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Lee LW, Shafiani S, Crossley B, Emerson RO, Williamson D, Bunin A, Vargas J, Han AS, Kaplan IM, Green PHR, Kirsch I, Bhagat G. Characterisation of T cell receptor repertoires in coeliac disease. J Clin Pathol 2024; 77:116-124. [PMID: 36522177 PMCID: PMC10850686 DOI: 10.1136/jcp-2022-208541] [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: 08/08/2022] [Accepted: 11/23/2022] [Indexed: 12/16/2022]
Abstract
AIMS Characterise T-cell receptor gene (TR) repertoires of small intestinal T cells of patients with newly diagnosed (active) coeliac disease (ACD), refractory CD type I (RCD I) and patients with CD on a gluten-free diet (GFD). METHODS Next-generation sequencing of complementarity-determining region 3 (CDR3) of rearranged T cell receptor β (TRB) and γ (TRG) genes was performed using DNA extracted from intraepithelial cell (IEC) and lamina propria cell (LPC) fractions and a small subset of peripheral blood mononuclear cell (PBMC) samples obtained from CD and non-CD (control) patients. Several parameters were assessed, including relative abundance and enrichment. RESULTS TRB and TRG repertoires of CD IEC and LPC samples demonstrated lower clonality but higher frequency of rearranged TRs compared with controls. No CD-related differences were detected in the limited number of PBMC samples. Previously published LP gliadin-specific TRB sequences were more frequently detected in LPC samples from patients with CD compared with non-CD controls. TRG repertoires of IECs from both ACD and GFD patients demonstrated increased abundance of certain CDR3 amino acid (AA) motifs compared with controls, which were encoded by multiple nucleotide variants, including one motif that was enriched in duodenal IECs versus the PBMCs of CD patients. CONCLUSIONS Small intestinal TRB and TRG repertoires of patients with CD are more diverse than individuals without CD, likely due to mucosal recruitment and accumulation of T cells because of protracted inflammation. Enrichment of the unique TRG CDR3 AA sequence in the mucosa of patients with CD may suggest disease-associated changes in the TCRγδ IE lymphocyte (IEL) landscape.
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Affiliation(s)
- Lik Wee Lee
- Computational Biology and Translational Medicine, Adaptive Biotechnologies Corp, Seattle, Washington, USA
| | - Shahin Shafiani
- Computational Biology and Translational Medicine, Adaptive Biotechnologies Corp, Seattle, Washington, USA
| | - Beryl Crossley
- Computational Biology and Translational Medicine, Adaptive Biotechnologies Corp, Seattle, Washington, USA
| | - Ryan O Emerson
- Computational Biology and Translational Medicine, Adaptive Biotechnologies Corp, Seattle, Washington, USA
| | - David Williamson
- Computational Biology and Translational Medicine, Adaptive Biotechnologies Corp, Seattle, Washington, USA
| | - Anna Bunin
- Department of Medicine, Celiac Disease Center, Columbia University Irving Medical Center, New York, New York, USA
| | - Justin Vargas
- Department of Medicine, Celiac Disease Center, Columbia University Irving Medical Center, New York, New York, USA
| | - Arnold S Han
- Department of Medicine, Celiac Disease Center, Columbia University Irving Medical Center, New York, New York, USA
| | - Ian M Kaplan
- Computational Biology and Translational Medicine, Adaptive Biotechnologies Corp, Seattle, Washington, USA
| | - Peter H R Green
- Department of Medicine, Celiac Disease Center, Columbia University Irving Medical Center, New York, New York, USA
| | - Ilan Kirsch
- Computational Biology and Translational Medicine, Adaptive Biotechnologies Corp, Seattle, Washington, USA
| | - Govind Bhagat
- Department of Pathology and Cell Biology and Department of Medicine, Celiac Disease Center, Columbia University Irving Medical Center, New York, New York, USA
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2
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Delmonte OM, Oguz C, Dobbs K, Myint-Hpu K, Palterer B, Abers MS, Draper D, Truong M, Kaplan IM, Gittelman RM, Zhang Y, Rosen LB, Snow AL, Dalgard CL, Burbelo PD, Imberti L, Sottini A, Quiros-Roldan E, Castelli F, Rossi C, Brugnoni D, Biondi A, Bettini LR, D'Angio M, Bonfanti P, Anderson MV, Saracino A, Chironna M, Di Stefano M, Fiore JR, Santantonio T, Castagnoli R, Marseglia GL, Magliocco M, Bosticardo M, Pala F, Shaw E, Matthews H, Weber SE, Xirasagar S, Barnett J, Oler AJ, Dimitrova D, Bergerson JRE, McDermott DH, Rao VK, Murphy PM, Holland SM, Lisco A, Su HC, Lionakis MS, Cohen JI, Freeman AF, Snyder TM, Lack J, Notarangelo LD. Perturbations of the T-cell receptor repertoire in response to SARS-CoV-2 in immunocompetent and immunocompromised individuals. J Allergy Clin Immunol 2023:S0091-6749(23)02544-7. [PMID: 38154666 DOI: 10.1016/j.jaci.2023.12.011] [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: 05/29/2023] [Revised: 12/13/2023] [Accepted: 12/19/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND Functional T-cell responses are essential for virus clearance and long-term protection after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, whereas certain clinical factors, such as older age and immunocompromise, are associated with worse outcome. OBJECTIVE We sought to study the breadth and magnitude of T-cell responses in patients with coronavirus disease 2019 (COVID-19) and in individuals with inborn errors of immunity (IEIs) who had received COVID-19 mRNA vaccine. METHODS Using high-throughput sequencing and bioinformatics tools to characterize the T-cell receptor β repertoire signatures in 540 individuals after SARS-CoV-2 infection, 31 IEI recipients of COVID-19 mRNA vaccine, and healthy controls, we quantified HLA class I- and class II-restricted SARS-CoV-2-specific responses and also identified several HLA allele-clonotype motif associations in patients with COVID-19, including a subcohort of anti-type 1 interferon (IFN-1)-positive patients. RESULTS Our analysis revealed that elderly patients with COVID-19 with critical disease manifested lower SARS-CoV-2 T-cell clonotype diversity as well as T-cell responses with reduced magnitude, whereas the SARS-CoV-2-specific clonotypes targeted a broad range of HLA class I- and class II-restricted epitopes across the viral proteome. The presence of anti-IFN-I antibodies was associated with certain HLA alleles. Finally, COVID-19 mRNA immunization induced an increase in the breadth of SARS-CoV-2-specific clonotypes in patients with IEIs, including those who had failed to seroconvert. CONCLUSIONS Elderly individuals have impaired capacity to develop broad and sustained T-cell responses after SARS-CoV-2 infection. Genetic factors may play a role in the production of anti-IFN-1 antibodies. COVID-19 mRNA vaccines are effective in inducing T-cell responses in patients with IEIs.
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Affiliation(s)
- Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
| | - Cihan Oguz
- Integrated Data Sciences Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Katherine Myint-Hpu
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Boaz Palterer
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michael S Abers
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Deborah Draper
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Meng Truong
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | | | | | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Lindsey B Rosen
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrew L Snow
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md; Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, Md; The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Md
| | - Peter D Burbelo
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Md
| | - Luisa Imberti
- Section of Microbiology, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Alessandra Sottini
- Section of Microbiology, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Department of Infectious and Tropical Diseases, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Francesco Castelli
- Department of Infectious and Tropical Diseases, University of Brescia, ASST Spedali Civili, Brescia, Italy
| | - Camillo Rossi
- Direzione Sanitaria, ASST Spedali Civili, Brescia, Italy
| | - Duilio Brugnoni
- Laboratorio Analisi Chimico-Cliniche, ASST Spedali Civili, Brescia, Italy
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Laura Rachele Bettini
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Mariella D'Angio
- Pediatric Department and Centro Tettamanti-European Reference Network on Paediatric Cancer, European Reference Network on Haematological Diseases, and European Reference Network on Hereditary Metabolic Disorders, University of Milano-Bicocca-Fondazione MBBM, Monza, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Megan V Anderson
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, University of Bari, Bari, Italy
| | - Maria Chironna
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Mariantonietta Di Stefano
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Jose Ramon Fiore
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Teresa Santantonio
- Department of Medical and Surgical Sciences, Section of Infectious Diseases, University of Foggia, Foggia, Italy
| | - Riccardo Castagnoli
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Gian Luigi Marseglia
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Mary Magliocco
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Elana Shaw
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Helen Matthews
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sarah E Weber
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sandhya Xirasagar
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Jason Barnett
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Dimana Dimitrova
- Center for Immuno-Oncology, National Cancer Institute, National Institutes of Health, Bethesda, Md
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - David H McDermott
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - V Koneti Rao
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Philip M Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Andrea Lisco
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | | | - Justin Lack
- Integrated Data Sciences Section, Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
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3
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Fjelltveit EB, Blomberg B, Kuwelker K, Zhou F, Onyango TB, Brokstad KA, Elyanow R, Kaplan IM, Tøndel C, Mohn KGI, Özgümüş T, Cox RJ, Langeland N. Symptom Burden and Immune Dynamics 6 to 18 Months Following Mild Severe Acute Respiratory Syndrome Coronavirus 2 Infection (SARS-CoV-2): A Case-control Study. Clin Infect Dis 2022; 76:e60-e70. [PMID: 35959897 PMCID: PMC9384725 DOI: 10.1093/cid/ciac655] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/13/2022] [Accepted: 08/10/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The burden and duration of persistent symptoms after nonsevere coronavirus disease 2019 (COVID-19) remains uncertain. This study aimed to assess postinfection symptom trajectories in home-isolated COVID-19 cases compared with age- and time- matched seronegative controls, and investigate immunological correlates of long COVID. METHODS A prospective case-control study included home-isolated COVID-19 cases between February 28 and April 4, 2020, and followed for 12 (n = 233) to 18 (n = 149) months, and 189 age-matched severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-naive controls. We collected clinical data at baseline, 6, 12, and 18 months postinfection, and blood samples at 2, 4, 6, and 12 months for analysis of SARS-CoV-2-specific humoral and cellular responses. RESULTS Overall, 46% (108/233) had persisting symptoms 12 months after COVID-19. Compared with controls, adult cases had a high risk of fatigue (27% excess risk, sex, and comorbidity adjusted odds ratio [aOR] 5.86; 95% confidence interval [CI], 3.27-10.5), memory problems (21% excess risk; aOR 7.42; CI, 3.51-15.67), concentration problems (20% excess risk; aOR 8.88; 95% CI, 3.88-20.35), and dyspnea (10% excess risk; aOR 2.66; 95% CI, 1.22-5.79). The prevalence of memory problems increased overall from 6 to 18 months (excess risk 11.5%; 95% CI, 1.5-21.5; P = .024) and among women (excess risk 18.7%; 95% CI, 4.4-32.9; P = .010). Longitudinal spike immunoglobulin G was significantly associated with dyspnea at 12 months. The spike-specific clonal CD4+ T-cell receptor β depth was significantly associated with both dyspnea and number of symptoms at 12 months. CONCLUSIONS This study documents a high burden of persisting symptoms after mild COVID-19 and suggests that infection induced SARS-CoV-2-specific immune responses may influence long-term symptoms.
