wener
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology
| | | | | | - Michael Gale
- Department of Immunology
- Department of Microbiology, and
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Michael R. Holbrook
- National Institute of Allergy and Infectious Diseases (NIAID) Integrated Research Facility, Frederick, Maryland, USA
| | | | | | - Damon H. May
- Adaptive Biotechnologies, Seattle, Washington, USA
| | | | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington, USA
| | | | | | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
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28
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Reid T, Godornes C, Tong D, Koelle DM. Treponema pallidum specific CD4 T cell epitope discovery. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.170.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Despite curative therapy and multiple public health campaigns to eliminate syphilis in the US, the incidence of Syphilis is rising in diverse groups: men who have sex with men, women, and children. An effective syphilis vaccine will be a key tool in the eradication of this disease. Prior efforts to create a protective syphilis vaccine focused on raising antibodies against rare outer membrane proteins to facilitate antibody mediated opsonophagocytosis of Treponema pallidum (Tp) in infectious lesions. The inclusion of immunodominant T cell antigens in a subunit vaccine can provide CD4 T cell help to B cells to produce opsonic antibodies. We sought to identify human Tp T cell antigens validated to the epitope level as there are none reported in the literature. Tp specific CD4 T cells were isolated from persons with active or treated syphilis infection by CD137 and CD69 activation–based FACS and polyclonal expansion. These cells were then probed with a panel of 39 recombinantly expressed Tp proteins. Preliminary data show that activation-induced-marker-enriched, expanded T cells can be probed to discover novel CD4 T cell antigens and epitopes using proliferation experiments. The first 4 CD4 T cell antigens identified included antibody targets Tp0435 and Tp0574, a flagellar apparatus protein Tp0870, and a metabolite transporter Tp0684. Further refinement of minimal T cell antigens within these proteins and expansion of the Tp protein panel is ongoing. These are the first human Tp specific T cell epitopes described. Incorporating this information into vaccine design may further increase protection against infection.
Supported by T32AI007140-44
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Affiliation(s)
- Tara Reid
- 1Medicine/Allergy and Infectious Disease, Univ. of Washington
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29
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Koelle DM, Dong L, Jing L, Laing KJ, Zhu J, Jin L, Selke S, Wald A, Varon D, Huang ML, Johnston C, Corey L, Posavad CM. HSV-2-Specific Human Female Reproductive Tract Tissue Resident Memory T Cells Recognize Diverse HSV Antigens. Front Immunol 2022; 13:867962. [PMID: 35432373 PMCID: PMC9009524 DOI: 10.3389/fimmu.2022.867962] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/07/2022] [Indexed: 01/05/2023] Open
Abstract
Antigen-specific TRM persist and protect against skin or female reproductive tract (FRT) HSV infection. As the pathogenesis of HSV differs between humans and model organisms, we focus on humans with well-characterized recurrent genital HSV-2 infection. Human CD8+ TRM persisting at sites of healed human HSV-2 lesions have an activated phenotype but it is unclear if TRM can be cultivated in vitro. We recovered HSV-specific TRM from genital skin and ectocervix biopsies, obtained after recovery from recurrent genital HSV-2, using ex vivo activation by viral antigen. Up to several percent of local T cells were HSV-reactive ex vivo. CD4 and CD8 T cell lines were up to 50% HSV-2-specific after sorting-based enrichment. CD8 TRM displayed HLA-restricted reactivity to specific HSV-2 peptides with high functional avidities. Reactivity to defined peptides persisted locally over several month and was quite subject-specific. CD4 TRM derived from biopsies, and from an extended set of cervical cytobrush specimens, also recognized diverse HSV-2 antigens and peptides. Overall we found that HSV-2-specific TRM are abundant in the FRT between episodes of recurrent genital herpes and maintain competency for expansion. Mucosal sites are accessible for clinical monitoring during immune interventions such as therapeutic vaccination.
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Affiliation(s)
- David M Koelle
- Department of Medicine, University of Washington, Seattle, WA, United States.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Global Health, University of Washington, Seattle, WA, United States.,Department of Translational Research, Benaroya Research Institute, Seattle, WA, United States
| | - Lichun Dong
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Kerry J Laing
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jia Zhu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Lei Jin
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, WA, United States.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Dana Varon
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Meei-Li Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Christine Johnston
- Department of Medicine, University of Washington, Seattle, WA, United States.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Lawrence Corey
- Department of Medicine, University of Washington, Seattle, WA, United States.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Christine M Posavad
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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30
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Wu X, Roberto JB, Knupp A, Greninger AL, Truong CD, Hollingshead N, Kenerson HL, Tuefferd M, Chen A, Koelle DM, Horton H, Jerome KR, Polyak SJ, Yeung RS, Crispe IN. Response of Human Liver Tissue to Innate Immune Stimuli. Front Immunol 2022; 13:811551. [PMID: 35355993 PMCID: PMC8959492 DOI: 10.3389/fimmu.2022.811551] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Precision-cut human liver slice cultures (PCLS) have become an important alternative immunological platform in preclinical testing. To further evaluate the capacity of PCLS, we investigated the innate immune response to TLR3 agonist (poly-I:C) and TLR4 agonist (LPS) using normal and diseased liver tissue. Pathological liver tissue was obtained from patients with active chronic HCV infection, and patients with former chronic HCV infection cured by recent Direct-Acting Antiviral (DAA) drug therapy. We found that hepatic innate immunity in response to TLR3 and TLR4 agonists was not suppressed but enhanced in the HCV-infected tissue, compared with the healthy controls. Furthermore, despite recent HCV elimination, DAA-cured liver tissue manifested ongoing abnormalities in liver immunity: sustained abnormal immune gene expression in DAA-cured samples was identified in direct ex vivo measurements and in TLR3 and TLR4 stimulation assays. Genes that were up-regulated in chronic HCV-infected liver tissue were mostly characteristic of the non-parenchymal cell compartment. These results demonstrated the utility of PCLS in studying both liver pathology and innate immunity.
