1
|
Susanto TT, Hung V, Levine AG, Kerr CH, Yoo Y, Chen Y, Oses-Prieto JA, Fromm L, Fujii K, Wernig M, Burlingame AL, Ruggero D, Barna M. RAPIDASH: A tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues and stimulated macrophages. bioRxiv 2023:2023.12.07.570613. [PMID: 38106052 PMCID: PMC10723405 DOI: 10.1101/2023.12.07.570613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translational control. However, a lack of technologies to enrich RAPs across many sample types has prevented systematic analysis of RAP number, dynamics, and functions. Here, we have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including DHX30 and LLPH, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development that is linked to the translation of genes with long coding sequences. Finally, we characterized ribosome composition remodeling during immune activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs ranging from those with neuroregulatory functions to those activated by immune stimuli, thereby providing critical insights into how ribosomes are remodeled.
Collapse
Affiliation(s)
- Teodorus Theo Susanto
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Victoria Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Craig H Kerr
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yongjin Yoo
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yuxiang Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Lisa Fromm
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Kotaro Fujii
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Maria Barna
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| |
Collapse
|
2
|
Xu K, Yin N, Peng M, Stamatiades EG, Shyu A, Li P, Zhang X, Do MH, Wang Z, Capistrano KJ, Chou C, Levine AG, Rudensky AY, Li MO. Glycolysis fuels phosphoinositide 3-kinase signaling to bolster T cell immunity. Science 2021; 371:405-410. [PMID: 33479154 DOI: 10.1126/science.abb2683] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 08/29/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022]
Abstract
Infection triggers expansion and effector differentiation of T cells specific for microbial antigens in association with metabolic reprograming. We found that the glycolytic enzyme lactate dehydrogenase A (LDHA) is induced in CD8+ T effector cells through phosphoinositide 3-kinase (PI3K) signaling. In turn, ablation of LDHA inhibits PI3K-dependent phosphorylation of Akt and its transcription factor target Foxo1, causing defective antimicrobial immunity. LDHA deficiency cripples cellular redox control and diminishes adenosine triphosphate (ATP) production in effector T cells, resulting in attenuated PI3K signaling. Thus, nutrient metabolism and growth factor signaling are highly integrated processes, with glycolytic ATP serving as a rheostat to gauge PI3K-Akt-Foxo1 signaling in the control of T cell immunity. Such a bioenergetic mechanism for the regulation of signaling may explain the Warburg effect.
Collapse
Affiliation(s)
- Ke Xu
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Na Yin
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Min Peng
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Efstathios G Stamatiades
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Institute of Microbiology, Infectious Diseases and Immunology, Charité University Medical Centre, 12203 Berlin, Germany
| | - Amy Shyu
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Peng Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xian Zhang
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mytrang H Do
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Zhaoquan Wang
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | | | - Chun Chou
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew G Levine
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Alexander Y Rudensky
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA.,Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ming O Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. .,Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| |
Collapse
|
3
|
Ng DL, Granados AC, Santos YA, Servellita V, Goldgof GM, Meydan C, Sotomayor-Gonzalez A, Levine AG, Balcerek J, Han LM, Akagi N, Truong K, Neumann NM, Nguyen DN, Bapat SP, Cheng J, Martin CSS, Federman S, Foox J, Gopez A, Li T, Chan R, Chu CS, Wabl CA, Gliwa AS, Reyes K, Pan CY, Guevara H, Wadford D, Miller S, Mason CE, Chiu CY. A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood. Sci Adv 2021; 7:eabe5984. [PMID: 33536218 PMCID: PMC7857687 DOI: 10.1126/sciadv.abe5984] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/15/2020] [Indexed: 05/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease-19 (COVID-19), has emerged as the cause of a global pandemic. We used RNA sequencing to analyze 286 nasopharyngeal (NP) swab and 53 whole-blood (WB) samples from 333 patients with COVID-19 and controls. Overall, a muted immune response was observed in COVID-19 relative to other infections (influenza, other seasonal coronaviruses, and bacterial sepsis), with paradoxical down-regulation of several key differentially expressed genes. Hospitalized patients and outpatients exhibited up-regulation of interferon-associated pathways, although heightened and more robust inflammatory responses were observed in hospitalized patients with more clinically severe illness. Two-layer machine learning-based host classifiers consisting of complete (>1000 genes), medium (<100), and small (<20) gene biomarker panels identified COVID-19 disease with 85.1-86.5% accuracy when benchmarked using an independent test set. SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for COVID-19 diagnosis.