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Affiliation(s)
- Elisabeth B Fjelltveit
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Bjørn Blomberg
- Department of Clinical Science, University of Bergen, Bergen, Norway,National Advisory Unit for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Kanika Kuwelker
- Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Fan Zhou
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Therese B Onyango
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Karl A Brokstad
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | | | - Ian M Kaplan
- Adaptive Biotechnologies, Seattle, Washington, USA
| | - Camilla Tøndel
- Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Research and Development, Haukeland University Hospital, Bergen, Norway,Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Kristin G I Mohn
- Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Türküler Özgümüş
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | | | - Nina Langeland
- Correspondence: N. Langeland, Department of Clinical Science, University of Bergen, Norway, Postboks 7804, 5020 Bergen, Norway ()
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4
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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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5
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Dalai SC, Dines JN, Snyder TM, Gittelman RM, Eerkes T, Vaney P, Howard S, Akers K, Skewis L, Monteforte A, Witte PR, Wolf C, Nesse H, Herndon M, Qadeer J, Duffy S, Svejnoha E, Taromino C, Kaplan IM, Alsobrook J, Manley T, Baldo L. Clinical Validation of a Novel T-Cell Receptor Sequencing Assay for Identification of Recent or Prior Severe Acute Respiratory Syndrome Coronavirus 2 Infection. Clin Infect Dis 2022; 75:2079-2087. [PMID: 35521791 PMCID: PMC9129217 DOI: 10.1093/cid/ciac353] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 04/08/2022] [Accepted: 04/29/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND While diagnostic, therapeutic, and vaccine development in the coronavirus disease 2019 (COVID-19) pandemic has proceeded at unprecedented speed, critical gaps in our understanding of the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain unaddressed by current diagnostic strategies. METHODS A statistical classifier for identifying prior SARS-CoV-2 infection was trained using >4000 SARS-CoV-2-associated T-cell receptor (TCR) β sequences identified by comparing 784 cases and 2447 controls from 5 independent cohorts. The T-Detect COVID (Adaptive Biotechnologies) assay applies this classifier to TCR repertoires sequenced from blood samples to yield a binary assessment of past infection. Assay performance was assessed in 2 retrospective (n = 346; n = 69) and 1 prospective cohort (n = 87) to determine positive percent agreement (PPA) and negative percent agreement (NPA). PPA was compared with 2 commercial serology assays, and pathogen cross-reactivity was evaluated. RESULTS T-Detect COVID demonstrated high PPA in individuals with prior reverse transcription-polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infection (97.1% 15+ days from diagnosis; 94.5% 15+ days from symptom onset), high NPA (∼100%) in presumed or confirmed SARS-CoV-2 negative cases, equivalent or higher PPA than 2 commercial serology tests, and no evidence of pathogen cross-reactivity. CONCLUSIONS T-Detect COVID is a novel T-cell immunosequencing assay demonstrating high clinical performance for identification of recent or prior SARS-CoV-2 infection from blood samples, with implications for clinical management, risk stratification, surveillance, and understanding of protective immunity and long-term sequelae.
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Affiliation(s)
- Sudeb C. Dalai
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jennifer N. Dines
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | | | - Rachel M. Gittelman
- Research, Adaptive Biotechnologies, Seattle, Washington, USA,CORRESPONDING AUTHOR: Rachel M. Gittelman, PhD Adaptive Biotechnologies 1551 Eastlake Ave E Seattle, WA, 98102 USA
| | - Tera Eerkes
- Regulatory Affairs, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Pashmi Vaney
- Regulatory Affairs, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Sally Howard
- Regulatory Affairs, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Kipp Akers
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Lynell Skewis
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Anthony Monteforte
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Pamela R. Witte
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Cristina Wolf
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Hans Nesse
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Megan Herndon
- Molecular Product Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Jia Qadeer
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Sarah Duffy
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Emily Svejnoha
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Caroline Taromino
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Ian M. Kaplan
- T-Detect Product Management, Adaptive Biotechnologies, Seattle, Washington, USA
| | - John Alsobrook
- Molecular Lab Management, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Thomas Manley
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
| | - Lance Baldo
- Medical Affairs and Clinical Development, Adaptive Biotechnologies, Seattle, Washington, USA
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Sacco K, Castagnoli R, Vakkilainen S, Liu C, Delmonte OM, Oguz C, Kaplan IM, Alehashemi S, Burbelo PD, Bhuyan F, de Jesus AA, Dobbs K, Rosen LB, Cheng A, Shaw E, Vakkilainen MS, Pala F, Lack J, Zhang Y, Fink DL, Oikonomou V, Snow AL, Dalgard CL, Chen J, Sellers BA, Montealegre Sanchez GA, Barron K, Rey-Jurado E, Vial C, Poli MC, Licari A, Montagna D, Marseglia GL, Licciardi F, Ramenghi U, Discepolo V, Lo Vecchio A, Guarino A, Eisenstein EM, Imberti L, Sottini A, Biondi A, Mató S, Gerstbacher D, Truong M, Stack MA, Magliocco M, Bosticardo M, Kawai T, Danielson JJ, Hulett T, Askenazi M, Hu S, Cohen JI, Su HC, Kuhns DB, Lionakis MS, Snyder TM, Holland SM, Goldbach-Mansky R, Tsang JS, Notarangelo LD. Immunopathological signatures in multisystem inflammatory syndrome in children and pediatric COVID-19. Nat Med 2022; 28:1050-1062. [PMID: 35177862 PMCID: PMC9119950 DOI: 10.1038/s41591-022-01724-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [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: 09/24/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022]
Abstract
Pediatric Coronavirus Disease 2019 (pCOVID-19) is rarely severe; however, a minority of children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) might develop multisystem inflammatory syndrome in children (MIS-C), with substantial morbidity. In this longitudinal multi-institutional study, we applied multi-omics (analysis of soluble biomarkers, proteomics, single-cell gene expression and immune repertoire analysis) to profile children with COVID-19 (n = 110) and MIS-C (n = 76), along with pediatric healthy controls (pHCs; n = 76). pCOVID-19 was characterized by robust type I interferon (IFN) responses, whereas prominent type II IFN-dependent and NF-κB-dependent signatures, matrisome activation and increased levels of circulating spike protein were detected in MIS-C, with no correlation with SARS-CoV-2 PCR status around the time of admission. Transient expansion of TRBV11-2 T cell clonotypes in MIS-C was associated with signatures of inflammation and T cell activation. The association of MIS-C with the combination of HLA A*02, B*35 and C*04 alleles suggests genetic susceptibility. MIS-C B cells showed higher mutation load than pCOVID-19 and pHC. These results identify distinct immunopathological signatures in pCOVID-19 and MIS-C that might help better define the pathophysiology of these disorders and guide therapy.
