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Melocchi A, Schmittlein B, Jones AL, Ainane Y, Rizvi A, Chan D, Dickey E, Pool K, Harsono K, Szymkiewicz D, Scarfogliero U, Bhatia V, Sivanantham A, Kreciglowa N, Hunter A, Gomez M, Tanner A, Uboldi M, Batish A, Balcerek J, Kutova-Stoilova M, Paruthiyil S, Acevedo LA, Stadnitskiy R, Carmichael S, Aulbach H, Hewitt M, Jeu XDMD, Robilant BD, Parietti F, Esensten JH. Development of a robotic cluster for automated and scalable cell therapy manufacturing. Cytotherapy 2024:S1465-3249(24)00098-7. [PMID: 38647505 DOI: 10.1016/j.jcyt.2024.03.010] [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: 12/14/2023] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND AIMS The production of commercial autologous cell therapies such as chimeric antigen receptor T cells requires complex manual manufacturing processes. Skilled labor costs and challenges in manufacturing scale-out have contributed to high prices for these products. METHODS We present a robotic system that uses industry-standard cell therapy manufacturing equipment to automate the steps involved in cell therapy manufacturing. The robotic cluster consists of a robotic arm and customized modules, allowing the robot to manipulate a variety of standard cell therapy instruments and materials such as incubators, bioreactors, and reagent bags. This system enables existing manual manufacturing processes to be rapidly adapted to robotic manufacturing, without having to adopt a completely new technology platform. Proof-of-concept for the robotic cluster's expansion module was demonstrated by expanding human CD8+ T cells. RESULTS The robotic cultures showed comparable cell yields, viability, and identity to those manually performed. In addition, the robotic system was able to maintain culture sterility. CONCLUSIONS Such modular robotic solutions may support scale-up and scale-out of cell therapies that are developed using classical manual methods in academic laboratories and biotechnology companies. This approach offers a pathway for overcoming manufacturing challenges associated with manual processes, ultimately contributing to the broader accessibility and affordability for personalized immunotherapies.
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Affiliation(s)
- Alice Melocchi
- Multiply Labs, San Francisco, California, USA; Sezione di Tecnologia e Legislazione Farmaceutiche "M. E. Sangalli", Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy.
| | | | - Alexis L Jones
- Multiply Labs, San Francisco, California, USA; Department of Health Sciences and Technology, Harvard-Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Ali Rizvi
- Multiply Labs, San Francisco, California, USA
| | - Darius Chan
- Multiply Labs, San Francisco, California, USA
| | | | - Kelsey Pool
- Multiply Labs, San Francisco, California, USA
| | | | | | | | | | | | | | | | | | | | - Marco Uboldi
- Multiply Labs, San Francisco, California, USA; Sezione di Tecnologia e Legislazione Farmaceutiche "M. E. Sangalli", Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Milano, Italy
| | - Arpit Batish
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Mariella Kutova-Stoilova
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Sreenivasan Paruthiyil
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Luis A Acevedo
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | - Rachel Stadnitskiy
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA
| | | | | | - Matthew Hewitt
- Charles River Scientific, Wilmington, Massachusetts, USA
| | | | | | | | - Jonathan H Esensten
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, USA; The Advanced Biotherapy Center (ABC), Sheba Medical Center, Tel Hashomer, Israel
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2
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Balcerek J, Shy BR, Putnam AL, Masiello LM, Lares A, Dekovic F, Acevedo L, Lee MR, Nguyen V, Liu W, Paruthiyil S, Xu J, Leinbach AS, Bluestone JA, Tang Q, Esensten JH. Polyclonal Regulatory T Cell Manufacturing Under cGMP: A Decade of Experience. Front Immunol 2021; 12:744763. [PMID: 34867967 PMCID: PMC8636860 DOI: 10.3389/fimmu.2021.744763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/01/2021] [Indexed: 12/29/2022] Open
Abstract
We report on manufacturing outcomes for 41 autologous polyclonal regulatory T cell (PolyTreg) products for 7 different Phase 1 clinical trials over a 10-year period (2011-2020). Data on patient characteristics, manufacturing parameters, and manufacturing outcomes were collected from manufacturing batch records and entered into a secure database. Overall, 88% (36/41) of PolyTreg products met release criteria and 83% (34/41) of products were successfully infused into patients. Of the 7 not infused, 5 failed release criteria, and 2 were not infused because the patient became ineligible due to a change in clinical status. The median fold expansion over the 14-day manufacturing process was 434.8 -fold (range 29.8-2,232), resulting in a median post-expansion cell count of 1,841 x 106 (range 56.9-16,179 x 106). The main correlate of post-expansion cell number was starting cell number, which positively correlates with absolute circulating Treg cell count. Other parameters, including date of PolyTreg production, patient sex, and patient age did not significantly correlate with fold expansion of Treg during product manufacturing. In conclusion, PolyTreg manufacturing outcomes are consistent across trials and dates of production.