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Affiliation(s)
- Xia Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States.,Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jessica B Roberto
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Allison Knupp
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Institute, Seattle, WA, United States
| | - Camtu D Truong
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Nicole Hollingshead
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Heidi L Kenerson
- Department of Surgery, University of Washington, Seattle, WA, United States
| | - Marianne Tuefferd
- Infectious Diseases and Vaccines, Janssen Research and Development, Beerse, Belgium
| | - Antony Chen
- Infectious Diseases and Vaccines, Janssen Research and Development, Beerse, Belgium
| | - David M Koelle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States.,Department of Medicine, University of Washington, Seattle, WA, United States.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Institute, Seattle, WA, United States.,Department of Translational Research, Benaroya Research Institute, Seattle, WA, United States.,Department of Global Health, University of Washington, Seattle, WA, United States
| | - Helen Horton
- Infectious Diseases and Vaccines, Janssen Research and Development, Beerse, Belgium
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Institute, Seattle, WA, United States
| | - Stephen J Polyak
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States.,Department of Global Health, University of Washington, Seattle, WA, United States
| | - Raymond S Yeung
- Department of Surgery, University of Washington, Seattle, WA, United States
| | - Ian N Crispe
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
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31
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Jing L, Wu X, Krist MP, Hsiang TY, Campbell VL, McClurkan CL, Favors SM, Hemingway LA, Godornes C, Tong DQ, Selke S, LeClair AC, Pyo CW, Geraghty DE, Laing KJ, Wald A, Gale M, Koelle DM. T cell response to intact SARS-CoV-2 includes coronavirus cross-reactive and variant-specific components. JCI Insight 2022; 7:e158126. [PMID: 35133988 PMCID: PMC8986086 DOI: 10.1172/jci.insight.158126] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 01/04/2022] [Accepted: 02/02/2022] [Indexed: 12/03/2022] Open
Abstract
SARS-CoV-2 provokes a robust T cell response. Peptide-based studies exclude antigen processing and presentation biology, which may influence T cell detection studies. To focus on responses to whole virus and complex antigens, we used intact SARS-CoV-2 and full-length proteins with DCs to activate CD8 and CD4 T cells from convalescent people. T cell receptor (TCR) sequencing showed partial repertoire preservation after expansion. Resultant CD8 T cells recognize SARS-CoV-2-infected respiratory tract cells, and CD4 T cells detect inactivated whole viral antigen. Specificity scans with proteome-covering protein/peptide arrays show that CD8 T cells are oligospecific per subject and that CD4 T cell breadth is higher. Some CD4 T cell lines enriched using SARS-CoV-2 cross-recognize whole seasonal coronavirus (sCoV) antigens, with protein, peptide, and HLA restriction validation. Conversely, recognition of some epitopes is eliminated for SARS-CoV-2 variants, including spike (S) epitopes in the Alpha, Beta, Gamma, and Delta variant lineages.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | | | - Chu-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Daniel E. Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Anna Wald
- Department of Medicine
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Michael Gale
- Department of Immunology, and
- Center for Innate Immunity of Immune Disease, Department of Immunology, and
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - David M. Koelle
- Department of Medicine
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
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32
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Sooda A, Rwandamuriye F, Wanjalla CN, Jing L, Koelle DM, Peters B, Leary S, Chopra A, Calderwood MA, Mallal SA, Pavlos R, Watson M, Phillips EJ, Redwood AJ. Abacavir inhibits but does not cause self-reactivity to HLA-B*57:01-restricted EBV specific T cell receptors. Commun Biol 2022; 5:133. [PMID: 35173258 PMCID: PMC8850454 DOI: 10.1038/s42003-022-03058-9] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 01/14/2022] [Indexed: 01/11/2023] Open
Abstract
Pre-existing pathogen-specific memory T cell responses can contribute to multiple adverse outcomes including autoimmunity and drug hypersensitivity. How the specificity of the T cell receptor (TCR) is subverted or seconded in many of these diseases remains unclear. Here, we apply abacavir hypersensitivity (AHS) as a model to address this question because the disease is linked to memory T cell responses and the HLA risk allele, HLA-B*57:01, and the initiating insult, abacavir, are known. To investigate the role of pathogen-specific TCR specificity in mediating AHS we performed a genome-wide screen for HLA-B*57:01 restricted T cell responses to Epstein-Barr virus (EBV), one of the most prevalent human pathogens. T cell epitope mapping revealed HLA-B*57:01 restricted responses to 17 EBV open reading frames and identified an epitope encoded by EBNA3C. Using these data, we cloned the dominant TCR for EBNA3C and a previously defined epitope within EBNA3B. TCR specificity to each epitope was confirmed, however, cloned TCRs did not cross-react with abacavir plus self-peptide. Nevertheless, abacavir inhibited TCR interactions with their cognate ligands, demonstrating that TCR specificity may be subverted by a drug molecule. These results provide an experimental road map for future studies addressing the heterologous immune responses of TCRs including T cell mediated adverse drug reactions. HLA-B*57:01 restricted EBV-specific T-cell receptor specificity is altered by abacavir, suggesting a potentially inhibitory effect of abacavir on HLA-B*57:01 restricted TCR recognition.
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Affiliation(s)
- Anuradha Sooda
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Francois Rwandamuriye
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia.,Telethon Kids Institute, Nedlands, WA, Australia
| | - Celestine N Wanjalla
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA.,Benaroya Research Institute, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Michael A Calderwood
- Department of Medicine, The Channing Laboratory, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Simon A Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia.,Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rebecca Pavlos
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia.,Telethon Kids Institute, Nedlands, WA, Australia
| | - Mark Watson
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Elizabeth J Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia. .,Center for Drug Safety & Immunology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Alec J Redwood
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia.,Institute for Respiratory Health, Level 2, 6 Verdun Street, Nedlands, WA, 6009, Australia.,School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
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33
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Jing L, Wu X, Krist MP, Hsiang TY, Campbell VL, McClurkan CL, Favors SM, Hemingway LA, Godornes C, Tong DQ, Selke S, LeClair AC, Pyo CW, Geraghty DE, Laing KJ, Wald A, Gale M, Koelle DM. T cell response to intact SARS-CoV-2 includes coronavirus cross-reactive and variant-specific components. medRxiv 2022:2022.01.23.22269497. [PMID: 35118477 PMCID: PMC8811910 DOI: 10.1101/2022.01.23.22269497] [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: 06/14/2023]
Abstract
SARS-CoV-2 provokes a brisk T cell response. Peptide-based studies exclude antigen processing and presentation biology and may influence T cell detection studies. To focus on responses to whole virus and complex antigens, we used intact SARS-CoV-2 and full-length proteins with DC to activate CD8 and CD4 T cells from convalescent persons. T cell receptor (TCR) sequencing showed partial repertoire preservation after expansion. Resultant CD8 T cells recognize SARS-CoV-2-infected respiratory cells, and CD4 T cells detect inactivated whole viral antigen. Specificity scans with proteome-covering protein/peptide arrays show that CD8 T cells are oligospecific per subject and that CD4 T cell breadth is higher. Some CD4 T cell lines enriched using SARS-CoV-2 cross-recognize whole seasonal coronavirus (sCoV) antigens, with protein, peptide, and HLA restriction validation. Conversely, recognition of some epitopes is eliminated for SARS-CoV-2 variants, including spike (S) epitopes in the alpha, beta, gamma, and delta variant lineages.
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34
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James CA, Xu Y, Aguilar MS, Jing L, Layton ED, Gilleron M, Minnaard AJ, Scriba TJ, Day CL, Warren EH, Koelle DM, Seshadri C. CD4 and CD8 co-receptors modulate functional avidity of CD1b-restricted T cells. Nat Commun 2022; 13:78. [PMID: 35013257 PMCID: PMC8748927 DOI: 10.1038/s41467-021-27764-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/10/2021] [Indexed: 12/13/2022] Open
Abstract
T cells recognize mycobacterial glycolipid (mycolipid) antigens presented by CD1b molecules, but the role of CD4 and CD8 co-receptors in mycolipid recognition is unknown. Here we show CD1b-mycolipid tetramers reveal a hierarchy in which circulating T cells expressing CD4 or CD8 co-receptor stain with a higher tetramer mean fluorescence intensity than CD4-CD8- T cells. CD4+ primary T cells transduced with mycolipid-specific T cell receptors bind CD1b-mycolipid tetramer with a higher fluorescence intensity than CD8+ primary T cells. The presence of either CD4 or CD8 also decreases the threshold for interferon-γ secretion. Co-receptor expression increases surface expression of CD3ε, suggesting a mechanism for increased tetramer binding and activation. Targeted transcriptional profiling of mycolipid-specific T cells from individuals with active tuberculosis reveals canonical markers associated with cytotoxicity among CD8+ compared to CD4+ T cells. Thus, expression of co-receptors modulates T cell receptor avidity for mycobacterial lipids, leading to in vivo functional diversity during tuberculosis disease.
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Affiliation(s)
- Charlotte A James
- Molecular Medicine and Mechanisms of Disease PhD Program (M3D), Department of Pathology, University of Washington, Seattle, WA, USA
| | - Yuexin Xu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Erik D Layton
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Martine Gilleron
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, 31077, Toulouse, France
| | - Adriaan J Minnaard
- Stratingh Institute for Chemistry, University of Groningen, Groningen, The Netherlands
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Cheryl L Day
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA
| | - Edus H Warren
- Molecular Medicine and Mechanisms of Disease PhD Program (M3D), Department of Pathology, University of Washington, Seattle, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David M Koelle
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Benaroya Research Institute, Seattle, WA, USA
| | - Chetan Seshadri
- Department of Medicine, University of Washington, Seattle, WA, USA.
- Tuberculosis Research and Training Center, Seattle, WA, USA.