Collapse
Affiliation(s)
- Dianna L Ng
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lucy M Han
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Naomi Akagi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Kent Truong
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Neil M Neumann
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - David N Nguyen
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Jing Cheng
- Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Claudia Sanchez-San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Tony Li
- Department of Medicine, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Ray Chan
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Cynthia S Chu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chiara A Wabl
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Chao-Yang Pan
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Hugo Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Debra Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| |
Collapse
|
4
|
Lynch KL, Whitman JD, Lacanienta NP, Beckerdite EW, Kastner SA, Shy BR, Goldgof GM, Levine AG, Bapat SP, Stramer SL, Esensten JH, Hightower AW, Bern C, Wu AHB. Magnitude and Kinetics of Anti-Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Responses and Their Relationship to Disease Severity. Clin Infect Dis 2021; 72:301-308. [PMID: 33501951 PMCID: PMC7454426 DOI: 10.1093/cid/ciaa979] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [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: 06/09/2020] [Accepted: 07/09/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can be detected indirectly by measuring the host immune response. For some viruses, antibody concentrations correlate with host protection and viral neutralization, but in rare cases, antiviral antibodies can promote disease progression. Elucidation of the kinetics and magnitude of the SARS-CoV-2 antibody response is essential to understand the pathogenesis of coronavirus disease 2019 (COVID-19) and identify potential therapeutic targets. METHODS Sera (n = 533) from patients with real-time polymerase chain reaction-confirmed COVID-19 (n = 94 with acute infections and n = 59 convalescent patients) were tested using a high-throughput quantitative immunoglobulin M (IgM) and immunoglobulin G (IgG) assay that detects antibodies to the spike protein receptor binding domain and nucleocapsid protein. Individual and serial samples covered the time of initial diagnosis, during the disease course, and following recovery. We evaluated antibody kinetics and correlation between magnitude of the response and disease severity. RESULTS Patterns of SARS-CoV-2 antibody production varied considerably. Among 52 patients with 3 or more serial specimens, 44 (84.6%) and 42 (80.8%) had observed IgM and IgG seroconversion at a median of 8 and 10 days, respectively. Compared to those with milder disease, peak measurements were significantly higher for patients admitted to the intensive care unit for all time intervals between 6 and 20 days for IgM, and all intervals after 5 days for IgG. CONCLUSIONS High-sensitivity assays with a robust dynamic range provide a comprehensive picture of host antibody response to SARS-CoV-2. IgM and IgG responses were significantly higher in patients with severe than mild disease. These differences may affect strategies for seroprevalence studies, therapeutics, and vaccine development.
Collapse
Affiliation(s)
- Kara L Lynch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Jeffrey D Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Noreen P Lacanienta
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Erica W Beckerdite
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Shannon A Kastner
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Brian R Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Susan L Stramer
- Scientific Affairs, American Red Cross, Gaithersberg, Maryland, USA
| | - Jonathan H Esensten
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| | | | - Caryn Bern
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Alan H B Wu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, USA
| |
Collapse
|
5
|
Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AWY, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk RP, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Nat Biotechnol 2020; 38:1174-1183. [PMID: 32855547 PMCID: PMC7740072 DOI: 10.1038/s41587-020-0659-0] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 07/29/2020] [Indexed: 12/18/2022]
Abstract
Appropriate use and interpretation of serological tests for assessments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure, infection and potential immunity require accurate data on assay performance. We conducted a head-to-head evaluation of ten point-of-care-style lateral flow assays (LFAs) and two laboratory-based enzyme-linked immunosorbent assays to detect anti-SARS-CoV-2 IgM and IgG antibodies in 5-d time intervals from symptom onset and studied the specificity of each assay in pre-coronavirus disease 2019 specimens. The percent of seropositive individuals increased with time, peaking in the latest time interval tested (>20 d after symptom onset). Test specificity ranged from 84.3% to 100.0% and was predominantly affected by variability in IgM results. LFA specificity could be increased by considering weak bands as negative, but this decreased detection of antibodies (sensitivity) in a subset of SARS-CoV-2 real-time PCR-positive cases. Our results underline the importance of seropositivity threshold determination and reader training for reliable LFA deployment. Although there was no standout serological assay, four tests achieved more than 80% positivity at later time points tested and more than 95% specificity.