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Affiliation(s)
- Keith Sacco
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Riccardo Castagnoli
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Svetlana Vakkilainen
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Can Liu
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Graduate Program in Biological Sciences, University of Maryland, College Park, MD, USA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Cihan Oguz
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | | | - Sara Alehashemi
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Farzana Bhuyan
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adriana A de Jesus
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lindsey B Rosen
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Aristine Cheng
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elana Shaw
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Justin Lack
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Danielle L Fink
- Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Vasileios Oikonomou
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew L Snow
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jinguo Chen
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD, USA
| | - Brian A Sellers
- Trans-NIH Center for Human Immunology, Autoimmunity, and Inflammation (CHI), National Institutes of Health, Bethesda, MD, USA
| | - Gina A Montealegre Sanchez
- Intramural Clinical Management and Operation Branch (ICMOB), Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karyl Barron
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emma Rey-Jurado
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Cecilia Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Maria Cecilia Poli
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
- Unidad de Inmunología y Reumatología, Hospital de niños Dr. Roberto del Río, Santiago, Chile
| | - Amelia Licari
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Daniela Montagna
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
- Laboratory of Immunology and Transplantation, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Gian Luigi Marseglia
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Francesco Licciardi
- Department of Pediatric and Public Health Sciences, Regina Margherita Children's Hospital, A.O.U. Città Della Salute E Della Scienza Di Torino, University of Turin, Turin, Italy
| | - Ugo Ramenghi
- Department of Pediatric and Public Health Sciences, Regina Margherita Children's Hospital, A.O.U. Città Della Salute E Della Scienza Di Torino, University of Turin, Turin, Italy
| | - Valentina Discepolo
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Andrea Lo Vecchio
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Alfredo Guarino
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples Federico II, Napoli, Italy
| | - Eli M Eisenstein
- Department of Pediatrics, Hadassah-Hebrew University Medical Center, Mount Scopus, Jerusalem, Israel
| | - Luisa Imberti
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Alessandra Sottini
- CREA Laboratory (AIL Center for Hemato-Oncologic Research), Diagnostic Department, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN, University of Milano Bicocca, Fondazione MBBM, Ospedale San Gerardo, Monza, Italy
| | - Sayonara Mató
- Randall Children's Hospital at Legacy Emanuel, Portland, OR, USA
| | - Dana Gerstbacher
- Division of Pediatric Rheumatology, Stanford Children's Hospital, Stanford, CA, USA
| | - Meng Truong
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael A Stack
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mary Magliocco
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tomoki Kawai
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey J Danielson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tyler Hulett
- CDI Laboratories, Antygen Division, Baltimore, MD, USA
| | | | - Shaohui Hu
- CDI Laboratories, Antygen Division, Baltimore, MD, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Helen C Su
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Douglas B Kuhns
- Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michail S Lionakis
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Raphaela Goldbach-Mansky
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John S Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- NIH Center for Human Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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7
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Capelle CM, Ciré S, Domingues O, Ernens I, Hedin F, Fischer A, Snoeck CJ, Ammerlaan W, Konstantinou M, Grzyb K, Skupin A, Carty CL, Hilger C, Gilson G, Celebic A, Wilmes P, Del Sol A, Kaplan IM, Betsou F, Abdelrahman T, Cosma A, Vaillant M, Fagherazzi G, Ollert M, Hefeng FQ. Combinatorial analysis reveals highly coordinated early-stage immune reactions that predict later antiviral immunity in mild COVID-19 patients. Cell Rep Med 2022; 3:100600. [PMID: 35480624 PMCID: PMC8960124 DOI: 10.1016/j.xcrm.2022.100600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 02/18/2022] [Accepted: 03/18/2022] [Indexed: 12/12/2022]
Abstract
While immunopathology has been widely studied in patients with severe COVID-19, immune responses in non-hospitalized patients have remained largely elusive. We systematically analyze 484 peripheral cellular or soluble immune features in a longitudinal cohort of 63 mild and 15 hospitalized patients versus 14 asymptomatic and 26 household controls. We observe a transient increase of IP10/CXCL10 and interferon-β levels, coordinated responses of dominant SARS-CoV-2-specific CD4 and fewer CD8 T cells, and various antigen-presenting and antibody-secreting cells in mild patients within 3 days of PCR diagnosis. The frequency of key innate immune cells and their functional marker expression are impaired in hospitalized patients at day 1 of inclusion. T cell and dendritic cell responses at day 1 are highly predictive for SARS-CoV-2-specific antibody responses after 3 weeks in mild but not hospitalized patients. Our systematic analysis reveals a combinatorial picture and trajectory of various arms of the highly coordinated early-stage immune responses in mild COVID-19 patients.
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Affiliation(s)
- Christophe M Capelle
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg; Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Séverine Ciré
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg
| | - Olivia Domingues
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg
| | - Isabelle Ernens
- Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Fanny Hedin
- National Cytometry Platform, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Aurélie Fischer
- Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Chantal J Snoeck
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg
| | - Wim Ammerlaan
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Maria Konstantinou
- National Cytometry Platform, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg; Department of Neuroscience, University California San Diego, La Jolla, CA, USA
| | | | - Christiane Hilger
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg
| | - Georges Gilson
- Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg
| | - Aljosa Celebic
- Translational Medicine Operations Hub, Competence Centre for Methodology and Statistics, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Paul Wilmes
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg; CIC bioGUNE, Bizkaia Technology Park, Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | | | - Fay Betsou
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg; Laboratoire National de Santé (LNS), Dudelange, Luxembourg
| | | | - Antonio Cosma
- National Cytometry Platform, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Michel Vaillant
- Translational Medicine Operations Hub, Competence Centre for Methodology and Statistics, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Guy Fagherazzi
- Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg; Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis (ORCA), University of Southern Denmark, Odense, Denmark.
| | - Feng Q Hefeng
- Department of Infection and Immunity, Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg.
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8
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Li D, Xu A, Mengesha E, Elyanow R, Gittelman RM, Chapman H, Prostko JC, Frias EC, Stewart JL, Pozdnyakova V, Debbas P, Mujukian A, Horizon AA, Merin N, Joung S, Botwin GJ, Sobhani K, Figueiredo JC, Cheng S, Kaplan IM, McGovern DPB, Merchant A, Melmed GY, Braun J. The T-Cell Response to SARS-CoV-2 Vaccination in Inflammatory Bowel Disease is Augmented with Anti-TNF Therapy. Inflamm Bowel Dis 2022; 28:1130-1133. [PMID: 35397000 PMCID: PMC9047232 DOI: 10.1093/ibd/izac071] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Indexed: 12/12/2022]
Abstract
Lay Summary
T-cell and antibody responses to severe acute respiratory syndrome coronavirus 2 vaccination in inflammatory bowel disease patients are poorly correlated. T-cell responses are preserved by most biologic therapies, but augmented by anti-tumor necrosis factor (anti-TNF) treatment. While anti-TNF therapy blunts the antibody response, cellular immunity after vaccination is robust.
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Affiliation(s)
- Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alexander Xu
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | | | - John C Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL
| | - Edwin C Frias
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL
| | - James L Stewart
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL
| | - Valeriya Pozdnyakova
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Philip Debbas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Angela Mujukian
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Noah Merin
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sandy Joung
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gregory J Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jane C Figueiredo
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ian M Kaplan
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Akil Merchant
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gil Y Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jonathan Braun
- Address correspondence to: Jonathan Braun, MD, PhD, Inflammatory Bowel and Immunobiology Research Institute, Karsh Division of Digestive and Liver Diseases, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA ()
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9
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Xu AM, Li D, Ebinger JE, Mengesha E, Elyanow R, Gittelman RM, Chapman H, Joung S, Botwin GJ, Pozdnyakova V, Debbas P, Mujukian A, Prostko JC, Frias EC, Stewart JL, Horizon AA, Merin N, Sobhani K, Figueiredo JC, Cheng S, Kaplan IM, McGovern DPB, Merchant A, Melmed GY, Braun J. Differences in SARS-CoV-2 Vaccine Response Dynamics Between Class-I- and Class-II-Specific T-Cell Receptors in Inflammatory Bowel Disease. Front Immunol 2022; 13:880190. [PMID: 35464463 PMCID: PMC9024211 DOI: 10.3389/fimmu.2022.880190] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/18/2022] [Indexed: 12/01/2022] Open
Abstract
T-cells specifically bind antigens to induce adaptive immune responses using highly specific molecular recognition, and a diverse T-cell repertoire with expansion of antigen-specific clones can indicate robust immune responses after infection or vaccination. For patients with inflammatory bowel disease (IBD), a spectrum of chronic intestinal inflammatory diseases usually requiring immunomodulatory treatment, the T-cell response has not been well characterized. Understanding the patient factors that result in strong vaccination responses is critical to guiding vaccination schedules and identifying mechanisms of T-cell responses in IBD and other immune-mediated conditions. Here we used T-cell receptor sequencing to show that T-cell responses in an IBD cohort were influenced by demographic and immune factors, relative to a control cohort of health care workers (HCWs). Subjects were sampled at the time of SARS-CoV-2 vaccination, and longitudinally afterwards; TCR Vβ gene repertoires were sequenced and analyzed for COVID-19-specific clones. We observed significant differences in the overall strength of the T-cell response by age and vaccine type. We further stratified the T-cell response into Class-I- and Class-II-specific responses, showing that Ad26.COV2.S vector vaccine induced Class-I-biased T-cell responses, whereas mRNA vaccine types led to different responses, with mRNA-1273 vaccine inducing a more Class-I-deficient T-cell response compared to BNT162b2. Finally, we showed that these T-cell patterns were consistent with antibody levels from the same patients. Our results account for the surprising success of vaccination in nominally immuno-compromised IBD patients, while suggesting that a subset of IBD patients prone to deficiencies in T-cell response may warrant enhanced booster protocols.