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35
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Mesic A, Jackson EK, Lalika M, Koelle DM, Patel RC. Interferon-based agents for current and future viral respiratory infections: A scoping literature review of human studies. PLOS Glob Public Health 2022; 2:e0000231. [PMID: 36962150 PMCID: PMC10022196 DOI: 10.1371/journal.pgph.0000231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/17/2022] [Indexed: 11/19/2022]
Abstract
The interferon (IFN) system is a potent line of defense against viral infections. IFN-based agents already tested may be of use in COVID-19 or future viral respiratory outbreaks. Here we review the comparative efficacy, safety/tolerability, and future potential of IFN-based therapeutics. We reviewed human studies in which IFN or IFN pathway-interacting agents were used for viral respiratory infections. We identified 977 articles, of which 194 were included for full-text review. Of these, we deemed 35 articles to be relevant. The use of IFN-based agents for pre-exposure prophylaxis (n = 19) and treatment (n = 15) were most common, with intranasal (n = 22) as the most common route. We found IFN-α (n = 23) was used most often, and rhinovirus (n = 14) was the most common causative agent. Studies demonstrated mixed efficacy but generally positive safety and tolerability. Host-directed therapies, such as IFN or IFN inducers, are worthy of additional research to target viral respiratory infections lacking direct-acting antivirals.
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Affiliation(s)
- Aldina Mesic
- Department of Global Health, The Strategic Analysis, Research & Training (START) Center, University of Washington, Seattle, WA, United States of America
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - Emahlea K Jackson
- Department of Global Health, The Strategic Analysis, Research & Training (START) Center, University of Washington, Seattle, WA, United States of America
- Department of Epidemiology, University of Washington, Seattle, WA, United States of America
| | - Mathias Lalika
- Department of Global Health, The Strategic Analysis, Research & Training (START) Center, University of Washington, Seattle, WA, United States of America
- Department of Global Health, University of Washington, Seattle, WA, United States of America
| | - David M Koelle
- Department of Global Health, University of Washington, Seattle, WA, United States of America
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- Benaroya Research Institute, Seattle, WA, United States of America
| | - Rena C Patel
- Department of Global Health, The Strategic Analysis, Research & Training (START) Center, University of Washington, Seattle, WA, United States of America
- Department of Global Health, University of Washington, Seattle, WA, United States of America
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States of America
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36
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Johansson AM, Malhotra U, Kim YG, Gomez R, Krist MP, Wald A, Koelle DM, Kwok WW. Cross-reactive and mono-reactive SARS-CoV-2 CD4+ T cells in prepandemic and COVID-19 convalescent individuals. PLoS Pathog 2021; 17:e1010203. [PMID: 34965282 PMCID: PMC8769337 DOI: 10.1371/journal.ppat.1010203] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/19/2022] [Accepted: 12/14/2021] [Indexed: 12/15/2022] Open
Abstract
Class II tetramer reagents for eleven common DR alleles and a DP allele prevalent in the world population were used to identify SARS-CoV-2 CD4+ T cell epitopes. A total of 112, 28 and 42 epitopes specific for Spike, Membrane and Nucleocapsid, respectively, with defined HLA-restriction were identified. Direct ex vivo staining of PBMC with tetramer reagents was used to define immunodominant and subdominant T cell epitopes and estimate the frequencies of these T cells in SARS-CoV-2 exposed and naïve individuals. Majority of SARS-CoV-2 epitopes identified have <67% amino acid sequence identity with endemic coronaviruses and are unlikely to elicit high avidity cross-reactive T cell responses. Four SARS-CoV-2 Spike reactive epitopes, including a DPB1*04:01 restricted epitope, with ≥67% amino acid sequence identity to endemic coronavirus were identified. SARS-CoV-2 T cell lines for three of these epitopes elicited cross-reactive T cell responses to endemic cold viruses. An endemic coronavirus Spike T cell line showed cross-reactivity to the fourth SARS-CoV-2 epitope. Three of the Spike cross-reactive epitopes were subdominant epitopes, while the DPB1*04:01 restricted epitope was a dominant epitope. Frequency analyses showed Spike cross-reactive T cells as detected by tetramers were present at relatively low frequency in unexposed people and only contributed a small proportion of the overall Spike-specific CD4+ T cells in COVID-19 convalescent individuals. In total, these results suggested a very limited number of SARS-CoV-2 T cells as detected by tetramers are capable of recognizing ccCoV with relative high avidity and vice versa. The potentially supportive role of these high avidity cross-reactive T cells in protective immunity against SARS-CoV-2 needs further studies.
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Affiliation(s)
- Alexandra M. Johansson
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
| | - Uma Malhotra
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
- Virginia Mason Franciscan Health, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Yeseul G. Kim
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
| | - Rebecca Gomez
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
| | - Maxwell P. Krist
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - David M. Koelle
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - William W. Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
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37
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Chang WC, Abe R, Anderson P, Anderson W, Ardern-Jones MR, Beachkofsky TM, Bellón T, Biala AK, Bouchard C, Cavalleri GL, Chapman N, Chodosh J, Choi HK, Cibotti RR, Divito SJ, Dewar K, Dehaeck U, Etminan M, Forbes D, Fuchs E, Goldman JL, Holmes JH, Hope EA, Hung SI, Hsieh CL, Iovieno A, Jagdeo J, Kim MK, Koelle DM, Lacouture ME, Le Pallec S, Lehloenya RJ, Lim R, Lowe A, McCawley J, McCawley J, Micheletti RG, Mockenhaupt M, Niemeyer K, Norcross MA, Oboh D, Olteanu C, Pasieka HB, Peter J, Pirmohamed M, Rieder M, Saeed HN, Shear NH, Shieh C, Straus S, Sukasem C, Sung C, Trubiano JA, Tsou SY, Ueta M, Volpi S, Wan C, Wang H, Wang ZQ, Weintraub J, Whale C, Wheatley LM, Whyte-Croasdaile S, Williams KB, Wright G, Yeung SN, Zhou L, Chung WH, Phillips EJ, Carleton BC. Corrigendum to 'SJS/TEN 2019: From science to translation' [J. Dermatol. Sci. 98/1 (2020) 2-12]. J Dermatol Sci 2021; 104:146-147. [PMID: 34763988 PMCID: PMC9371621 DOI: 10.1016/j.jdermsci.2021.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Wan-Chun Chang
- Division of Translational Therapeutics, Department of
Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC,
Canada,British Columbia Children’s Hospital Research
Institute, Vancouver, BC, Canada
| | - Riichiro Abe
- Niigata University Graduate School of Medical and Dental
Sciences, Niigata, Japan
| | - Paul Anderson
- Stevens-Johnson Syndrome Foundation, Westminster, CO,
USA
| | | | - Michael R. Ardern-Jones
- Faculty of Medicine, University of Southampton, Southampton
General Hospital, Southampton, UK
| | | | - Teresa Bellón
- Drug Hypersensitivity Group. Hospital La Paz Institute for
Health Research (IdiPAZ), Madrid, Spain
| | - Agnieszka K. Biala
- Division of Translational Therapeutics, Department of
Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC,
Canada
| | | | - Gianpiero L. Cavalleri
- School of Pharmacy and Molecular and Cellular Therapeutics,
Royal College of Surgeons in Ireland, Dublin, Ireland,FutureNeuro SFI Research Centre, Royal College of
Surgeons in Ireland, Dublin, Ireland
| | | | - James Chodosh
- Massachusetts Eye and Ear, Harvard Medical School, Boston,
MA, USA
| | - Hyon K. Choi
- Division of Rheumatology, Allergy and Immunology,