Collapse
Affiliation(s)
- Jeffrey D Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph Hiatt
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Cody T Mowery
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Brian R Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ruby Yu
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Tori N Yamamoto
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ujjwal Rathore
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Caroline Whitty
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan M Woo
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Antonia E Gallman
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, USA
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - David N Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sophia A Bylsma
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Ana M Lyons
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Stacy Li
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Allison Wai-Yi Wong
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
| | - Eva Mae Gillis-Buck
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Zachary B Steinhart
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Youjin Lee
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Ryan Apathy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Mitchell J Lipke
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer Anne Smith
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Tina Zheng
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ian C Boothby
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Erin Isaza
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Jackie Chan
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Dante D Acenas
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jinwoo Lee
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Trisha A Macrae
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Than S Kyaw
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - David Wu
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Dianna L Ng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Vanessa A York
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Haig Alexander Eskandarian
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Perri C Callaway
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Infectious Diseases and Immunity Graduate Group, University of California, Berkeley, Berkeley, CA, USA
| | - Lakshmi Warrier
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Mary E Moreno
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Justine Levan
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Leonel Torres
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lila A Farrington
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rita P Loudermilk
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Kanishka Koshal
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Diane Yang
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Michael G Astudillo
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Jeffrey A Gelfand
- Division of Infectious Diseases, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Susan L Stramer
- Scientific Affairs, American Red Cross, Gaithersburg, MD, USA
| | - Michael R Wilson
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Aashish Manglik
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jason G Cyster
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, USA
| | - Joel D Ernst
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Alan H B Wu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kara L Lynch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Caryn Bern
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
| | - Patrick D Hsu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Alexander Marson
- J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
6
|
Ng DL, Goldgof GM, Shy BR, Levine AG, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai SK, Sotomayor-Gonzalez A, Servellita V, Martin CSS, Granados A, Glasner DR, Han LM, Truong K, Akagi N, Nguyen DN, Neumann NM, Qazi D, Hsu E, Gu W, Santos YA, Custer B, Green V, Williamson P, Hills NK, Lu CM, Whitman JD, Stramer SL, Wang C, Reyes K, Hakim JMC, Sujishi K, Alazzeh F, Pham L, Thornborrow E, Oon CY, Miller S, Kurtz T, Simmons G, Hackett J, Busch MP, Chiu CY. SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood. Nat Commun 2020; 11:4698. [PMID: 32943630 PMCID: PMC7499171 DOI: 10.1038/s41467-020-18468-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/18/2020] [Indexed: 01/08/2023] Open
Abstract
Given the limited availability of serological testing to date, the seroprevalence of SARS-CoV-2-specific antibodies in different populations has remained unclear. Here, we report very low SARS-CoV-2 seroprevalence in two San Francisco Bay Area populations. Seroreactivity was 0.26% in 387 hospitalized patients admitted for non-respiratory indications and 0.1% in 1,000 blood donors in early April 2020. We additionally describe the longitudinal dynamics of immunoglobulin-G (IgG), immunoglobulin-M (IgM), and in vitro neutralizing antibody titers in COVID-19 patients. The median time to seroconversion ranged from 10.3-11.0 days for these 3 assays. Neutralizing antibodies rose in tandem with immunoglobulin titers following symptom onset, and positive percent agreement between detection of IgG and neutralizing titers was >93%. These findings emphasize the importance of using highly accurate tests for surveillance studies in low-prevalence populations, and provide evidence that seroreactivity using SARS-CoV-2 anti-nucleocapsid protein IgG and anti-spike IgM assays are generally predictive of in vitro neutralizing capacity.