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Affiliation(s)
- Joanna Balcerek
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Brian R Shy
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Amy L Putnam
- Diabetes Center, University of California San Francisco, San Francisco, CA, United States
| | - Lisa M Masiello
- Diabetes Center, University of California San Francisco, San Francisco, CA, United States
| | - Angela Lares
- Diabetes Center, University of California San Francisco, San Francisco, CA, United States
| | - Florinna Dekovic
- Diabetes Center, University of California San Francisco, San Francisco, CA, United States
| | - Luis Acevedo
- Diabetes Center, University of California San Francisco, San Francisco, CA, United States
| | - Michael R Lee
- Diabetes Center, University of California San Francisco, San Francisco, CA, United States
| | - Vinh Nguyen
- Department of Surgery, University of California San Francisco, San Francisco, CA, United States
| | - Weihong Liu
- Diabetes Center, University of California San Francisco, San Francisco, CA, United States
| | - Sreenivasan Paruthiyil
- Diabetes Center, University of California San Francisco, San Francisco, CA, United States
| | - Jingying Xu
- Diabetes Center, University of California San Francisco, San Francisco, CA, United States
| | - Ashley S Leinbach
- Diabetes Center, University of California San Francisco, San Francisco, CA, United States
| | - Jeffrey A Bluestone
- Diabetes Center, University of California San Francisco, San Francisco, CA, United States.,Sean N. Parker Autoimmune Research Laboratory, University of California San Francisco, San Francisco, CA, United States
| | - Qizhi Tang
- Diabetes Center, University of California San Francisco, San Francisco, CA, United States.,Department of Surgery, University of California San Francisco, San Francisco, CA, United States
| | - Jonathan H Esensten
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, United States
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3
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Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Sanchez San Martin C, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst JA, Miller S, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi JM, Simoneau CR, Kumar GR, McMahon S, Lidsky PV, Xiao Y, Hemarajata P, Green NM, Espinosa A, Kath C, Haw M, Bell J, Hacker JK, Hanson C, Wadford DA, Anaya C, Ferguson D, Frankino PA, Shivram H, Lareau LF, Wyman SK, Ott M, Andino R, Chiu CY. Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant. Cell 2021; 184:3426-3437.e8. [PMID: 33991487 PMCID: PMC8057738 DOI: 10.1016/j.cell.2021.04.025] [Citation(s) in RCA: 313] [Impact Index Per Article: 104.3] [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: 03/03/2021] [Revised: 04/02/2021] [Accepted: 04/15/2021] [Indexed: 01/07/2023]
Abstract
We identified an emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California, a state in the western United States. Named B.1.427/B.1.429 to denote its two lineages, the variant emerged in May 2020 and increased from 0% to >50% of sequenced cases from September 2020 to January 2021, showing 18.6%-24% increased transmissibility relative to wild-type circulating strains. The variant carries three mutations in the spike protein, including an L452R substitution. We found 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation common to variants B.1.1.7, B.1.351, and P.1. Antibody neutralization assays revealed 4.0- to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California exhibiting decreased antibody neutralization warrants further investigation.