Massachusetts General Hospital, Boston, MA, USA
| | - Ricardo R. Cibotti
- National Institute of Arthritis and Musculoskeletal and
Skin Diseases, NIH, USA
| | - Sherrie J. Divito
- Department of Dermatology, Brigham and Women’s
Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Ulrike Dehaeck
- Department of Obstetrics and Gynecology, University of
British Columbia, Vancouver, BC, Canada
| | - Mahyar Etminan
- Department of Ophthalmology and Visual Sciences,
University of British Columbia, Vancouver, BC, Canada
| | - Diane Forbes
- Canadian Institutes of Health Research, Ottawa, ON,
Canada
| | - Esther Fuchs
- Department of Obstetrics and Gynecology, University of
Washington, Seattle, WA, USA
| | | | - James H. Holmes
- Wake Forest University School of Medicine, WFBMC Burn
Center, Winston-Salem, NC, USA
| | | | - Shuen-Iu Hung
- Cancer Vaccine and Immune Cell Therapy Core Laboratory,
Chang Gung Immunology Consortium, Chang Gung Memorial Hospital, Linkou, Taoyuan,
Taiwan,Institute of Pharmacology, National Yang-Ming University,
Taipei, Taiwan
| | | | - Alfonso Iovieno
- Department of Ophthalmology and Visual Sciences,
University of British Columbia, Vancouver General Hospital Eye Care Center,
Vancouver, BC, Canada
| | | | - Mee Kum Kim
- Department of Ophthalmology, Seoul National University
College of Medicine, Seoul, South Korea
| | - David M. Koelle
- Department of Medicine, University of Washington, Seattle,
WA, USA
| | | | - Sophie Le Pallec
- Association des malades des syndromes de Lyell et de
Stevens-Johnson (Amalyste), Paris, France
| | - Rannakoe J. Lehloenya
- Division of Dermatology, Department of Medicine,
University of Cape Town, Cape Town, South Africa
| | - Robyn Lim
- Health Products and Food Branch, Health Canada, Ottawa,
ON, Canada
| | - Angie Lowe
- SJS/TEN International Awareness (STIA), Lucky Lake, SK,
Canada
| | - Jean McCawley
- Stevens-Johnson Syndrome Foundation, Westminster, CO,
USA
| | - Julie McCawley
- Stevens-Johnson Syndrome Foundation, Westminster, CO,
USA
| | - Robert G. Micheletti
- Department of Dermatology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
| | - Maja Mockenhaupt
- Dokumentationszentrum schwerer Hautreaktionen (dZh),
Department of Dermatology, Medical Center and Medical Faculty, University of
Freiburg, Freiburg, Germany
| | | | - Michael A. Norcross
- Laboratory of Immunology, Division of Biotechnology
Review and Research III (DBRR III), Office of Biotechnology Products (OBP), Office
of Pharmaceutical Quality (OPQ), Center for Drug Evaluation and Research (CDER),
FDA, Silver Spring, MD, USA
| | - Douglas Oboh
- Stevens-Johnson Syndrome Foundation, Westminster, CO,
USA
| | - Cristina Olteanu
- Division of Dermatology, Department of Medicine,
University of Alberta, Edmonton, AB, Canada
| | - Helena B. Pasieka
- Department of Der matology, MedStar Washington Hospital
Center, Washington, DC, USA
| | - Jonathan Peter
- Division of Allergy and Clinical Immunology, Department
of Medicine, University of Cape Town, Cape Town, South Africa
| | - Munir Pirmohamed
- Department of Molecular and Clinical Pharmacology,
University of Liverpool, Liverpool, UK
| | - Michael Rieder
- Department of Paediatrics, Children’s
Hospital/London Health Sciences Centre, Schulich School of Medicine & Dentistry,
Western University, London, ON, Canada
| | - Hajirah N. Saeed
- Massachusetts Eye and Ear, Harvard Medical School, Boston,
MA, USA
| | - Neil H. Shear
- Sunnybrook Health Sciences Centre, University of Toronto,
ON, Canada
| | - Christine Shieh
- Department of Ophthalmology, Vanderbilt Eye Institute,
Nashville, TN, USA
| | - Sabine Straus
- Dutch Medicines Evaluation Board, Pharmacovigilance Risk
Assessment Committee, European Medicines Agency, Utrecht, Netherlands
| | | | - Cynthia Sung
- Health Products Regulation Group, Health Sciences
Authority Singapore, Duke-NUS Medical School, Singapore
| | - Jason A. Trubiano
- Department of Infectious Diseases, Austin Health,
Heidelberg, Germany,Department of Medicine, University of Melbourne,
Victoria, Australia
| | | | - Mayumi Ueta
- Department of Frontier Medical Science and Technology for
Ophthalmology, Kyoto Pre fectural University of Medicine, Kyoto, Japan
| | - Simona Volpi
- National Human Genome Research Institute, NIH, Bethesda,
ML, USA
| | - Chen Wan
- Genome British Columbia, Vancouver, BC, Canada
| | - Hongsheng Wang
- Institute of Dermatology, Chinese Academy of Medical
Sciences, National Center for STD and Leprosy Control, China CDC, Nanjing,
China
| | | | - Jessica Weintraub
- Division of Pharmacovigilance I, Office of Surveillance
and Epidemiology, Center for Drug Evaluation and Research, US Food and Drug
Administration, USA
| | | | - Lisa M. Wheatley
- National Institute of Allergy and Infectious Diseases,
NIH, Bethesda, ML, USA
| | | | - Kristina B. Williams
- Department of Pathology, Microbiology and Immunology,
Vanderbilt University Medical Center, Nashville, TN, USA
| | - Galen Wright
- Division of Translational Therapeutics, Department of
Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC,
Canada
| | - Sonia N. Yeung
- Department of Ophthalmology and Visual Sciences,
University of British Columbia, Vancouver General Hospital Eye Care Center,
Vancouver, BC, Canada
| | - Li Zhou
- Division of General Internal Medicine and Primary Care,
Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Wen-Hung Chung
- Department of Dermatology, Drug Hypersensitivity Clinical
and Research Center, Chang Gung Memorial Hospital, Linkou, Taipei, Keelung, Taoyuan,
Taiwan,Cancer Vaccine and Immune Cell Therapy Core Laboratory,
Chang Gung Immunology Consortium, Chang Gung Memorial Hospital, Linkou, Taoyuan,
Taiwan,College of Medicine, Chang Gung University, Taoyuan,
Taiwan,Whole-Genome Research Core Laboratory of Human Diseases,
Chang Gung Memorial Hospital, Keelung, Taiwan,Department of Dermatology, Xiamen Chang Gung Hospital,
Xiamen, China
| | - Elizabeth J. Phillips
- Department of Pathology, Microbiology and Immunology,
Vanderbilt University Medical Center, Nashville, TN, USA,Institute for Immunology and Infectious Diseases, Murdoch
University, Murdoch, Australia,Division of Infectious Diseases, Department of Medicine,
Vanderbilt University Medical Center, Nashville, TN, USA,Department of Pharmacology, Vanderbilt University Medical
Center, Nashville, TN, USA
| | - Bruce C. Carleton
- Division of Translational Therapeutics, Department of
Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC,
Canada,British Columbia Children’s Hospital Research
Institute, Vancouver, BC, Canada
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38
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Wainberg M, Luquez T, Koelle DM, Readhead B, Johnston C, Darvas M, Funk CC. The viral hypothesis: how herpesviruses may contribute to Alzheimer's disease. Mol Psychiatry 2021; 26:5476-5480. [PMID: 33972690 PMCID: PMC8758477 DOI: 10.1038/s41380-021-01138-6] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 12/14/2022]
Abstract
The hypothesis that infectious agents, particularly herpesviruses, contribute to Alzheimer's disease (AD) pathogenesis has been investigated for decades but has long engendered controversy. In the past 3 years, several studies in mouse models, human tissue models, and population cohorts have reignited interest in this hypothesis. Collectively, these studies suggest that many of the hallmarks of AD, like amyloid beta production and neuroinflammation, can arise as a protective response to acute infection that becomes maladaptive in the case of chronic infection. We place this work in its historical context and explore its etiological implications.
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Affiliation(s)
| | - Tain Luquez
- Institute for Systems Biology, Seattle, WA, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Benaroya Research Institute, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Ben Readhead
- Arizona State University-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Christine Johnston
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Martin Darvas
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Cory C Funk
- Institute for Systems Biology, Seattle, WA, USA.