Collapse
Affiliation(s)
- Dianna L Ng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Brian R Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Mary Rodgers
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Kelly Coller
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Sandra Pearce
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Sergej Franz
- Vitalant Research Institute, San Francisco, CA, USA
| | - Li Du
- Vitalant Research Institute, San Francisco, CA, USA
| | - Mars Stone
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | | | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Andrea Granados
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Dustin R Glasner
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Lucy M Han
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Kent Truong
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Naomi Akagi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - David N Nguyen
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Neil M Neumann
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Qazi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
| | | | | | - Nancy K Hills
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Chuanyi M Lu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Laboratory Medicine Service, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Jeffrey D Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jill M C Hakim
- Department of Medicine at ZSFG, The Division of HIV, ID & Global Medicine, San Francisco, CA, USA
| | - Kirk Sujishi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Fariba Alazzeh
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lori Pham
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Edward Thornborrow
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ching-Ying Oon
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Theodore Kurtz
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Graham Simmons
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - John Hackett
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Michael P Busch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
7
|
Ng DL, Goldgof GM, Shy BR, Levine AG, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai SK, Sotomayor-Gonzalez A, Servellita V, Martin CSS, Granados A, Glasner DR, Han LM, Truong K, Akagi N, Nguyen DN, Neumann NM, Qazi D, Hsu E, Gu W, Santos YA, Custer B, Green V, Williamson P, Hills NK, Lu CM, Whitman JD, Stramer S, Wang C, Reyes K, Hakim JM, Sujishi K, Alazzeh F, Pham L, Oon CY, Miller S, Kurtz T, Hackett J, Simmons G, Busch MP, Chiu CY. SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area. medRxiv 2020:2020.05.19.20107482. [PMID: 32511477 PMCID: PMC7273245 DOI: 10.1101/2020.05.19.20107482] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 01/09/2023]
Abstract
We report very low SARS-CoV-2 seroprevalence in two San Francisco Bay Area populations. Seropositivity was 0.26% in 387 hospitalized patients admitted for non-respiratory indications and 0.1% in 1,000 blood donors. We additionally describe the longitudinal dynamics of immunoglobulin-G, immunoglobulin-M, and in vitro neutralizing antibody titers in COVID-19 patients. Neutralizing antibodies rise in tandem with immunoglobulin levels following symptom onset, exhibiting median time to seroconversion within one day of each other, and there is >93% positive percent agreement between detection of immunoglobulin-G and neutralizing titers.