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Affiliation(s)
- Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Miguel A Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mir M Khalid
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | | | - Alicia Sotomayor-González
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Dustin R Glasner
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Kevin R Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Nikitha P Reddy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA
| | - Scot Federman
- Laboratory for Genomics Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jing Cheng
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jordan Taylor
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jessica A Streithorst
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bharath Sreekumar
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Pei-Yi Chen
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Ursula Schulze-Gahmen
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Taha Y Taha
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Jennifer M Hayashi
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Camille R Simoneau
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - G Renuka Kumar
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Sarah McMahon
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Peera Hemarajata
- Los Angeles County Public Health Laboratories, Downey, CA 90242, USA
| | - Nicole M Green
- Los Angeles County Public Health Laboratories, Downey, CA 90242, USA
| | - Alex Espinosa
- California Department of Public Health, Richmond, CA 94804, USA
| | - Chantha Kath
- California Department of Public Health, Richmond, CA 94804, USA
| | - Monica Haw
- California Department of Public Health, Richmond, CA 94804, USA
| | - John Bell
- California Department of Public Health, Richmond, CA 94804, USA
| | - Jill K Hacker
- California Department of Public Health, Richmond, CA 94804, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, CA 94804, USA
| | - Debra A Wadford
- California Department of Public Health, Richmond, CA 94804, USA
| | - Carlos Anaya
- Monterey County Department of Public Health, Monterey, CA 93906, USA
| | - Donna Ferguson
- Monterey County Department of Public Health, Monterey, CA 93906, USA
| | - Phillip A Frankino
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Haridha Shivram
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Liana F Lareau
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Melanie Ott
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institute of Virology, San Francisco, CA 94158, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Raul Andino
- Department of Microbiology and Immunology, 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 94158, USA; UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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4
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Balcerek J, Trejo E, Levine K, Couey P, Kornberg ZV, Rogine C, Young C, Li PJ, Shy BR, Taylor JE, Bakhtary S, Friedlander T, Lynch KL, Bern C, Esensten JH. Hospital-Based Donor Recruitment and Predonation Serologic Testing for COVID-19 Convalescent Plasma. Am J Clin Pathol 2021; 155:515-521. [PMID: 33399201 PMCID: PMC7929413 DOI: 10.1093/ajcp/aqaa268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Objectives Serologic testing for antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in potential donors of coronavirus disease 2019 (COVID-19) convalescent plasma (CCP) may not be performed until after blood donation. A hospital-based recruitment program for CCP may be an efficient way to identify potential donors prospectively Methods Patients who recovered from known or suspected COVID-19 were identified and recruited through medical record searches and public appeals in March and April 2020. Participants were screened with a modified donor history questionnaire and, if eligible, were asked for consent and tested for SARS-CoV-2 antibodies (IgG and IgM). Participants positive for SARS-CoV-2 IgG were referred for CCP collection. Results Of 179 patients screened, 128 completed serologic testing and 89 were referred for CCP donation. IgG antibodies to SARS-CoV-2 were detected in 23 of 51 participants with suspected COVID-19 and 66 of 77 participants with self-reported COVID-19 confirmed by polymerase chain reaction (PCR). The anti–SARS-CoV-2 IgG level met the US Food and Drug Administration criteria for “high-titer” CCP in 39% of participants confirmed by PCR, as measured by the Ortho VITROS IgG assay. A wide range of SARS-CoV-2 IgG levels were observed. Conclusions A hospital-based CCP donor recruitment program can prospectively identify potential CCP donors. Variability in SARS-CoV-2 IgG levels has implications for the selection of CCP units for transfusion.