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39
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Peng T, Phasouk K, Sodroski CN, Sun S, Hwangbo Y, Layton ED, Jin L, Klock A, Diem K, Magaret AS, Jing L, Laing K, Li A, Huang ML, Mertens M, Johnston C, Jerome KR, Koelle DM, Wald A, Knipe DM, Corey L, Zhu J. Tissue-Resident-Memory CD8 + T Cells Bridge Innate Immune Responses in Neighboring Epithelial Cells to Control Human Genital Herpes. Front Immunol 2021; 12:735643. [PMID: 34552595 PMCID: PMC8450389 DOI: 10.3389/fimmu.2021.735643] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/11/2021] [Indexed: 12/02/2022] Open
Abstract
Tissue-resident-memory T cells (TRM) populate the body’s barrier surfaces, functioning as frontline responders against reencountered pathogens. Understanding of the mechanisms by which CD8TRM achieve effective immune protection remains incomplete in a naturally recurring human disease. Using laser capture microdissection and transcriptional profiling, we investigate the impact of CD8TRM on the tissue microenvironment in skin biopsies sequentially obtained from a clinical cohort of diverse disease expression during herpes simplex virus 2 (HSV-2) reactivation. Epithelial cells neighboring CD8TRM display elevated and widespread innate and cell-intrinsic antiviral signature expression, largely related to IFNG expression. Detailed evaluation via T-cell receptor reconstruction confirms that CD8TRM recognize viral-infected cells at the specific HSV-2 peptide/HLA level. The hierarchical pattern of core IFN-γ signature expression is well-conserved in normal human skin across various anatomic sites, while elevation of IFI16, TRIM 22, IFITM2, IFITM3, MX1, MX2, STAT1, IRF7, ISG15, IFI44, CXCL10 and CCL5 expression is associated with HSV-2-affected asymptomatic tissue. In primary human cells, IFN-γ pretreatment reduces gene transcription at the immediate-early stage of virus lifecycle, enhances IFI16 restriction of wild-type HSV-2 replication and renders favorable kinetics for host protection. Thus, the adaptive immune response through antigen-specific recognition instructs innate and cell-intrinsic antiviral machinery to control herpes reactivation, a reversal of the canonical thinking of innate activating adaptive immunity in primary infection. Communication from CD8TRM to surrounding epithelial cells to activate broad innate resistance might be critical in restraining various viral diseases.
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Affiliation(s)
- Tao Peng
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Khamsone Phasouk
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Catherine N Sodroski
- Department of Microbiology and Virology Program, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Sijie Sun
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Yon Hwangbo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Erik D Layton
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Lei Jin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Alexis Klock
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Kurt Diem
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Amalia S Magaret
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Lichen Jing
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Kerry Laing
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Alvason Li
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States
| | - Meei-Li Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Max Mertens
- Department of Microbiology and Virology Program, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Christine Johnston
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - David M Koelle
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States.,Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States.,Benaroya Research Institute, Seattle, WA, United States
| | - Anna Wald
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States.,Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - David M Knipe
- Department of Microbiology and Virology Program, Blavatnik Institute, Harvard Medical School, Boston, MA, United States
| | - Lawrence Corey
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Department of Medicine, University of Washington School of Medicine, Seattle, WA, United States.,Department of Global Health, University of Washington School of Medicine, Seattle, WA, United States
| | - Jia Zhu
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, United States.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States.,Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, United States
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40
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St. Leger AJ, Koelle DM, Kinchington PR, Verjans GMGM. Local Immune Control of Latent Herpes Simplex Virus Type 1 in Ganglia of Mice and Man. Front Immunol 2021; 12:723809. [PMID: 34603296 PMCID: PMC8479180 DOI: 10.3389/fimmu.2021.723809] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/26/2021] [Indexed: 12/28/2022] Open
Abstract
Herpes simplex virus type 1 (HSV-1) is a prevalent human pathogen. HSV-1 genomes persist in trigeminal ganglia neuronal nuclei as chromatinized episomes, while epithelial cells are typically killed by lytic infection. Fluctuations in anti-viral responses, broadly defined, may underlay periodic reactivations. The ganglionic immune response to HSV-1 infection includes cell-intrinsic responses in neurons, innate sensing by several cell types, and the infiltration and persistence of antigen-specific T-cells. The mechanisms specifying the contrasting fates of HSV-1 in neurons and epithelial cells may include differential genome silencing and chromatinization, dictated by variation in access of immune modulating viral tegument proteins to the cell body, and protection of neurons by autophagy. Innate responses have the capacity of recruiting additional immune cells and paracrine activity on parenchymal cells, for example via chemokines and type I interferons. In both mice and humans, HSV-1-specific CD8 and CD4 T-cells are recruited to ganglia, with mechanistic studies suggesting active roles in immune surveillance and control of reactivation. In this review we focus mainly on HSV-1 and the TG, comparing and contrasting where possible observational, interventional, and in vitro studies between humans and animal hosts.
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Affiliation(s)
- Anthony J. St. Leger
- Department of Ophthalmology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Benaroya Research Institute, Seattle, WA, United States
| | - Paul R. Kinchington
- Department of Ophthalmology and Molecular Microbiology and Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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41
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Plymate LC, Pepper G, Krist MP, Koelle DM. Immunogenicity of repeat COVID-19 mRNA vaccinations in a patient with myasthenia gravis receiving mycophenolate, prednisone, and eculizumab. J Transl Autoimmun 2021; 4:100114. [PMID: 34426798 PMCID: PMC8375276 DOI: 10.1016/j.jtauto.2021.100114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023] Open
Abstract
Vaccination can prevent infection and disease due to SARS-CoV-2. Early reports indicate that immune suppressed or immune compromised populations have reduced immune responses to US emergency use authorized (EUA) vaccines. Patients with autoimmune disorders are at risk for severe COVID-19, and are frequently immune suppressed related to therapy, the underlying disease, or both. Myasthenia gravis (MG) is an autoimmune disorder characterized by antibodies that interrupt neuromuscular transmission. Chronic immune suppressive therapy is typically required. We report the case of a 74 year old woman with MG receiving mycophenolate, prednisone, and eculizumab in whom mRNA vaccination failed to elicit detectable circulating vaccine-specific IgG or IFN-γ T cell responses. Eculizumab was discontinued, and repeat vaccination with two doses of an alternative EUA mRNA vaccine led to circulating IgG specific for the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein, and to detectable S-specific T cell responses. While it is not known if these responses will protect against SARS-CoV-2 infection or disease, a repeat course of mRNA vaccination appears to be safe and was broadly immunogenic in this individual. T and B cell immune responses to SARS-CoV-2 mRNA vaccine reduced in an immune suppressed patient. Repeat vaccination course with an alternative mRNA vaccine led to detectable, specific T and B cell responses. Persons with autoimmune disease receiving immune suppression may benefit from additional doses of vaccine.
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Affiliation(s)
| | - Gregory Pepper
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Maxwell P Krist
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - David M Koelle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Benaroya Research Institute, Seattle, WA, USA
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42
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Peng T, Phasouk K, Bossard E, Klock A, Jin L, Laing KJ, Johnston C, Williams NA, Czartoski JL, Varon D, Long AN, Bielas JH, Snyder TM, Robins H, Koelle DM, McElrath MJ, Wald A, Corey L, Zhu J. Distinct populations of antigen-specific tissue-resident CD8+ T cells in human cervix mucosa. JCI Insight 2021; 6:e149950. [PMID: 34156975 PMCID: PMC8410090 DOI: 10.1172/jci.insight.149950] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 03/25/2021] [Accepted: 06/18/2021] [Indexed: 11/17/2022] Open
Abstract
The ectocervix is part of the lower female reproductive tract (FRT), which is susceptible to sexually transmitted infections (STIs). Comprehensive knowledge of the phenotypes and T cell receptor (TCR) repertoire of tissue-resident memory T cells (TRMs) in the human FRT is lacking. We took single-cell RNA-Seq approaches to simultaneously define gene expression and TCR clonotypes of the human ectocervix. There were significantly more CD8+ than CD4+ T cells. Unsupervised clustering and trajectory analysis identified distinct populations of CD8+ T cells with IFNGhiGZMBloCD69hiCD103lo or IFNGloGZMBhiCD69medCD103hi phenotypes. Little overlap was seen between their TCR repertoires. Immunofluorescence staining showed that CD103+CD8+ TRMs were preferentially localized in the epithelium, whereas CD69+CD8+ TRMs were distributed evenly in the epithelium and stroma. Ex vivo assays indicated that up to 14% of cervical CD8+ TRM clonotypes were HSV-2 reactive in HSV-2-seropositive persons, reflecting physiologically relevant localization. Our studies identified subgroups of CD8+ TRMs in the human ectocervix that exhibited distinct expression of antiviral defense and tissue residency markers, anatomic locations, and TCR repertoires that target anatomically relevant viral antigens. Optimization of the location, number, and function of FRT TRMs is an important approach for improving host defenses to STIs.