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Affiliation(s)
- Alexander M. Xu
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Joseph E. Ebinger
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | | | | | - Heidi Chapman
- Adaptive Biotechnologies, Seattle, WA, United States
| | - Sandy Joung
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Gregory J. Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Valeriya Pozdnyakova
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Philip Debbas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Angela Mujukian
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - John C. Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, United States
| | - Edwin C. Frias
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, United States
| | - James L. Stewart
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, United States
| | - Arash A. Horizon
- Center for Rheumatology Medical Group, Los Angeles, CA, United States
| | - Noah Merin
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Jane C. Figueiredo
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Ian M. Kaplan
- Adaptive Biotechnologies, Seattle, WA, United States
| | - Dermot P. B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Akil Merchant
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Gil Y. Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
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10
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Li D, Xu A, Mengesha E, Elyanow R, Gittelman RM, Chapman H, Prostko JC, Frias EC, Stewart JL, Pozdnyakova V, Debbas P, Mujukian A, Horizon AA, Merin N, Joung S, Botwin GJ, Sobhani K, Figueiredo JC, Cheng S, Kaplan IM, McGovern DP, Merchant A, Melmed GY, Braun J. The T-cell clonal response to SARS-CoV-2 vaccination in inflammatory bowel disease patients is augmented by anti-TNF therapy and often deficient in antibody-responders. medRxiv 2021:2021.12.08.21267444. [PMID: 34909785 PMCID: PMC8669852 DOI: 10.1101/2021.12.08.21267444] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Vaccination against SARS-CoV-2 is a highly effective strategy to protect against infection, which is predominantly mediated by vaccine-induced antibodies. Postvaccination antibodies are robustly produced by those with inflammatory bowel disease (IBD) even on immune-modifying therapies but are blunted by anti-TNF therapy. In contrast, T-cell response which primarily determines long-term efficacy against disease progression,, is less well understood. We aimed to assess the post-vaccination T-cell response and its relationship to antibody responses in patients with inflammatory bowel disease (IBD) on immune-modifying therapies. METHODS We evaluated IBD patients who completed SARS-CoV-2 vaccination using samples collected at four time points (dose 1, dose 2, 2 weeks after dose 2, 8 weeks after dose 2). T-cell clonal analysis was performed by T-cell Receptor (TCR) immunosequencing. The breadth (number of unique sequences to a given protein) and depth (relative abundance of all the unique sequences to a given protein) of the T-cell clonal response were quantified using reference datasets and were compared to antibody responses. RESULTS Overall, 303 subjects were included (55% female; 5% with prior COVID) (Table). 53% received BNT262b (Pfizer), 42% mRNA-1273 (Moderna) and 5% Ad26CoV2 (J&J). The Spike-specific clonal response peaked 2 weeks after completion of the vaccine regimen (3- and 5-fold for breadth and depth, respectively); no changes were seen for non-Spike clones, suggesting vaccine specificity. Reduced T-cell clonal depth was associated with chronologic age, male sex, and immunomodulator treatment. It was preserved by non-anti-TNF biologic therapies, and augmented clonal depth was associated with anti-TNF treatment. TCR depth and breadth were associated with vaccine type; after adjusting for age and gender, Ad26CoV2 (J&J) exhibited weaker metrics than mRNA-1273 (Moderna) (p=0.01 for each) or BNT262b (Pfizer) (p=0.056 for depth). Antibody and T-cell responses were only modestly correlated. While those with robust humoral responses also had robust TCR clonal expansion, a substantial fraction of patients with high antibody levels had only a minimal T-cell clonal response. CONCLUSION Age, sex and select immunotherapies are associated with the T-cell clonal response to SARS-CoV-2 vaccines, and T-cell responses are low in many patients despite high antibody levels. These factors, as well as differences seen by vaccine type may help guide reimmunization vaccine strategy in immune-impaired populations. Further study of the effects of anti-TNF therapy on vaccine responses are warranted.
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Affiliation(s)
- Dalin Li
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alexander Xu
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | | | | | - John C. Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL
| | - Edwin C. Frias
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL
| | - James L. Stewart
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL
| | - Valeriya Pozdnyakova
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Philip Debbas
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Angela Mujukian
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Noah Merin
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sandy Joung
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gregory J. Botwin
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kimia Sobhani
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jane C. Figueiredo
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Akil Merchant
- Cedars Sinai Cancer and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Gil Y. Melmed
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jonathan Braun
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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11
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Dalai SC, Dines JN, Snyder TM, Gittelman RM, Eerkes T, Vaney P, Howard S, Akers K, Skewis L, Monteforte A, Witte PR, Wolf C, Nesse H, Qadeer J, Duffy S, Svejnoha E, Taromino C, Kagen M, Kaplan IM, Alsobrook J, Manley T, Baldo L. 144. Clinical Validation and Performance of a T-cell Immunosequencing Assay to Identify Past SARS-CoV-2 Infection. Open Forum Infect Dis 2021. [PMCID: PMC8643828 DOI: 10.1093/ofid/ofab466.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Our understanding of the SARS-CoV-2 immune response has critical gaps that are inadequately addressed with available tools. We report the clinical performance of T-Detect COVID, the first T-cell assay to identify prior SARS-CoV-2 infection using T-cell receptor (TCR) sequencing and repertoire profiling from whole blood samples. Methods The T-Detect COVID assay combines high-throughput immunosequencing of the TCRß gene from blood samples with a statistical classifier demonstrating 99.8% specificity for identifying prior SARS-CoV-2 infection. The assay was employed in several retrospective and prospective cohorts to assess primary and secondary Positive Percent Agreement (PPA) with SARS-CoV-2 RT-PCR (N=205; N=77); primary and secondary Negative Percent Agreement (NPA; N=87; N=79); PPA compared to SARS-CoV-2 serology (N=55); and pathogen cross-reactivity (N=38). The real-world performance of the test was also evaluated in a retrospective review of test ordering (N=69) at a single primary care clinic in Park City, Utah. Results In validation studies, T-Detect COVID demonstrated high PPA (97.1% ≥15 days from diagnosis) in subjects with prior PCR-confirmed SARS-CoV-2 infection; high NPA (~100%) in SARS-CoV-2 negative cases; equivalent or higher PPA with RT-PCR compared to two commercial EUA antibody tests; and no evidence of pathogen cross-reactivity. Review of assay use in a single clinic showed 100% PPA with RT-PCR in individuals with past confirmed SARS-CoV-2 vs. 85.7% for antibody testing, 100% agreement with positive antibody results, and positive results in 2/4 convalescent subjects with seroreversion to a negative antibody. In addition, 12/69 (17.3%) individuals with absent or negative RT-PCR tested positive by T-Detect COVID, nearly all of whom had compatible symptoms and/or exposure. TCR positivity was observed up to 12+ months (median 118 days) from the date of positive RT-PCR. Conclusion A T-cell immunosequencing assay shows high clinical performance for identifying past SARS-CoV-2 infection from whole blood samples. This assay can provide additional insights on the SARS-CoV-2 immune response, with practical implications for clinical management, risk stratification, surveillance, assessing vaccine immunity, and understanding long-term sequelae. Disclosures Sudeb C. Dalai, MD, PhD, Adaptive Biotechnologies (Employee, Shareholder) Jennifer N. Dines, MD, Adaptive Biotechnologies (Employee, Shareholder) Thomas M. Snyder, PhD, Adaptive Biotechnologies (Employee, Shareholder) Rachel M. Gittelman, PhD, Adaptive Biotechnologies (Employee, Shareholder) Tera Eerkes, PhD, Adaptive Biotechnologies (Employee, Shareholder) Pashmi Vaney, PhD, Adaptive Biotechnologies (Employee, Shareholder) Sally Howard, PhD, Adaptive Biotechnologies (Employee, Shareholder) Kipp Akers, PhD, Adaptive Biotechnologies (Employee, Shareholder) Lynell Skewis, PhD, Adaptive Biotechnologies (Employee, Shareholder) Anthony Monteforte, PhD, Adaptive Biotechnologies (Employee, Shareholder) Pamela R. Witte, PhD, Adaptive Biotechnologies (Employee, Shareholder) Cristina Wolf, PhD, Adaptive Biotechnologies (Employee, Shareholder) Hans Nesse, PhD, Adaptive Biotechnologies (Employee, Shareholder) Jia Qadeer, PhD, Adaptive Biotechnologies (Employee, Shareholder) Sarah Duffy, PhD, Adaptive Biotechnologies (Employee, Shareholder) Emily Svejnoha, PhD, Adaptive Biotechnologies (Employee, Shareholder) Caroline Taromino, PhD, Adaptive Biotechnologies (Employee, Shareholder) Ian M. Kaplan, PhD, Adaptive Biotechnologies (Employee, Shareholder) John Alsobrook, MD, Adaptive Biotechnologies (Employee, Shareholder) Thomas Manley, MD, Adaptive Biotechnologies (Employee, Shareholder) Lance Baldo, MD, Adaptive Biotechnologies (Employee, Shareholder, Leadership Interest)