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Affiliation(s)
| | - Evelin Trejo
- Division of Hematology/Oncology, Department of Medicine
| | | | - Paul Couey
- Division of Hematology/Oncology, Department of Medicine
| | - Zoe V Kornberg
- School of Medicine, University of California San Francisco
| | - Camille Rogine
- School of Medicine, University of California San Francisco
| | | | - P Jonathan Li
- School of Medicine, University of California San Francisco
| | | | | | | | | | | | - Caryn Bern
- Department of Epidemiology and Biostatistics
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5
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Deng X, Garcia-Knight MA, Khalid MM, Servellita V, Wang C, Morris MK, Sotomayor-González A, Glasner DR, Reyes KR, Gliwa AS, Reddy NP, Martin CSS, Federman S, Cheng J, Balcerek J, Taylor J, Streithorst JA, Miller S, Kumar GR, Sreekumar B, Chen PY, Schulze-Gahmen U, Taha TY, Hayashi J, Simoneau CR, McMahon S, Lidsky PV, Xiao Y, Hemarajata P, Green NM, Espinosa A, Kath C, Haw M, Bell J, Hacker JK, Hanson C, Wadford DA, Anaya C, Ferguson D, Lareau LF, Frankino PA, Shivram H, Wyman SK, Ott M, Andino R, Chiu CY. Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation. medRxiv 2021:2021.03.07.21252647. [PMID: 33758899 PMCID: PMC7987058 DOI: 10.1101/2021.03.07.21252647] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We identified a novel SARS-CoV-2 variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California. Named B.1.427/B.1.429 to denote its 2 lineages, the variant emerged around May 2020 and increased from 0% to >50% of sequenced cases from September 1, 2020 to January 29, 2021, exhibiting an 18.6-24% increase in transmissibility relative to wild-type circulating strains. The variant carries 3 mutations in the spike protein, including an L452R substitution. Our analyses revealed 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation found in the B.1.1.7, B.1.351, and P.1 variants. Antibody neutralization assays showed 4.0 to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California associated with decreased antibody neutralization warrants further investigation.
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Affiliation(s)
- Xianding Deng
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Miguel A Garcia-Knight
- Department of Microbiology and Immunology, University of California San Francisco, California, USA
| | - Mir M Khalid
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Candace Wang
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Mary Kate Morris
- California Department of Public Health, Richmond, California, USA
| | - Alicia Sotomayor-González
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Dustin R Glasner
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Kevin R Reyes
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Nikitha P Reddy
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
| | - Scot Federman
- Laboratory for Genomics Research, University of California San Francisco, California, USA
| | - Jing Cheng
- Department of Medicine, University of California San Francisco, California, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California San Francisco, California, USA
| | - Jordan Taylor
- Department of Laboratory Medicine, University of California San Francisco, California, USA
| | - Jessica A Streithorst
- Department of Laboratory Medicine, University of California San Francisco, California, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, California, USA
| | - G Renuka Kumar
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Bharath Sreekumar
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Pei-Yi Chen
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Ursula Schulze-Gahmen
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Taha Y Taha
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Jennifer Hayashi
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Camille R Simoneau
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Sarah McMahon
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California San Francisco, California, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California San Francisco, California, USA
| | - Peera Hemarajata
- Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - Nicole M Green
- Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - Alex Espinosa
- California Department of Public Health, Richmond, California, USA
| | - Chantha Kath
- California Department of Public Health, Richmond, California, USA
| | - Monica Haw
- California Department of Public Health, Richmond, California, USA
| | - John Bell
- California Department of Public Health, Richmond, California, USA
| | - Jill K Hacker
- California Department of Public Health, Richmond, California, USA
| | - Carl Hanson
- California Department of Public Health, Richmond, California, USA
| | - Debra A Wadford
- California Department of Public Health, Richmond, California, USA
| | - Carlos Anaya
- Monterey County Department of Public Health, Monterey, California, USA
| | - Donna Ferguson
- Monterey County Department of Public Health, Monterey, California, USA
| | - Liana F Lareau
- Department of Bioengineering, University of California Berkeley, Berkeley, California, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Phillip A Frankino
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Haridha Shivram
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Melanie Ott
- Department of Medicine, University of California San Francisco, California, USA
- Gladstone Institute of Virology, San Francisco, California, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California San Francisco, California, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, California, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, USA
- Department of Medicine, University of California San Francisco, California, USA
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
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6
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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.
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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
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7
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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.
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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.
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8
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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.
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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.
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9
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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.
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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
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10
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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.