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Affiliation(s)
- Tao Peng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology and
| | - Khamsone Phasouk
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Emily Bossard
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Alexis Klock
- Department of Laboratory Medicine and Pathology and
| | - Lei Jin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Kerry J Laing
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Christine Johnston
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Noel A Williams
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Julie L Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Dana Varon
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Annalyssa N Long
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jason H Bielas
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | | | - David M Koelle
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology and.,Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA.,Benaroya Research Institute, Seattle, Washington, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology and.,Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Anna Wald
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology and.,Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Lawrence Corey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology and.,Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jia Zhu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology and
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43
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Elyanow R, Snyder TM, Dalai SC, Gittelman RM, Boonyaratanakornkit J, Wald A, Selke S, Wener MH, Morishima C, Greninger AL, Holbrook MR, Kaplan IM, Zahid HJ, Carlson JM, Baldo L, Manley T, Robins HS, Koelle DM. T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity. medRxiv 2021:2021.03.19.21251426. [PMID: 33791723 PMCID: PMC8010755 DOI: 10.1101/2021.03.19.21251426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Measuring the adaptive immune response to SARS-CoV-2 can enable the assessment of past infection as well as protective immunity and the risk of reinfection. While neutralizing antibody (nAb) titers are one measure of protection, such assays are challenging to perform at a large scale and the longevity of the SARS-CoV-2 nAb response is not fully understood. Here, we apply a T-cell receptor (TCR) sequencing assay that can be performed on a small volume standard blood sample to assess the adaptive T-cell response to SARS-CoV-2 infection. Samples were collected from a cohort of 302 individuals recovered from COVID-19 up to 6 months after infection. Previously published findings in this cohort showed that two commercially available SARS-CoV-2 serologic assays correlate well with nAb testing. We demonstrate that the magnitude of the SARS-CoV-2-specific T-cell response strongly correlates with nAb titer, as well as clinical indicators of disease severity including hospitalization, fever, or difficulty breathing. While the depth and breadth of the T-cell response declines during convalescence, the T-cell signal remains well above background with high sensitivity up to at least 6 months following initial infection. Compared to serology tests detecting binding antibodies to SARS-CoV-2 spike and nucleoprotein, the overall sensitivity of the TCR-based assay across the entire cohort and all timepoints was approximately 5% greater for identifying prior SARS-CoV-2 infection. Notably, the improved performance of T-cell testing compared to serology was most apparent in recovered individuals who were not hospitalized and were sampled beyond 150 days of their initial illness, suggesting that antibody testing may have reduced sensitivity in individuals who experienced less severe COVID-19 illness and at later timepoints. Finally, T-cell testing was able to identify SARS-CoV-2 infection in 68% (55/81) of convalescent samples having nAb titers below the lower limit of detection, as well as 37% (13/35) of samples testing negative by all three antibody assays. These results demonstrate the utility of a TCR-based assay as a scalable, reliable measure of past SARS-CoV-2 infection across a spectrum of disease severity. Additionally, the TCR repertoire may be useful as a surrogate for protective immunity with additive clinical value beyond serologic or nAb testing methods.
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Affiliation(s)
| | | | - Sudeb C. Dalai
- Adaptive Biotechnologies, Seattle, Washington, USA
- Stanford University School of Medicine, Stanford, California, USA
| | | | - Jim Boonyaratanakornkit
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Mark H. Wener
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Chihiro Morishima
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Alex L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Michael R. Holbrook
- National Institute of Allergy and Infectious Diseases Integrated Research Facility, Frederick, Maryland, USA
| | | | | | | | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington, USA
| | | | | | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
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44
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Yu KK, Fischinger S, Smith MT, Atyeo C, Cizmeci D, Wolf CR, Layton ED, Logue JK, Aguilar MS, Shuey K, Loos C, Yu J, Franko N, Choi RY, Wald A, Barouch DH, Koelle DM, Lauffenburger D, Chu HY, Alter G, Seshadri C. Comorbid illnesses are associated with altered adaptive immune responses to SARS-CoV-2. JCI Insight 2021; 6:146242. [PMID: 33621211 PMCID: PMC8026190 DOI: 10.1172/jci.insight.146242] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 11/19/2020] [Accepted: 02/17/2021] [Indexed: 12/16/2022] Open
Abstract
Comorbid medical illnesses, such as obesity and diabetes, are associated with more severe COVID-19, hospitalization, and death. However, the role of the immune system in mediating these clinical outcomes has not been determined. We used multiparameter flow cytometry and systems serology to comprehensively profile the functions of T cells and antibodies targeting spike, nucleocapsid, and envelope proteins in a convalescent cohort of COVID-19 subjects who were either hospitalized (n = 20) or not hospitalized (n = 40). To avoid confounding, subjects were matched by age, sex, ethnicity, and date of symptom onset. Surprisingly, we found that the magnitude and functional breadth of virus-specific CD4+ T cell and antibody responses were consistently higher among hospitalized subjects, particularly those with medical comorbidities. However, an integrated analysis identified more coordination between polyfunctional CD4+ T cells and antibodies targeting the S1 domain of spike among subjects who were not hospitalized. These data reveal a functionally diverse and coordinated response between T cells and antibodies targeting SARS-CoV-2, which is reduced in the presence of comorbid illnesses that are known risk factors for severe COVID-19.
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Affiliation(s)
- Krystle Kq Yu
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,PhD program in Immunology and Virology, University of Duisburg-Essen, Essen, Germany
| | - Malisa T Smith
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,PhD program in Virology, Division of Medical Sciences, Harvard University, Boston, Massachusetts, USA
| | - Deniz Cizmeci
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Caitlin R Wolf
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Erik D Layton
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Jennifer K Logue
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Melissa S Aguilar
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kiel Shuey
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicholas Franko
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Anna Wald
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Epidemiology and.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Dan H Barouch
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - David M Koelle
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA.,Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA.,Benaroya Research Institute, Seattle, Washington, USA
| | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
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45
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Phan IQ, Subramanian S, Kim D, Murphy M, Pettie D, Carter L, Anishchenko I, Barrett LK, Craig J, Tillery L, Shek R, Harrington WE, Koelle DM, Wald A, Veesler D, King N, Boonyaratanakornkit J, Isoherranen N, Greninger AL, Jerome KR, Chu H, Staker B, Stewart L, Myler PJ, Van Voorhis WC. In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19. Sci Rep 2021; 11:4290. [PMID: 33619344 PMCID: PMC7900118 DOI: 10.1038/s41598-021-83730-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 02/03/2021] [Indexed: 02/07/2023] Open
Abstract
Rapid generation of diagnostics is paramount to understand epidemiology and to control the spread of emerging infectious diseases such as COVID-19. Computational methods to predict serodiagnostic epitopes that are specific for the pathogen could help accelerate the development of new diagnostics. A systematic survey of 27 SARS-CoV-2 proteins was conducted to assess whether existing B-cell epitope prediction methods, combined with comprehensive mining of sequence databases and structural data, could predict whether a particular protein would be suitable for serodiagnosis. Nine of the predictions were validated with recombinant SARS-CoV-2 proteins in the ELISA format using plasma and sera from patients with SARS-CoV-2 infection, and a further 11 predictions were compared to the recent literature. Results appeared to be in agreement with 12 of the predictions, in disagreement with 3, while a further 5 were deemed inconclusive. We showed that two of our top five candidates, the N-terminal fragment of the nucleoprotein and the receptor-binding domain of the spike protein, have the highest sensitivity and specificity and signal-to-noise ratio for detecting COVID-19 sera/plasma by ELISA. Mixing the two antigens together for coating ELISA plates led to a sensitivity of 94% (N = 80 samples from persons with RT-PCR confirmed SARS-CoV-2 infection), and a specificity of 97.2% (N = 106 control samples).