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Affiliation(s)
- Sudeb C Dalai
- Adaptive Biotechnologies and Stanford University School of Medicine, Seattle, Washington
| | | | | | | | - Tera Eerkes
- Adaptive Biotechnologies, Seattle, Washington
| | | | | | - Kipp Akers
- Adaptive Biotechnologies, Seattle, Washington
| | | | | | | | | | - Hans Nesse
- Adaptive Biotechnologies, Seattle, Washington
| | - Jia Qadeer
- Adaptive Biotechnologies, Seattle, Washington
| | - Sarah Duffy
- Adaptive Biotechnologies, Seattle, Washington
| | | | | | | | | | | | | | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington
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12
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Dalai SC, Greissl J, Pesesky M, Rebman AW, Soloski MJ, Horn EJ, Dines JN, Gittelman RM, Snyder TM, Emerson RO, Meeds E, Manley T, Kaplan IM, Baldo L, Carlson JM, Robins HS, Aucott J. LB17. Immunosequencing of the T-Cell Receptor Repertoire Reveals Signatures Specific for Diagnosis and Characterization of Early Lyme Disease. Open Forum Infect Dis 2021. [PMCID: PMC8644055 DOI: 10.1093/ofid/ofab466.1653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background Changing climate and demographic trends have led to recent increases in the incidence of tick-borne illnesses. Early diagnosis of Lyme disease (LD) is critical for initiation of antibiotics to mitigate symptoms and prevent late manifestations. In patients not presenting with a typical erythema migrans rash, 2-tiered serologic testing is recommended to support a diagnosis of LD. However, 2-tiered testing is limited by ambiguity in interpretation and low sensitivity in early disease, highlighting an unmet clinical need for alternative diagnostic approaches. We identified a clinical signal for early LD based on evaluation of the T-cell response to B. burgdorferi infection. Methods We immunosequenced T-cell receptor (TCR) repertoires in blood samples from 3 independent cohorts of patients with laboratory-confirmed or clinically diagnosed early LD and endemic/non-endemic controls to identify 251 public, LD-associated TCRs. These TCRs were used to train a classifier that identified early LD with 99% specificity. Classifier sensitivity was evaluated in 211 LD cases and 2631 endemic controls and compared to that of standard 2-tiered testing (STTT). Biologic specificity was assessed by correlating TCR assay scores with clinical measures and by mapping the antigen specificity of Lyme-associated TCRs to B. burgdorferi antigens. Figure 1. LD-associated TCRs distinguish cases (orange) from controls (blue) in training cohorts. (A) Logistic-growth curve used to define a scoring function. (B) Positive-call threshold (99th percentile in endemic controls). ![]()
Results In early LD, TCR testing demonstrated a 1.9-fold increase in sensitivity compared to STTT (56% vs 30%), with a 3.1-fold increase ≤4 days from the onset of symptoms (44% vs 14%). TCR positivity predicted subsequent seroconversion in 37% of initially STTT-negative patients, suggesting the T-cell response is detectable before the humoral response. While positivity for both tests declined following treatment, greater declines in posttreatment sensitivity were observed for STTT compared to TCR testing. Higher TCR scores were associated with measures of disease severity, including abnormal liver function tests, disseminated rash, and number of symptoms. A subset of LD-associated TCRs mapped to B. burgdorferi antigens, demonstrating the high specificity of a TCR immunosequencing approach. ![]()
Figure 2. Validation of the TCR classifier in the JHU cohort and other holdout endemic controls. Distribution of model scores (A) and assay sensitivity (B). Model scores (C) and ROC (D) curves by serostatus. ![]()
Figure 3. Clinical correlates of TCR scoring. (A) Liver function test; (B) lymphocyte count, (C) rash presentation, (D) number of symptoms. ![]()
Conclusion T-cell-based testing has potential clinical utility as a sensitive and specific diagnostic for early LD, particularly in the initial days of illness. Disclosures Sudeb C. Dalai, MD, PhD, Adaptive Biotechnologies (Employee, Shareholder) Julia Greissl, PhD, Microsoft (Employee, Shareholder) Mitch Pesesky, PhD, Adaptive Biotechnologies (Employee, Shareholder) Allison W. Rebman, MPH, Global Lyme Alliance (Research Grant or Support)Steven and Alexandra Cohen Foundation (Research Grant or Support) Mark J. Soloski, PhD, NIH grant P30 AR070254 (Grant/Research Support)Steven and Alexandra Cohen Foundation (Research Grant or Support) Elizabeth J. Horn, PhD, Adaptive Biotechnologies (Research Grant or Support)Bay Area Lyme Foundation (Research Grant or Support)Lyme Disease Biobank (Employee)Steven and Alexandra Cohen Foundation (Research Grant or Support) Jennifer N. Dines, MD, Adaptive Biotechnologies (Employee, Shareholder) Rachel M. Gittelman, PhD, Adaptive Biotechnologies (Employee, Shareholder) Thomas M. Snyder, PhD, Adaptive Biotechnologies (Employee, Shareholder) Ryan O. Emerson, PhD, Adaptive Biotechnologies (Other Financial or Material Support, Employment with Adaptive Biotechnologies during the time of this study) Edward Meeds, PhD, Microsoft (Employee, Shareholder) Thomas Manley, MD, Adaptive Biotechnologies (Other Financial or Material Support, Declares employment with Adaptive Biotechnologies during the time of this study) Ian M. Kaplan, PhD, Adaptive Biotechnologies (Employee, Shareholder) Lance Baldo, MD, Adaptive Biotechnologies (Employee, Shareholder, Leadership Interest) Jonathan M. Carlson, PhD, Microsoft (Employee, Shareholder) Harlan S. Robins, PhD, Adaptive Biotechnologies (Board Member, Employee, Shareholder) John Aucott, MD, Adaptive Biotechnologies (Advisor or Review Panel member)Bay Area Lyme Foundation (Other Financial or Material Support, Scientific Advisory Board member)Department of Health and Human Services (Other Financial or Material Support, Past Chair, 2018, HHS Tick-borne Disease Working Group, Office of HIV/AIDS and Infectious Disease Policy, Office of the Assistant Secretary of Health)Expert testimony (Other Financial or Material Support, Expert testimony)Global Lyme Alliance (Research Grant or Support)Pfizer (Consultant)Steven and Alexandra Cohen Foundation (Research Grant or Support)Tarsus Pharmaceuticals (Consultant)
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Affiliation(s)
- Sudeb C Dalai
- Adaptive Biotechnologies and Stanford University School of Medicine, Seattle, WA
| | | | | | - Allison W Rebman
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Mark J Soloski
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | | | | | | | | | | | | | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington
| | | | | | - John Aucott
- Johns Hopkins University School of Medicine, Baltimore, Maryland
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13
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Snyder TM, Gittelman RM, Klinger M, May DH, Osborne EJ, Taniguchi R, Jabran Zahid H, Elyanow R, Dalai SC, Kaplan IM, Dines JN, Noakes MT, Pandya R, Baldo L, Semprini S, Cerchione C, Nicolini F, Mazza M, Delmonte OM, Dobbs K, Laguna-Goya R, Carreño-Tarragona G, Barrio S, Imberti L, Sottini A, Quiros-Roldan E, Rossi C, Biondi A, Bettini LR, D’Angio M, Bonfanti P, Tompkins MF, Alba C, Dalgard C, Sambri V, Martinelli G, Goldman JD, Heath JR, Su HC, Notarangelo LD, Paz-Artal E, Martinez-Lopez J, Carlson JM, Robins HS. 126. Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection and Vaccination. Open Forum Infect Dis 2021. [PMCID: PMC8690367 DOI: 10.1093/ofid/ofab466.