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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
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11
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Balcerek J, Jiang J, Li Y, Jiang Q, Holdreith N, Singh B, Chandra V, Lv K, Ren JG, Rozenova K, Li W, Greenberg RA, Tong W. Lnk/Sh2b3 deficiency restores hematopoietic stem cell function and genome integrity in Fancd2 deficient Fanconi anemia. Nat Commun 2018; 9:3915. [PMID: 30254368 PMCID: PMC6156422 DOI: 10.1038/s41467-018-06380-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 06/30/2017] [Accepted: 09/03/2018] [Indexed: 12/20/2022] Open
Abstract
Fanconi anemia (FA) is a bone marrow failure (BMF) syndrome that arises from mutations in a network of FA genes essential for DNA interstrand crosslink (ICL) repair and replication stress tolerance. While allogeneic stem cell transplantation can replace defective HSCs, interventions to mitigate HSC defects in FA do not exist. Remarkably, we reveal here that Lnk (Sh2b3) deficiency restores HSC function in Fancd2−/− mice. Lnk deficiency does not impact ICL repair, but instead stabilizes stalled replication forks in a manner, in part, dependent upon alleviating blocks to cytokine−mediated JAK2 signaling. Lnk deficiency restores proliferation and survival of Fancd2−/− HSCs, while reducing replication stress and genomic instability. Furthermore, deletion of LNK in human FA-like HSCs promotes clonogenic growth. These findings highlight a new role for cytokine/JAK signaling in promoting replication fork stability, illuminate replication stress as a major underlying origin of BMF in FA, and have strong therapeutic implications. Loss of Fancd2 leads to replication stress intolerance and Fanconi Anemia, where haematopoietic stem cell (HSC) function is compromised. Here, the authors show that Lnk/Sh2b3 loss restores HSC proliferation and survival in Fancd2 knockout mice and ameliorates replication stress in a cytokine/JAK2 signaling dependent manner.
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Affiliation(s)
- Joanna Balcerek
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jing Jiang
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.,Institute of Translational Medicine, School of Medicine, Yangzhou University, 225001, Yangzhou, Jiangsu, China
| | - Yang Li
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qinqin Jiang
- Department of Cancer Biology, Abramson Cancer Research Institute and Basser Center for BRCA, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nicholas Holdreith
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Brijendra Singh
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Vemika Chandra
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kaosheng Lv
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jian-Gang Ren
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Krasimira Rozenova
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Weihua Li
- Department of Cancer Biology, Abramson Cancer Research Institute and Basser Center for BRCA, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Roger A Greenberg
- Department of Cancer Biology, Abramson Cancer Research Institute and Basser Center for BRCA, and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Wei Tong
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Tong W, Balcerek J, Jiang Q, Jiang J, Greenberg R. LNK(SH2B3) ameliorates hematopoietic stem and progenitor defects in fanconi anemia. Exp Hematol 2016. [DOI: 10.1016/j.exphem.2016.06.226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Wang W, Tang Y, Wang Y, Tascau L, Balcerek J, Tong W, Levine RL, Welch C, Tall AR, Wang N. LNK/SH2B3 Loss of Function Promotes Atherosclerosis and Thrombosis. Circ Res 2016; 119:e91-e103. [PMID: 27430239 DOI: 10.1161/circresaha.116.308955] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/15/2016] [Indexed: 01/01/2023]
Abstract
RATIONALE Human genome-wide association studies have revealed novel genetic loci that are associated with coronary heart disease. One such locus resides in LNK/SH2B3, which in mice is expressed in hematopoietic cells and suppresses thrombopoietin signaling via its receptor myeloproliferative leukemia virus oncogene. However, the mechanisms underlying the association of LNK single-nucleotide polymorphisms with coronary heart disease are poorly understood. OBJECTIVE To understand the functional effects of LNK single-nucleotide polymorphisms and explore the mechanisms whereby LNK loss of function impacts atherosclerosis and thrombosis. METHODS AND RESULTS Using human cord blood, we show that the common TT risk genotype (R262W) of LNK is associated with expansion of hematopoietic stem cells and enhanced megakaryopoiesis, demonstrating reduced LNK function and increased myeloproliferative leukemia virus oncogene signaling. In mice, hematopoietic Lnk deficiency leads to accelerated arterial thrombosis and atherosclerosis, but only in the setting of hypercholesterolemia. Hypercholesterolemia acts synergistically with LNK deficiency to increase interleukin 3/granulocyte-macrophage colony-stimulating factor receptor signaling in bone marrow myeloid