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Affiliation(s)
- Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - David Kim
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Michael Murphy
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA
| | - Deleah Pettie
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA
| | - Ivan Anishchenko
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA
| | - Lynn K Barrett
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA
| | - Justin Craig
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA
| | - Logan Tillery
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA
| | - Roger Shek
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA
| | - Whitney E Harrington
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - David M Koelle
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Benaroya Research Institute, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
| | - Anna Wald
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Neil King
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA
| | - Jim Boonyaratanakornkit
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nina Isoherranen
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Helen Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington, Seattle, WA, USA
| | - Bart Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Lance Stewart
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design (IPD), University of Washington, Seattle, WA, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA.,Department of Medical Education and Biomedical Informatics & Department of Global Health, University of Washington, Seattle, WA, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. .,Department of Microbiology, University of Washington, Seattle, WA, USA. .,Department of Global Health, University of Washington, Seattle, WA, USA.
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46
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Thomason JL, Obih UM, Koelle DM, Lood C, Hughes AG. An interferon-gamma release assay as a novel biomarker in systemic lupus erythematosus. Rheumatology (Oxford) 2021; 59:3479-3487. [PMID: 32375180 DOI: 10.1093/rheumatology/keaa161] [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: 08/02/2019] [Revised: 02/22/2020] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE The mycobacterium tuberculosis (TB) IFN-γ release assay (TB-IGRA) assesses peripheral blood cell release of IFN-γ upon ex vivo exposure to mitogen (IGRA-MT), TB antigen or a negative/nil control (IGRA-NL); IGRA-NL is a measure of spontaneous IFN-γ release (SIR). Here, we investigate the diagnostic associations of elevated SIR and the potential use of IGRA-NL as a novel biomarker in SLE. METHODS We analysed diagnostic code frequencies among 11 823 individuals undergoing TB-IGRA testing between 2010 and 2015 in a large urban US health-care system. To study the relationship between IGRA-NL and SLE, we identified 99 individuals with SLE and TB-IGRA test results then assessed correlations between IGRA-NL, normalized IGRA-NL (the quotient of IGRA-NL/IGRA-MT), disease manifestations and disease activity. RESULTS We identified a discovery cohort of 108 individuals with elevated SIR (>5 S.d. above median) that was significantly enriched for a limited set of diagnoses, including SLE, TB infection, haemophagocytic lymphohistiocytosis and HIV infection. In SLE patients undergoing TB-IGRA testing, normalized IGRA-NL correlated better with disease activity than did anti-dsDNA or complement levels. This relationship appeared to reflect interactions between normalized IGRA-NL and the presence of acute skin disease, hypocomplementemia, fever and thrombocytopenia. CONCLUSION Elevated SIR appears to be associated with a limited number of disease processes, including SLE. The diagnostic utility of SIR remains to be determined. IFN-γ activation, as measured by the TB-IGRA test, may offer a readily available tool for assessing disease activity in patients with SLE.
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Affiliation(s)
- Jenna L Thomason
- Department of Medicine, Division of Rheumatology, University of Washington
| | - Uchechukwu M Obih
- Department of Medicine, Division of Rheumatology, University of Washington.,Department of Rheumatology, Swedish Medical Center
| | - David M Koelle
- Department of Medicine, Division of Infectious Diseases, University of Washington.,Department of Laboratory Medicine, University of Washington.,Department of Global Health, University of Washington.,Fred Hutchinson Cancer Research Center.,Benaroya Research Institute, Seattle, WA, USA
| | - Christian Lood
- Department of Medicine, Division of Rheumatology, University of Washington
| | - And Grant Hughes
- Department of Medicine, Division of Rheumatology, University of Washington
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47
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Boonyaratanakornkit J, Morishima C, Selke S, Zamora D, McGuffin S, Shapiro AE, Campbell VL, McClurkan CL, Jing L, Gross R, Liang J, Postnikova E, Mazur S, Lukin VV, Chaudhary A, Das MK, Fink SL, Bryan A, Greninger AL, Jerome KR, Holbrook MR, Gernsheimer TB, Wener MH, Wald A, Koelle DM. Clinical, laboratory, and temporal predictors of neutralizing antibodies against SARS-CoV-2 among COVID-19 convalescent plasma donor candidates. J Clin Invest 2021; 131:144930. [PMID: 33320842 PMCID: PMC7843229 DOI: 10.1172/jci144930] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [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: 10/07/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUNDSARS-CoV-2-specific antibodies may protect from reinfection and disease, providing rationale for administration of plasma containing SARS-CoV-2-neutralizing antibodies (nAbs) as a treatment for COVID-19. Clinical factors and laboratory assays to streamline plasma donor selection, and the durability of nAb responses, are incompletely understood.METHODSPotential convalescent plasma donors with virologically documented SARS-CoV-2 infection were tested for serum IgG against SARS-CoV-2 spike protein S1 domain and against nucleoprotein (NP), and for nAb.RESULTSAmong 250 consecutive persons, including 27 (11%) requiring hospitalization, who were studied a median of 67 days since symptom onset, 97% were seropositive on 1 or more assays. Sixty percent of donors had nAb titers ≥1:80. Correlates of higher nAb titers included older age (adjusted OR [AOR] 1.03 per year of age, 95% CI 1.00-1.06), male sex (AOR 2.08, 95% CI 1.13-3.82), fever during illness (AOR 2.73, 95% CI 1.25-5.97), and disease severity represented by hospitalization (AOR 6.59, 95% CI 1.32-32.96). Receiver operating characteristic analyses of anti-S1 and anti-NP antibody results yielded cutoffs that corresponded well with nAb titers, with the anti-S1 assay being slightly more predictive. nAb titers declined in 37 of 41 paired specimens collected a median of 98 days (range 77-120) apart (P < 0.001). Seven individuals (2.8%) were persistently seronegative and lacked T cell responses.CONCLUSIONnAb titers correlated with COVID-19 severity, age, and sex. SARS-CoV-2 IgG results can serve as useful surrogates for nAb testing. Functional nAb levels declined, and a small proportion of convalescent individuals lacked adaptive immune responses.FUNDINGThe project was supported by the Frederick National Laboratory for Cancer Research with support from the NIAID under contract number 75N91019D00024, and was supported by the Fred Hutchinson Joel Meyers Endowment, Fast-Grants, a New Investigator award from the American Society for Transplantation and Cellular Therapy, and NIH contracts 75N93019C0063, 75N91019D00024, and HHSN272201800013C, and NIH grants T32-AI118690, T32-AI007044, K08-AI119142, and K23-AI140918.