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background T cells are central to the early identification and clearance of viral infections and support antibody generation by B cells, making them desirable for assessing the immune response to SARS-CoV-2 infection and vaccines. We combined 2 high-throughput immune profiling methods to create a quantitative picture of the SARS-CoV-2 T-cell response that is highly sensitive, durable, diagnostic, and discriminatory between natural infection and vaccination. Methods We deeply characterized 116 convalescent COVID-19 subjects by experimentally mapping CD8 and CD4 T-cell responses via antigen stimulation to 545 Human Leukocyte Antigen (HLA) class I and 284 class II viral peptides. We also performed T-cell receptor (TCR) repertoire sequencing on 1815 samples from 1521 PCR-confirmed SARS-CoV-2 cases and 3500 controls to identify shared public TCRs from SARS-CoV-2-associated CD8 and CD4 T cells. Combining these approaches with additional samples from vaccinated individuals, we characterized the response to natural infection as well as vaccination by separating responses to spike protein from other viral targets. Results We find that T-cell responses are often driven by a few immunodominant, HLA-restricted epitopes. As expected, the SARS-CoV-2 T-cell response peaks about 1-2 weeks after infection and is detectable at least several months after recovery. Applying these data, we trained a classifier to diagnose past SARS-CoV-2 infection based solely on TCR sequencing from blood samples and observed, at 99.8% specificity, high sensitivity soon after diagnosis (Day 3–7 = 85.1%; Day 8–14 = 94.8%) that persists after recovery (Day 29+/convalescent = 95.4%). Finally, by evaluating TCRs binding epitopes targeting all non-spike SARS-CoV-2 proteins, we were able to separate natural infection from vaccination with > 99% specificity. Conclusion TCR repertoire sequencing from whole blood reliably measures the adaptive immune response to SARS-CoV-2 soon after viral antigenic exposure (before antibodies are typically detectable) as well as at later time points, and distinguishes post-infection vs. vaccine immune responses with high specificity. This approach to characterizing the cellular immune response has applications in clinical diagnostics as well as vaccine development and monitoring. Disclosures Thomas M. Snyder, PhD, Adaptive Biotechnologies (Employee, Shareholder) Rachel M. Gittelman, PhD, Adaptive Biotechnologies (Employee, Shareholder) Mark Klinger, PhD, Adaptive Biotechnologies (Employee, Shareholder) Damon H. May, PhD, Adaptive Biotechnologies (Employee, Shareholder) Edward J. Osborne, PhD, Adaptive Biotechnologies (Employee, Shareholder) Ruth Taniguchi, PhD, Adaptive Biotechnologies (Employee, Shareholder) H. Jabran Zahid, PhD, Microsoft Research (Employee, Shareholder) Rebecca Elyanow, PhD, Adaptive Biotechnologies (Employee, Shareholder) Sudeb C. Dalai, MD, PhD, Adaptive Biotechnologies (Employee, Shareholder) Ian M. Kaplan, PhD, Adaptive Biotechnologies (Employee, Shareholder) Jennifer N. Dines, MD, Adaptive Biotechnologies (Employee, Shareholder) Matthew T. Noakes, PhD, Adaptive Biotechnologies (Employee, Shareholder) Ravi Pandya, PhD, Microsoft Research (Employee, Shareholder) Lance Baldo, MD, Adaptive Biotechnologies (Employee, Shareholder, Leadership Interest) James R. Heath, PhD, Merck (Research Grant or Support, Funding (from BARDA) for the ISB INCOV project, but had no role in planning the research or in writing the paper.) Joaquin Martinez-Lopez, MD, PhD, Adaptive Biotechnologies (Consultant) Jonathan M. Carlson, PhD, Microsoft Research (Employee, Shareholder) Harlan S. Robins, PhD, Adaptive Biotechnologies (Board Member, Employee, Shareholder)
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Affiliation(s)
| | | | | | - Damon H May
- Adaptive Biotechnologies, Seattle, Washington
| | | | | | | | | | - Sudeb C Dalai
- Adaptive Biotechnologies and Stanford University School of Medicine, Seattle, Washington
| | | | | | | | | | - Lance Baldo
- Adaptive Biotechnologies, Seattle, Washington
| | - Simona Semprini
- Unit of Microbiology - The Great Romagna Hub Laboratory, Pievesestina ITALY and DIMES, University of Bologna, Bologna, Emilia-Romagna, Italy
| | - Claudio Cerchione
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Medola, Lombardia, Italy
| | - Fabio Nicolini
- Immunotherapy, Cell Therapy and Biobank (ITCB), Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Medola, Lombardia, Italy
| | - Massimiliano Mazza
- Immunotherapy, Cell Therapy and Biobank (ITCB), Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Medola, Lombardia, Italy
| | - Ottavia M Delmonte
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Kerry Dobbs
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Rocio Laguna-Goya
- Department of Immunology, Hospital 12de Octubre, i+12, Madrid, Madrid, Spain
| | | | - Santiago Barrio
- Hematology Department, Hospital 12de Octubre, i+12, CNIO, Complutense University, Madrid, Madrid, Spain
| | - Luisa Imberti
- Laboratorio CREA, Department of Infectious and Tropical Diseases, and Medical Officer, ASST Spedali Civili di Brescia and University of Brescia, Brescia, Lombardia, Italy
| | - Alessandra Sottini
- Laboratorio CREA, Department of Infectious and Tropical Diseases, and Medical Officer, ASST Spedali Civili di Brescia and University of Brescia, Brescia, Lombardia, Italy
| | - Eugenia Quiros-Roldan
- Laboratorio CREA, Department of Infectious and Tropical Diseases, and Medical Officer, ASST Spedali Civili di Brescia and University of Brescia, Brescia, Lombardia, Italy
| | - Camillo Rossi
- Department of Pediatrics and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Lombardia, Italy
| | - Andrea Biondi
- Hematology Department, Hospital 12de Octubre, i+12, CNIO, Complutense University, Madrid, Madrid, Spain
| | - Laura Rachele Bettini
- Department of Pediatrics and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Lombardia, Italy
| | - Mariella D’Angio
- Department of Pediatrics and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, Lombardia, Italy
| | - Paolo Bonfanti
- Department of Infectious Diseases, University of Milano-Bicocca-Ospedale San Gerardo, Monza, Lombardia, Italy
| | - Miranda F Tompkins
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Camille Alba
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Clifton Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Vittorio Sambri
- Unit of Microbiology - The Great Romagna Hub Laboratory, Pievesestina ITALY and DIMES, University of Bologna, Bologna, Emilia-Romagna, Italy
| | - Giovanni Martinelli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Medola, Lombardia, Italy
| | - Jason D Goldman
- Swedish Medical Center, Seattle, WA, USA, and Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington
| | - James R Heath
- Institute for Systems Biology, Seattle, WA, USA, Seattle, Washington
| | - Helen C Su
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Luigi D Notarangelo
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Estela Paz-Artal
- Department of Immunology, Hospital 12de Octubre, i+12, Madrid, Madrid, Spain
| | - Joaquin Martinez-Lopez
- Hematology Department, Hospital 12de Octubre, i+12, CNIO, Complutense University, Madrid, Madrid, Spain
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14
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El Meskini R, Atkinson D, Kulaga A, Abdelmaksoud A, Gumprecht M, Pate N, Hayes S, Oberst M, Kaplan IM, Raber P, Van Dyke T, Sharan SK, Hollingsworth R, Day CP, Merlino G, Weaver Ohler Z. Distinct Biomarker Profiles and TCR Sequence Diversity Characterize the Response to PD-L1 Blockade in a Mouse Melanoma Model. Mol Cancer Res 2021; 19:1422-1436. [PMID: 33888600 DOI: 10.1158/1541-7786.mcr-20-0881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/09/2021] [Accepted: 04/19/2021] [Indexed: 11/16/2022]
Abstract
Only a subset of patients responds to immune checkpoint blockade (ICB) in melanoma. A preclinical model recapitulating the clinical activity of ICB would provide a valuable platform for mechanistic studies. We used melanoma tumors arising from an Hgftg;Cdk4R24C/R24C genetically engineered mouse (GEM) model to evaluate the efficacy of an anti-mouse PD-L1 antibody similar to the anti-human PD-L1 antibodies durvalumab and atezolizumab. Consistent with clinical observations for ICB in melanoma, anti-PD-L1 treatment elicited complete and durable response in a subset of melanoma-bearing mice. We also observed tumor growth delay or regression followed by recurrence. For early treatment assessment, we analyzed gene expression profiles, T-cell infiltration, and T-cell receptor (TCR) signatures in regressing tumors compared with tumors exhibiting no response to anti-PD-L1 treatment. We found that CD8+ T-cell tumor infiltration corresponded to response to treatment, and that anti-PD-L1 gene signature response indicated an increase in antigen processing and presentation, cytokine-cytokine receptor interaction, and natural killer cell-mediated cytotoxicity. TCR sequence data suggest that an anti-PD-L1-mediated melanoma regression response requires not only an expansion of the TCR repertoire that is unique to individual mice, but also tumor access to the appropriate TCRs. Thus, this melanoma model recapitulated the variable response to ICB observed in patients and exhibited biomarkers that differentiate between early response and resistance to treatment, providing a valuable platform for prediction of successful immunotherapy. IMPLICATIONS: Our melanoma model recapitulates the variable response to anti-PD-L1 observed in patients and exhibits biomarkers that characterize early antibody response, including expansion of the TCR repertoire.
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Affiliation(s)
- Rajaa El Meskini
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
| | - Devon Atkinson
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Alan Kulaga
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Abdalla Abdelmaksoud
- Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research (CCR), National Cancer Institute, Bethesda, Maryland.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Michelle Gumprecht
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Nathan Pate
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | | | | | | | | | - Terry Van Dyke
- Mouse Cancer Genetics Program, CCR, NCI/NIH, Frederick, Maryland
| | - Shyam K Sharan
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland.,Mouse Cancer Genetics Program, CCR, NCI/NIH, Frederick, Maryland
| | | | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, CCR, NCI/NIH, Bethesda, Maryland
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, CCR, NCI/NIH, Bethesda, Maryland
| | - Zoë Weaver Ohler
- Center for Advanced Preclinical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland.