progenitors, whereas in platelets cholesterol loading combines with Lnk deficiency to increase activation. Platelet LNK deficiency increases myeloproliferative leukemia virus oncogene signaling and AKT activation, whereas cholesterol loading decreases SHIP-1 phosphorylation, acting convergently to increase AKT and platelet activation. Together with increased myelopoiesis, platelet activation promotes prothrombotic and proatherogenic platelet/leukocyte aggregate formation. CONCLUSIONS LNK (R262W) is a loss-of-function variant that promotes thrombopoietin/myeloproliferative leukemia virus oncogene signaling and platelet and leukocyte production. In mice, LNK deficiency is associated with both increased platelet production and activation. Hypercholesterolemia acts in platelets and hematopoietic progenitors to exacerbate thrombosis and atherosclerosis associated with LNK deficiency.
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Affiliation(s)
- Wei Wang
- From the Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY (W.W., Y.T., Y.W., L.T., C.W., A.R.T., N.W.); Division of Hematology, Children's Hospital of Philadelphia, PA (W.T.); Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia (J.B., W.T.); and Human Oncology and Pathogenesis Program (R.L.L.) and Leukemia Service, Department of Medicine (R.L.L.), Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yang Tang
- From the Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY (W.W., Y.T., Y.W., L.T., C.W., A.R.T., N.W.); Division of Hematology, Children's Hospital of Philadelphia, PA (W.T.); Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia (J.B., W.T.); and Human Oncology and Pathogenesis Program (R.L.L.) and Leukemia Service, Department of Medicine (R.L.L.), Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Wang
- From the Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY (W.W., Y.T., Y.W., L.T., C.W., A.R.T., N.W.); Division of Hematology, Children's Hospital of Philadelphia, PA (W.T.); Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia (J.B., W.T.); and Human Oncology and Pathogenesis Program (R.L.L.) and Leukemia Service, Department of Medicine (R.L.L.), Memorial Sloan Kettering Cancer Center, New York, NY
| | - Liana Tascau
- From the Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY (W.W., Y.T., Y.W., L.T., C.W., A.R.T., N.W.); Division of Hematology, Children's Hospital of Philadelphia, PA (W.T.); Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia (J.B., W.T.); and Human Oncology and Pathogenesis Program (R.L.L.) and Leukemia Service, Department of Medicine (R.L.L.), Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joanna Balcerek
- From the Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY (W.W., Y.T., Y.W., L.T., C.W., A.R.T., N.W.); Division of Hematology, Children's Hospital of Philadelphia, PA (W.T.); Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia (J.B., W.T.); and Human Oncology and Pathogenesis Program (R.L.L.) and Leukemia Service, Department of Medicine (R.L.L.), Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wei Tong
- From the Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY (W.W., Y.T., Y.W., L.T., C.W., A.R.T., N.W.); Division of Hematology, Children's Hospital of Philadelphia, PA (W.T.); Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia (J.B., W.T.); and Human Oncology and Pathogenesis Program (R.L.L.) and Leukemia Service, Department of Medicine (R.L.L.), Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross L Levine
- From the Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY (W.W., Y.T., Y.W., L.T., C.W., A.R.T., N.W.); Division of Hematology, Children's Hospital of Philadelphia, PA (W.T.); Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia (J.B., W.T.); and Human Oncology and Pathogenesis Program (R.L.L.) and Leukemia Service, Department of Medicine (R.L.L.), Memorial Sloan Kettering Cancer Center, New York, NY
| | - Carrie Welch
- From the Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY (W.W., Y.T., Y.W., L.T., C.W., A.R.T., N.W.); Division of Hematology, Children's Hospital of Philadelphia, PA (W.T.); Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia (J.B., W.T.); and Human Oncology and Pathogenesis Program (R.L.L.) and Leukemia Service, Department of Medicine (R.L.L.), Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alan R Tall
- From the Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY (W.W., Y.T., Y.W., L.T., C.W., A.R.T., N.W.); Division of Hematology, Children's Hospital of Philadelphia, PA (W.T.); Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia (J.B., W.T.); and Human Oncology and Pathogenesis Program (R.L.L.) and Leukemia Service, Department of Medicine (R.L.L.), Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nan Wang
- From the Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY (W.W., Y.T., Y.W., L.T., C.W., A.R.T., N.W.); Division of Hematology, Children's Hospital of Philadelphia, PA (W.T.); Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia (J.B., W.T.); and Human Oncology and Pathogenesis Program (R.L.L.) and Leukemia Service, Department of Medicine (R.L.L.), Memorial Sloan Kettering Cancer Center, New York, NY.