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Affiliation(s)
- Jim Boonyaratanakornkit
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Seattle Cancer Care Alliance, Seattle, Washington, USA
| | | | - Stacy Selke
- Department of Laboratory Medicine and Pathology, and
| | - Danniel Zamora
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sarah McGuffin
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Adrienne E. Shapiro
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | | | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Robin Gross
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Frederick, Maryland, USA
| | - Janie Liang
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Frederick, Maryland, USA
| | - Elena Postnikova
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Frederick, Maryland, USA
| | - Steven Mazur
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Frederick, Maryland, USA
| | | | - Anu Chaudhary
- Department of Laboratory Medicine and Pathology, and
| | - Marie K. Das
- Department of Laboratory Medicine and Pathology, and
| | - Susan L. Fink
- Department of Laboratory Medicine and Pathology, and
| | - Andrew Bryan
- Department of Laboratory Medicine and Pathology, and
| | | | - Keith R. Jerome
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, and
| | - Michael R. Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Frederick, Maryland, USA
| | - Terry B. Gernsheimer
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Seattle Cancer Care Alliance, Seattle, Washington, USA
| | - Mark H. Wener
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, and
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - David M. Koelle
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, and
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Benaroya Research Institute, Seattle, Washington, USA
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48
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Casto AM, Roychoudhury P, Xie H, Selke S, Perchetti GA, Wofford H, Huang ML, Verjans GMGM, Gottlieb GS, Wald A, Jerome KR, Koelle DM, Johnston C, Greninger AL. Large, Stable, Contemporary Interspecies Recombination Events in Circulating Human Herpes Simplex Viruses. J Infect Dis 2021; 221:1271-1279. [PMID: 31016321 DOI: 10.1093/infdis/jiz199] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/20/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The ubiquitous human pathogens, herpes simplex virus (HSV)-1 and HSV-2, are distinct viral species that diverged approximately 6 million years ago. At least 4 small, ancient HSV-1 × HSV-2 interspecies recombination events have affected the HSV-2 genome, with recombinants and nonrecombinants at each locus circulating today. However, it is unknown whether interspecies recombination can affect other loci and whether new recombinants continue to be generated. METHODS Using 255 newly sequenced and 230 existing HSV genome sequences, we comprehensively assessed interspecies recombination in HSV. RESULTS Our findings show that the sizes and locations of interspecies recombination events in HSV-2 are significantly more variable than previously appreciated and that they can impact species-specific T-cell recognition of HSV. CONCLUSIONS We describe 2 large (>5 kb) recombination events, one of which arose in its current host, demonstrating that interspecies recombination continues to occur today. These results raise concerns about the use of live-attenuated HSV-2 vaccines in high HSV-1 prevalence areas.
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Affiliation(s)
- Amanda M Casto
- Departments of Medicine, University of Washington, Seattle
| | | | - Hong Xie
- Laboratory Medicine, University of Washington, Seattle
| | - Stacy Selke
- Departments of Medicine, University of Washington, Seattle
| | | | - Haley Wofford
- Departments of Medicine, University of Washington, Seattle
| | - Meei-Li Huang
- Laboratory Medicine, University of Washington, Seattle
| | - Georges M G M Verjans
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands.,Research Center for Emerging Infectious and Zoonoses, University of Veterinary Medicine Hannover, Germany
| | - Geoffrey S Gottlieb
- Departments of Medicine, University of Washington, Seattle.,Global Health, University of Washington, Seattle.,Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle
| | - Anna Wald
- Departments of Medicine, University of Washington, Seattle
| | - Keith R Jerome
- Laboratory Medicine, University of Washington, Seattle.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - David M Koelle
- Departments of Medicine, University of Washington, Seattle.,Laboratory Medicine, University of Washington, Seattle.,Global Health, University of Washington, Seattle.,Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Benaroya Research Institute, Seattle, Washington
| | - Christine Johnston
- Departments of Medicine, University of Washington, Seattle.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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49
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Yu KK, Fischinger S, Smith MT, Atyeo C, Cizmeci D, Wolf CR, Layton ED, Logue JK, Aguilar MS, Shuey K, Loos C, Yu J, Franko N, Choi RY, Wald A, Barouch DH, Koelle DM, Lauffenburger D, Chu HY, Alter G, Seshadri C. T cell and antibody functional correlates of severe COVID-19. medRxiv 2020:2020.11.25.20235150. [PMID: 33269369 PMCID: PMC7709190 DOI: 10.1101/2020.11.25.20235150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Comorbid medical illnesses, such as obesity and diabetes, are associated with more severe COVID-19, hospitalization, and death. However, the role of the immune system in mediating these clinical outcomes has not been determined. We used multi-parameter flow cytometry and systems serology to comprehensively profile the functions of T cells and antibodies targeting spike, nucleocapsid, and envelope proteins in a convalescent cohort of COVID-19 subjects who were either hospitalized (n=20) or not hospitalized (n=40). To avoid confounding, subjects were matched by age, sex, ethnicity, and date of symptom onset. Surprisingly, we found that the magnitude and functional breadth of virus-specific CD4 T cell and antibody responses were consistently higher among hospitalized subjects, particularly those with medical comorbidities. However, an integrated analysis identified more coordination between polyfunctional CD4 T-cells and antibodies targeting the S1 domain of spike among subjects that were not hospitalized. These data reveal a functionally diverse and coordinated response between T cells and antibodies targeting SARS-CoV-2 which is reduced in the presence of comorbid illnesses that are known risk factors for severe COVID-19. Our data suggest that isolated measurements of the magnitudes of spike-specific immune responses are likely insufficient to anticipate vaccine efficacy in high-risk populations.
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Affiliation(s)
- Krystle K.Q. Yu
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- PhD program in Immunology and Virology, University of Duisburg-Essen, Essen, Germany
| | - Malisa T. Smith
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- PhD program in Virology, Division of Medical Sciences, Harvard University, Boston, MA, USA
| | - Deniz Cizmeci
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caitlin R. Wolf
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Erik D. Layton
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Jennifer K. Logue
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Melissa S. Aguilar
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Kiel Shuey
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Nicholas Franko
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Anna Wald
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dan H. Barouch
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - David M. Koelle
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Benaroya Research Institute, Seattle, WA, USA
| | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helen Y. Chu
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Chetan Seshadri
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
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50
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Boonyaratanakornkit J, Morishima C, Selke S, Zamora D, McGuffin S, Shapiro AE, Campbell VL, McClurkan CL, Jing L, Gross R, Liang J, Postnikova E, Mazur S, Chaudhary A, Das MK, Fink SL, Bryan A, Greninger AL, Jerome KR, Holbrook MR, Gernsheimer TB, Wener MH, Wald A, Koelle DM. Clinical, laboratory, and temporal predictors of neutralizing antibodies to SARS-CoV-2 after COVID-19. medRxiv 2020. [PMID: 33052361 DOI: 10.1101/2020.10.06.20207472] [Citation(s) in RCA: 4] [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: 01/06/2023]
Abstract
BACKGROUND SARS-CoV-2-specific antibodies may protect from reinfection and disease, providing the rationale for administration of plasma containing SARS-CoV-2 neutralizing antibodies (nAb) as a treatment for COVID-19. The clinical factors and laboratory assays to streamline plasma donor selection, and the durability of nAb responses, are incompletely understood. METHODS Adults with virologically-documented SARS-CoV-2 infection in a convalescent plasma donor screening program were tested for serum IgG to SARS-CoV-2 spike protein S1 domain, nucleoprotein (NP), and for nAb. RESULTS Amongst 250 consecutive persons studied a median of 67 days since symptom onset, 243/250 (97%) were seropositive on one or more assays. Sixty percent of donors had nAb titers ≥1:80. Correlates of higher nAb titer included older age (adjusted OR [AOR] 1.03/year of age, 95% CI 1.00-1.06), male sex (AOR 2.08, 95% CI 1.13-3.82), fever during acute illness (AOR 2.73, 95% CI 1.25-5.97), and disease severity represented by hospitalization (AOR 6.59, 95% CI 1.32-32.96). Receiver operating characteristic (ROC) analyses of anti-S1 and anti-NP antibody results yielded cutoffs that corresponded well with nAb titers, with the anti-S1 assay being slightly more predictive. NAb titers declined in 37 of 41 paired specimens collected a median of 98 days (range, 77-120) apart (P<0.001). Seven individuals (2.8%) were persistently seronegative and lacked T cell responses. CONCLUSIONS Nab titers correlated with COVID-19 severity, age, and sex. Standard commercially available SARS-CoV-2 IgG results can serve as useful surrogates for nAb testing. Functional nAb levels were found to decline and a small proportion of COVID-19 survivors lack adaptive immune responses.
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