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15
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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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16
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Snyder TM, Gittelman RM, Klinger M, May DH, Osborne EJ, Taniguchi R, Zahid HJ, Kaplan IM, Dines JN, Noakes MT, Pandya R, Chen X, Elasady S, Svejnoha E, Ebert P, Pesesky MW, De Almeida P, O'Donnell H, DeGottardi Q, Keitany G, Lu J, Vong A, Elyanow R, Fields P, Greissl J, Baldo L, Semprini S, Cerchione C, Nicolini F, Mazza M, Delmonte OM, Dobbs K, Laguna-Goya R, Carreño-Tarragona G, Barrio S, Imberti L, Sottini A, Quiros-Roldan E, Rossi C, Biondi A, Bettini LR, D'Angio M, Bonfanti P, Tompkins MF, Alba C, Dalgard C, Sambri V, Martinelli G, Goldman JD, Heath JR, Su HC, Notarangelo LD, Paz-Artal E, Martinez-Lopez J, Carlson JM, Robins HS. Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels. medRxiv 2020:2020.07.31.20165647. [PMID: 32793919 PMCID: PMC7418734 DOI: 10.1101/2020.07.31.20165647] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
T cells are involved in the early identification and clearance of viral infections and also support the development of antibodies by B cells. This central role for T cells makes them a desirable target for assessing the immune response to SARS-CoV-2 infection. Here, we combined two high-throughput immune profiling methods to create a quantitative picture of the T-cell response to SARS-CoV-2. First, at the individual level, we deeply characterized 3 acutely infected and 58 recovered COVID-19 subjects by experimentally mapping their CD8 T-cell response through antigen stimulation to 545 Human Leukocyte Antigen (HLA) class I presented viral peptides (class II data in a forthcoming study). Then, at the population level, we performed T-cell repertoire sequencing on 1,815 samples (from 1,521 COVID-19 subjects) as well as 3,500 controls to identify shared "public" T-cell receptors (TCRs) associated with SARS-CoV-2 infection from both CD8 and CD4 T cells. Collectively, our data reveal that CD8 T-cell responses are often driven by a few immunodominant, HLA-restricted epitopes. As expected, the T-cell response to SARS-CoV-2 peaks about one to two weeks after infection and is detectable for at least several months after recovery. As an application of these data, we trained a classifier to diagnose SARS-CoV-2 infection based solely on TCR sequencing from blood samples, and observed, at 99.8% specificity, high early sensitivity soon after diagnosis (Day 3-7 = 85.1% [95% CI = 79.9-89.7]; Day 8-14 = 94.8% [90.7-98.4]) as well as lasting sensitivity after recovery (Day 29+/convalescent = 95.4% [92.1-98.3]). These results demonstrate an approach to reliably assess the adaptive immune response both soon after viral antigenic exposure (before antibodies are typically detectable) as well as at later time points. This blood-based molecular approach to characterizing the cellular immune response has applications in clinical diagnostics as well as in vaccine development and monitoring.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Allen Vong
- Adaptive Biotechnologies, Seattle, WA, USA
| | | | | | | | | | - Simona Semprini
- Unit of Microbiology - The Great Romagna Hub Laboratory, Pievesestina ITALY and DIMES, University of Bologna, Bologna, Italy
| | - Claudio Cerchione
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Fabio Nicolini
- Immunotherapy, Cell Therapy and Biobank (ITCB), Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Massimiliano Mazza
- Immunotherapy, Cell Therapy and Biobank (ITCB), Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, FC, Italy
| | - Ottavia M Delmonte
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kerry Dobbs
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rocio Laguna-Goya
- Department of Immunology, Hospital 12 de Octubre, i+12, CNIO, Complutense University, Madrid, Spain
| | | | - Santiago Barrio
- Hematology Department, Hospital 12 de Octubre, i+12, CNIO, Complutense University, Madrid, Spain
| | - Luisa Imberti
- Laboratorio CREA, Department of Infectious and Tropical Diseases, and Medical Officer, ASST Spedali Civili di Brescia and University of Brescia, Brescia, Italy
| | - Alessandra Sottini
- Laboratorio CREA, Department of Infectious and Tropical Diseases, and Medical Officer, ASST Spedali Civili di Brescia and University of Brescia, Brescia, Italy
| | - Eugenia Quiros-Roldan
- Laboratorio CREA, Department of Infectious and Tropical Diseases, and Medical Officer, ASST Spedali Civili di Brescia and University of Brescia, Brescia, Italy
| | - Camillo Rossi
- Laboratorio CREA, Department of Infectious and Tropical Diseases, and Medical Officer, ASST Spedali Civili di Brescia and University of Brescia, Brescia, Italy
| | - Andrea Biondi
- Department of Pediatrics and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, IT
| | - Laura Rachele Bettini
- Department of Pediatrics and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, IT
| | - Mariella D'Angio
- Department of Pediatrics and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale San Gerardo, Monza, IT
| | - Paolo Bonfanti
- Department of Infectious Diseases, University of Milano-Bicocca-Ospedale San Gerardo, Monza, IT
| | - Miranda F Tompkins
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Camille Alba
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Vittorio Sambri
- Unit of Microbiology - The Great Romagna Hub Laboratory, Pievesestina ITALY and DIMES, University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| | - Jason D Goldman
- Swedish Medical Center, Seattle, WA, USA, and Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | | | - Helen C Su
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luigi D Notarangelo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Estela Paz-Artal
- Department of Immunology, Hospital 12 de Octubre, i+12, CNIO, Complutense University, Madrid, Spain
| | - Joaquin Martinez-Lopez
- Hematology Department, Hospital 12 de Octubre, i+12, CNIO, Complutense University, Madrid, Spain
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17
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Nolan S, Vignali M, Klinger M, Dines JN, Kaplan IM, Svejnoha E, Craft T, Boland K, Pesesky M, Gittelman RM, Snyder TM, Gooley CJ, Semprini S, Cerchione C, Mazza M, Delmonte OM, Dobbs K, Carreño-Tarragona G, Barrio S, Sambri V, Martinelli G, Goldman JD, Heath JR, Notarangelo LD, Carlson JM, Martinez-Lopez J, Robins HS. A large-scale database of T-cell receptor beta (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2. Res Sq 2020:rs.3.rs-51964. [PMID: 32793896 PMCID: PMC7418738 DOI: 10.21203/rs.3.rs-51964/v1] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We describe the establishment and current content of the ImmuneCODE™ database, which includes hundreds of millions of T-cell Receptor (TCR) sequences from over 1,400 subjects exposed to or infected with the SARS-CoV-2 virus, as well as over 135,000 high-confidence SARS-CoV-2-specific TCRs. This database is made freely available, and the data contained in it can be downloaded and analyzed online or offline to assist with the global efforts to understand the immune response to the SARS-CoV-2 virus and develop new interventions.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ottavia M Delmonte
- National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Kerry Dobbs
- National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | | | | | | | | | - Jason D Goldman
- Swedish Medical Center, Seattle, WA, USA and Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | | | - Luigi D Notarangelo
- National Institute of Allergy and Infectious Diseases, National Institutes of Health
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18
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Giaccone G, Kim C, Thompson J, McGuire C, Kallakury B, Chahine JJ, Manning M, Mogg R, Blumenschein WM, Tan MT, Subramaniam DS, Liu SV, Kaplan IM, McCutcheon JN. Pembrolizumab in patients with thymic carcinoma: a single-arm, single-centre, phase 2 study. Lancet Oncol 2018; 19:347-355. [PMID: 29395863 PMCID: PMC10683856 DOI: 10.1016/s1470-2045(18)30062-7] [Citation(s) in RCA: 236] [Impact Index Per Article: 39.3] [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: 10/04/2017] [Revised: 11/19/2017] [Accepted: 11/23/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Treatment options are limited for patients with thymic carcinoma. These aggressive tumours are not typically associated with paraneoplastic autoimmune disorders, and strong PD-L1 expression has been reported in thymic epithelial tumours. We aimed to assess the activity of pembrolizumab, a monoclonal antibody that targets PD-1, in patients with advanced thymic carcinoma. METHODS We completed a single-arm phase 2 study of pembrolizumab in patients with recurrent thymic carcinoma who had progressed after at least one line of chemotherapy. This was a single-centre study performed at Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA. Key inclusion criteria were an Eastern Cooperative Oncology Group performance status of 0-2, no history of autoimmune disease or other malignancy requiring treatment or laboratory abnormality, and adequate organ function. Patients received 200 mg of pembrolizumab every 3 weeks for up to 2 years. The primary objective of the study was the proportion of patients who had achieved a response assessed with Response Evaluation Criteria in Solid Tumors version 1.1. Analysis was per protocol, in all eligible patients. The study is registered with ClinicalTrials.gov, number NCT02364076, and is closed to accrual; we report the final analysis. FINDINGS 41 patients were enrolled from March 12, 2015, to Dec 16, 2016, of whom 40 were eligible and evaluable and one was excluded because of elevated liver enzymes at screening. The median follow-up was 20 months (IQR 14-26). The proportion of patients who achieved a response was 22·5% (95% CI 10·8-38·5); one (3%) patient achieved a complete response, eight (20%) patients achieved partial responses, and 21 (53%) patients achieved stable disease. The most common grade 3 or 4 adverse events were increased aspartate aminotransferase and alanine aminotransferase (five [13%] patients each). Six (15%) patients developed severe autoimmune toxicity, including two (5%) patients with myocarditis. There were 17 deaths at the time of analysis, but no deaths due to toxicity. INTERPRETATION Pembrolizumab is a promising treatment option in patients with thymic carcinoma. Because severe autoimmune disorders are more frequent in thymic carcinoma than in other tumour types, careful monitoring is essential. FUNDING Merck & Co.