Collapse
Affiliation(s)
- Dianna L. Ng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Gregory M. Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Brian R. Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew G. Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P. Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Mary Rodgers
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Kelly Coller
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Sandy Pearce
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Sergej Franz
- Vitalant Research Institute, San Francisco, CA, USA
| | - Li Du
- Vitalant Research Institute, San Francisco, CA, USA
| | - Mars Stone
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | | | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Andrea Granados
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Dustin R. Glasner
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Lucy M. Han
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Kent Truong
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Naomi Akagi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - David N. Nguyen
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Neil M. Neumann
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Qazi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yale A. Santos
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
| | | | | | - Nancy K. Hills
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Chuanyi M. Lu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Lab Medicine Service, San Francisco VA Healthcare System
| | - Jeffrey D. Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jill M.C. Hakim
- Department of Medicine at ZSFG, the Division of HIV, ID & Global Medicine
| | - Kirk Sujishi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Fariba Alazzeh
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lori Pham
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ching-Ying Oon
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Theodore Kurtz
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John Hackett
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Graham Simmons
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Michael P. Busch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Charles Y. Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| |
Collapse
|
8
|
Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AWY, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk R, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. Test performance evaluation of SARS-CoV-2 serological assays. medRxiv 2020. [PMID: 32511497 PMCID: PMC7273265 DOI: 10.1101/2020.04.25.20074856] [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: 12/29/2022]
Abstract
Background: Serological tests are crucial tools for assessments of SARS-CoV-2 exposure, infection and potential immunity. Their appropriate use and interpretation require accurate assay performance data. Method: We conducted an evaluation of 10 lateral flow assays (LFAs) and two ELISAs to detect anti-SARS-CoV-2 antibodies. The specimen set comprised 128 plasma or serum samples from 79 symptomatic SARS-CoV-2 RT-PCR-positive individuals; 108 pre-COVID-19 negative controls; and 52 recent samples from individuals who underwent respiratory viral testing but were not diagnosed with Coronavirus Disease 2019 (COVID-19). Samples were blinded and LFA results were interpreted by two independent readers, using a standardized intensity scoring system. Results: Among specimens from SARS-CoV-2 RT-PCR-positive individuals, the percent seropositive increased with time interval, peaking at 81.8–100.0% in samples taken >20 days after symptom onset. Test specificity ranged from 84.3–100.0% in pre-COVID-19 specimens. Specificity was higher when weak LFA bands were considered negative, but this decreased sensitivity. IgM detection was more variable than IgG, and detection was highest when IgM and IgG results were combined. Agreement between ELISAs and LFAs ranged from 75.7–94.8%. No consistent cross-reactivity was observed. Conclusion: Our evaluation showed heterogeneous assay performance. Reader training is key to reliable LFA performance, and can be tailored for survey goals. Informed use of serology will require evaluations covering the full spectrum of SARS-CoV-2 infections, from asymptomatic and mild infection to severe disease, and later convalescence. Well-designed studies to elucidate the mechanisms and serological correlates of protective immunity will be crucial to guide rational clinical and public health policies.
Collapse
Affiliation(s)
- Jeffrey D Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph Hiatt
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cody T Mowery
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brian R Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ruby Yu
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tori N Yamamoto
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ujjwal Rathore
- J. David Gladstone Institutes, San Francisco, CA 94158, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Caroline Whitty
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jonathan M Woo
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Antonia E Gallman
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David N Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sophia A Bylsma
- Department of Bioengineering, University of California, Berkeley, Berkeley CA 94720 USA
| | - Ana M Lyons
- Department of Integrative Biology, University of California, Berkeley, Berkeley CA 94720 USA
| | - Stacy Li
- Department of Integrative Biology, University of California, Berkeley, Berkeley CA 94720 USA
| | - Allison Wai-Yi Wong
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
| | - Eva Mae Gillis-Buck
- Department of Surgery, University of California, San Francisco, CA 94143, USA
| | - Zachary B Steinhart
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Youjin Lee
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
| | - Ryan Apathy
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mitchell J Lipke
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jennifer Anne Smith
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tina Zheng
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA.,Department of Neurology, University of California, San Francisco, CA 94158, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ian C Boothby
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Department of Dermatology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erin Isaza
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jackie Chan
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
| | - Dante D Acenas
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