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Affiliation(s)
- Giuseppe Giaccone
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
| | - Chul Kim
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Jillian Thompson
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Colleen McGuire
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Bhaskar Kallakury
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Joeffrey J Chahine
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Maria Manning
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | | | | | - Ming T Tan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Deepa S Subramaniam
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Stephen V Liu
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | | | - Justine N McCutcheon
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
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19
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Kaplan IM, Morisot S, Heiser D, Cheng WC, Kim MJ, Civin CI. Deletion of tristetraprolin caused spontaneous reactive granulopoiesis by a non-cell-autonomous mechanism without disturbing long-term hematopoietic stem cell quiescence. J Immunol 2011; 186:2826-34. [PMID: 21270394 DOI: 10.4049/jimmunol.1002806] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tristetraprolin (TTP, Zfp36, Nup475, Tis11) dramatically reduces the stability of target mRNAs by binding to AU-rich elements in their 3' untranslated regions. Through this mechanism, TTP functions as a rheostatic, temporal regulator of gene expression. TTP knockout (KO) mice exhibit completely penetrant granulocytic hyperplasia. We have shown that the hematopoietic stem-progenitor cell compartment in TTP KO mice is also altered. Although no change was detected in long-term hematopoietic stem cell (HSC) frequency or function, as assayed by immunophenotypic markers or limiting dilution transplants, we observed increases in the frequencies and numbers of short-term HSCs, multipotent progenitors, and granulocyte-monocyte progenitors. This pattern is consistent with "reactive granulopoiesis," in which committed myeloid progenitors and more primitive progenitors cycle more actively to increase production of mature granulocytes in response to infection or adjuvant. We created reverse chimeras by transplanting wild-type bone marrow into TTP KO mice and found the "reactive granulopoiesis" phenocopied, indicating a non-hematopoietic stem-progenitor cell-autonomous mechanism. Correspondingly, we found elevated levels of the granulopoietic TTP targets IL-1β, TNF-α, and IL-6 in the plasma of TTP KO mice. Consistent with the non-cell-autonomous nature of the phenotype, we found elevated levels of IL-1β, TNF-α, and IL-6 transcripts in the livers of TTP KO mice and no detectable difference in the bone marrows. These findings demonstrate the importance of TTP in inflammatory homeostasis and highlight the ability of the hematopoietic system to respond to stress without significant numbers of quiescent HSCs entering the cell cycle.
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Affiliation(s)
- Ian M Kaplan
- Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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20
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Morisot S, Wayne AS, Bohana-Kashtan O, Kaplan IM, Gocke CD, Hildreth R, Stetler-Stevenson M, Walker RL, Davis S, Meltzer PS, Wheelan SJ, Brown P, Jones RJ, Shultz LD, Civin CI. High frequencies of leukemia stem cells in poor-outcome childhood precursor-B acute lymphoblastic leukemias. Leukemia 2010; 24:1859-66. [PMID: 20739953 PMCID: PMC3035974 DOI: 10.1038/leu.2010.184] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In order to develop a xenograft model to determine the efficacy of new therapies against primary human precursor-B acute lymphoblastic leukemia (ALL) stem cells (LSCs), we used the highly immunodeficient non-obese diabetic (NOD).Cg-Prkdc(scid)IL2rg(tmlWjl)/SzJ (NOD-severe combined immune deficient (scid) IL2rg(-/-)) mouse strain. Intravenous transplantation of 2 of 2 ALL cell lines and 9 of 14 primary ALL cases generated leukemia-like proliferations in recipient mice by 1-7 months after transplant. Leukemias were retransplantable, and the immunophenotypes, gene rearrangements and expression profiles were identical or similar to those of the original primary samples. NOD-scid mice transplanted with the same primary samples developed similar leukemias with only a slightly longer latency than did NOD-scid-IL2Rg(-/-) mice. In this highly sensitive NOD-scid-IL2Rg(-/-)-based assay, 1-100 unsorted primary human ALL cells from five of five tested patients, four of whom eventually experienced leukemia relapse, generated leukemias in recipient mice. This very high frequency of LSCs suggests that a hierarchical LSC model is not valuable for poor-outcome ALL.
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Affiliation(s)
- S Morisot
- Department of Pediatrics, Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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21
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Alder JK, Georgantas RW, Hildreth RL, Kaplan IM, Morisot S, Yu X, McDevitt M, Civin CI. Kruppel-like factor 4 is essential for inflammatory monocyte differentiation in vivo. J Immunol 2008; 180:5645-52. [PMID: 18390749 DOI: 10.4049/jimmunol.180.8.5645] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Several members of the Kruppel-like factor (KLF) family of transcription factors play important roles in differentiation, survival, and trafficking of blood and immune cell types. We demonstrate in this study that hematopoietic cells from KLF4(-/-) fetal livers (FL) contained normal numbers of functional hematopoietic progenitor cells, were radioprotective, and performed as well as KLF4(+/+) cells in competitive repopulation assays. However, hematopoietic "KLF4(-/-) chimeras" generated by transplantation of KLF4(-/-) fetal livers cells into lethally irradiated wild-type mice completely lacked circulating inflammatory (CD115(+)Gr1(+)) monocytes, and had reduced numbers of resident (CD115(+)Gr1(-)) monocytes. Although the numbers and function of peritoneal macrophages were normal in KLF4(-/-) chimeras, bone marrow monocytic cells from KLF4(-/-) chimeras expressed lower levels of key trafficking molecules and were more apoptotic. Thus, our in vivo loss-of-function studies demonstrate that KLF4, previously shown to mediate proinflammatory signaling in human macrophages in vitro, is essential for differentiation of mouse inflammatory monocytes, and is involved in the differentiation of resident monocytes. In addition, inducible expression of KLF4 in the HL60 human acute myeloid leukemia cell line stimulated monocytic differentiation and enhanced 12-O-tetradecanoylphorbol 13-acetate induced macrophage differentiation, but blocked all-trans-retinoic acid induced granulocytic differentiation of HL60 cells. The inflammation-selective effects of loss-of-KLF4 and the gain-of-KLF4-induced monocytic differentiation in HL60 cells identify KLF4 as a key regulator of monocytic differentiation and a potential target for translational immune modulation.
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Affiliation(s)
- Jonathan K Alder
- Divisions of Immunology and Hematopoiesis, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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22
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Snyder EL, Saenz CC, Denicourt C, Meade BR, Cui XS, Kaplan IM, Dowdy SF. Enhanced Targeting and Killing of Tumor Cells Expressing the CXC Chemokine Receptor 4 by Transducible Anticancer Peptides. Cancer Res 2005; 65:10646-50. [PMID: 16322205 DOI: 10.1158/0008-5472.can-05-0118] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein transduction domains (PTDs), such as the TAT PTD, have been shown to deliver a wide variety of cargo in cell culture and to treat preclinical models of cancer and cerebral ischemia. The TAT PTD enters cells by a lipid raft-dependent macropinocytosis mechanism that all cells perform. Consequently, PTDs resemble small-molecule therapeutics in their lack of pharmacologic tissue specificity in vivo. However, several human malignancies overexpress specific receptors, including HER2 in breast cancer, GnRH in ovarian carcinomas, and CXC chemokine receptor 4 (CXCR4) in multiple malignancies. To target tumor cells that overexpress the CXCR4 receptor, we linked the CXCR4 DV3 ligand to two transducible anticancer peptides: a p53-activating peptide (DV3-TATp53C') and a cyclin-dependent kinase 2 antagonist peptide (DV3-TAT-RxL). Treatment of tumor cells expressing the CXCR4 receptor with either the DV3-TATp53C' or DV3-TAT-RxL targeted peptides resulted in an enhancement of tumor cell killing compared with treatment with nontargeted parental peptides. In contrast, there was no difference between DV3 targeted peptide and nontargeted, parental peptide treatment of non-CXCR4-expressing tumor cells. These observations show that a multidomain approach can be used to further refine and enhance the tumor selectivity of biologically active, transducible macromolecules for treating cancer.
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Affiliation(s)
- Eric L Snyder
- Howard Hughes Medical Institute and Department of Cellular and Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California 92037-0686, USA
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23
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Kaplan IM, Wadia JS, Dowdy SF. Corrigendum to “Cationic TAT peptide transduction domain enters cells by macropinocytosis” [J. Control. Release 102 (2005) 247–253]. J Control Release 2005. [DOI: 10.1016/j.jconrel.2005.06.003] [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: 11/24/2022]
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24
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Abstract
Naturally occurring and synthetic short arginine containing protein transduction domains (PTDs), including HIV1 TAT, poly-Arg and Antp, have been used to deliver a wide variety of macromolecular, biologically active therapeutic cargo into cells, including peptides, proteins, antisense oligonucleotides and liposomes, in vitro and to treat pre-clinical models of cancer and stroke. PTDs enter cells in a rapid, receptor-independent fashion. Recently, large TAT-fusion proteins (in excess of 30,000 Da) were shown to transduce into cells by fluid-phase macropinocytosis, a specialized form of endocytosis that is independent of caveolae, clathrin and dynamin. However, it remains controversial as to whether or not PTD peptides (1000-5000 Da) enter cells via macropinocytosis and/or through an unknown alternative mechanism. Due to strong ionic interactions with the cell surface, previous measurements of PTD peptide internalization were inaccurate. Cationic PTD peptides containing variable numbers of arginine residues and conditions entered cells exclusively through macropinocytosis. In addition, no PTD peptide was found to enter cells at 4 degrees C, a long held assumption of transduction. Taken together, these observations provide a solid scientific basis for the development of novel biologically active transducible anticancer PTD peptide therapeutics.
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Affiliation(s)
- Ian M Kaplan
- Howard Hughes Medical Institute and Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093-0686, USA
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O'Neil JS, Kaplan IM. Impact on Marine Species of New England Recreational Fishing Policies. Biol Bull 1995; 189:246-247. [PMID: 27768456 DOI: 10.1086/bblv189n2p246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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Kaplan IM, Boyer BC. Monitoring Marine Resources: Ecological and Policy Implications Affecting the Scientific Collecting and Commercial Value of New England Conch (Busycon). Biol Bull 1992; 183:379-380. [PMID: 29300647 DOI: 10.1086/bblv183n2p379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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27
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Kaplan IM, Levine HJ. "Pre-infarction syndrome". Am J Cardiol 1971; 27:233. [PMID: 5543148 DOI: 10.1016/0002-9149(71)90267-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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