| | - Jinwoo Lee
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Trisha A Macrae
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Than S Kyaw
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
| | - David Wu
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
| | - Dianna L Ng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Pathology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vanessa A York
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Haig Alexander Eskandarian
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Perri C Callaway
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA.,Infectious Diseases and Immunity Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Lakshmi Warrier
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Mary E Moreno
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Justine Levan
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Leonel Torres
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Lila A Farrington
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Rita Loudermilk
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Kanishka Koshal
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Diane Yang
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Michael G Astudillo
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Jeffrey A Gelfand
- Division of Infectious Diseases, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94143, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Michael R Wilson
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA.,Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | - Chun Jimmie Ye
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.,Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA 94158, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jason G Cyster
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco
| | - Joel D Ernst
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Alan H B Wu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kara L Lynch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Caryn Bern
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Patrick D Hsu
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley CA 94720 USA
| | - Alexander Marson
- J. David Gladstone Institutes, San Francisco, CA 94158, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| |
Collapse
|
9
|
Levine AG, Hemmers S, Baptista AP, Schizas M, Faire MB, Moltedo B, Konopacki C, Schmidt-Supprian M, Germain RN, Treuting PM, Rudensky AY. Suppression of lethal autoimmunity by regulatory T cells with a single TCR specificity. J Exp Med 2017; 214:609-622. [PMID: 28130403 PMCID: PMC5339675 DOI: 10.1084/jem.20161318] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 11/06/2016] [Accepted: 12/23/2016] [Indexed: 12/31/2022] Open
Abstract
Levine et al. investigate the extent to which regulatory T cells with either a monoclonal T cell receptor (TCR) or random TCR repertoire in place of their developmentally selected specificities maintain TCR-dependent gene expression and immunosuppressive function. The regulatory T cell (T reg cell) T cell receptor (TCR) repertoire is highly diverse and skewed toward recognition of self-antigens. TCR expression by T reg cells is continuously required for maintenance of immune tolerance and for a major part of their characteristic gene expression signature; however, it remains unknown to what degree diverse TCR-mediated interactions with cognate self-antigens are required for these processes. In this study, by experimentally switching the T reg cell TCR repertoire to a single T reg cell TCR, we demonstrate that T reg cell function and gene expression can be partially uncoupled from TCR diversity. An induced switch of the T reg cell TCR repertoire to a random repertoire also preserved, albeit to a limited degree, the ability to suppress lymphadenopathy and T helper cell type 2 activation. At the same time, these perturbations of the T reg cell TCR repertoire led to marked immune cell activation, tissue inflammation, and an ultimately severe autoimmunity, indicating the importance of diversity and specificity for optimal T reg cell function.
Collapse
Affiliation(s)
- Andrew G Levine
- Howard Hughes Medical Institute, Immunology Program, Ludwig Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Saskia Hemmers
- Howard Hughes Medical Institute, Immunology Program, Ludwig Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Antonio P Baptista
- Lymphocyte Biology Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Michail Schizas
- Howard Hughes Medical Institute, Immunology Program, Ludwig Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Mehlika B Faire
- Howard Hughes Medical Institute, Immunology Program, Ludwig Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Bruno Moltedo
- Howard Hughes Medical Institute, Immunology Program, Ludwig Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Catherine Konopacki
- Howard Hughes Medical Institute, Immunology Program, Ludwig Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Marc Schmidt-Supprian
- Hematology and Oncology, Klinikum rechts der Isar, Technische Universität München, 80333 Munich, Germany
| | - Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Piper M Treuting
- Department of Comparative Medicine, University of Washington School of Medicine, Seattle, WA 98195
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute, Immunology Program, Ludwig Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| |
Collapse
|
10
|
Chinen T, Kannan AK, Levine AG, Fan X, Klein U, Zheng Y, Gasteiger G, Feng Y, Fontenot JD, Rudensky AY. An essential role for the IL-2 receptor in T reg cell function. Nat Immunol 2016; 17:1322-1333. [PMID: 27595233 PMCID: PMC5071159 DOI: 10.1038/ni.3540] [Citation(s) in RCA: 535] [Impact Index Per Article: 66.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 07/27/2016] [Indexed: 12/12/2022]
Abstract
Regulatory T (Treg) cells, expressing abundant amounts of the IL-2 receptor (IL-2R), are reliant on IL-2 produced by activated T cells. This feature implied a key role for a simple network based on IL-2 consumption by Treg cells in their suppressor function. However, congenital deficiency in IL-2R results in reduced expression of the Treg cell lineage specification factor Foxp3, confounding experimental efforts to understand the role of IL-2R expression and signaling in Treg suppressor function. Using genetic gain and loss of function approaches, we demonstrate that IL-2 capture is dispensable for control of CD4+ T cells, but is important for limiting CD8+ T cell activation, and that IL-2R dependent STAT5 transcription factor activation plays an essential role in Treg cell suppressor function separable from T cell receptor signaling.
Collapse
Affiliation(s)
- Takatoshi Chinen
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Andrew G Levine
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiying Fan
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ulf Klein
- Herbert Irving Comprehensive Cancer Center, Department of Pathology and Cell Biology, and Department of Microbiology and Immunology, Columbia University, New York, NY, USA
| | - Ye Zheng
- Nomis Foundation Laboratories for Immunobiology and Microbial Pathogenesis, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Georg Gasteiger
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Institute for Medical Microbiology and Hygiene, University of Mainz Medical Centre, Mainz, Germany
| | - Yongqiang Feng
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
11
|
Liu Z, Gerner MY, Van Panhuys N, Levine AG, Rudensky AY, Germain RN. Immune homeostasis enforced by co-localized effector and regulatory T cells. Nature 2015; 528:225-30. [PMID: 26605524 PMCID: PMC4702500 DOI: 10.1038/nature16169] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [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: 04/19/2015] [Accepted: 11/02/2015] [Indexed: 12/17/2022]
Abstract
FOXP3(+) regulatory T cells (Treg cells) prevent autoimmunity by limiting the effector activity of T cells that have escaped thymic negative selection or peripheral inactivation. Despite the information available about molecular factors mediating the suppressive function of Treg cells, the relevant cellular events in intact tissues remain largely unexplored, and whether Treg cells prevent activation of self-specific T cells or primarily limit damage from such cells has not been determined. Here we use multiplex, quantitative imaging in mice to show that, within secondary lymphoid tissues, highly suppressive Treg cells expressing phosphorylated STAT5 exist in discrete clusters with rare IL-2-positive T cells that are activated by self-antigens. This local IL-2 induction of STAT5 phosphorylation in Treg cells is part of a feedback circuit that limits further autoimmune responses. Inducible ablation of T cell receptor expression by Treg cells reduces their regulatory capacity and disrupts their localization in clusters, resulting in uncontrolled effector T cell responses. Our data thus reveal that autoreactive T cells are activated to cytokine production on a regular basis, with physically co-clustering T cell receptor-stimulated Treg cells responding in a negative feedback manner to suppress incipient autoimmunity and maintain immune homeostasis.
Collapse
Affiliation(s)
- Zhiduo Liu
- Lymphocyte Biology Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-1892, USA
| | - Michael Y Gerner
- Lymphocyte Biology Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-1892, USA
| | - Nicholas Van Panhuys
- Lymphocyte Biology Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-1892, USA
| | - Andrew G Levine
- Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-1892, USA
| |
Collapse
|
12
|
Levine AG, Arvey A, Jin W, Rudensky AY. Continuous requirement for the TCR in regulatory T cell function. Nat Immunol 2014; 15:1070-8. [PMID: 25263123 PMCID: PMC4205268 DOI: 10.1038/ni.3004] [Citation(s) in RCA: 393] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/05/2014] [Indexed: 12/12/2022]
Abstract
Foxp3+ regulatory T cells (Treg cells) maintain immunological tolerance and their deficiency results in fatal multi-organ autoimmunity. Although heightened T cell receptor (TCR) signaling is critical for the differentiation of Treg cells, the role of TCR signaling in Treg cell function remains largely unknown. Here we demonstrate inducible ablation of the TCR results in Treg cell dysfunction which cannot be attributed to impaired Foxp3 expression, decreased expression of Treg cell signature genes or altered ability to sense and consume interleukin 2. Rather, TCR signaling was required for maintaining the expression of a limited subset of genes comprising 25% of the activated Treg cell transcriptional signature. Our results reveal a critical role for the TCR in Treg cell suppressor capacity.
Collapse
Affiliation(s)
- Andrew G Levine
- 1] Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. [2] Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Aaron Arvey
- 1] Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. [2] Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Wei Jin
- 1] Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. [2] Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Alexander Y Rudensky
- 1] Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. [2] Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA. [3] Ludwig Center, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
13
|
|
14
|
|