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Abstract
Upon aging, the number of hematopoietic stem cells (HSCs) in the bone marrow increases while their repopulation potential declines. Moreover, aged HSCs exhibit lineage bias in reconstitution experiments with an inclination toward myeloid at the expense of lymphoid potential. The adaptor protein Lnk is an important negative regulator of HSC homeostasis, as Lnk deficiency is associated with a 10-fold increase in HSC numbers in young mice. However, the age-related increase in functional HSC numbers found in wild-type HSCs was not observed in Lnk-deficient animals. Importantly, HSCs from aged Lnk null mice possess greatly enhanced self-renewal capacity and diminished exhaustion, as evidenced by serial transplant experiments. In addition, Lnk deficiency ameliorates the aging-associated lineage bias. Transcriptome analysis revealed that WT and Lnk-deficient HSCs share many aging-related changes in gene expression patterns. Nonetheless, Lnk null HSCs displayed altered expression of components in select signaling pathways with potential involvement in HSC self-renewal and aging. Taken together, these results suggest that loss of Lnk partially mitigates age-related HSC alterations.
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Affiliation(s)
- Alexey Bersenev
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104-4318, USA
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Jiang J, Balcerek J, Rozenova K, Cheng Y, Bersenev A, Wu C, Song Y, Tong W. 14-3-3 regulates the LNK/JAK2 pathway in mouse hematopoietic stem and progenitor cells. J Clin Invest 2012; 122:2079-91. [PMID: 22546852 DOI: 10.1172/jci59719] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 03/09/2012] [Indexed: 11/17/2022] Open
Abstract
Hematopoietic stem and progenitor cell (HSPC) functions are governed by intricate signaling networks. The tyrosine kinase JAK2 plays an essential role in cytokine signaling during hematopoiesis. The adaptor protein LNK is a critical determinant of this process through its inhibitory interaction with JAK2, thereby limiting HSPC self-renewal. LNK deficiency promotes myeloproliferative neoplasm (MPN) development in mice, and LNK loss-of-function mutations are found in human MPNs, emphasizing its pivotal role in normal and malignant HSPCs. Here, we report the identification of 14-3-3 proteins as LNK binding partners. 14-3-3 interfered with the LNK-JAK2 interaction, thereby alleviating LNK inhibition of JAK2 signaling and cell proliferation. Binding of 14-3-3 required 2 previously unappreciated serine phosphorylation sites in LNK, and we found that their phosphorylation is mediated by glycogen synthase kinase 3 and PKA kinases. Mutations of these residues abrogated the interaction and augmented the growth inhibitory function of LNK. Conversely, forced 14-3-3 binding constrained LNK function. Furthermore, interaction with 14-3-3 sequestered LNK in the cytoplasm away from the plasma membrane-proximal JAK2. Importantly, bone marrow transplantation studies revealed an essential role for 14-3-3 in HSPC reconstitution that can be partially mitigated by LNK deficiency. We believe that, together, this work implicates 14-3-3 proteins as novel and positive HSPC regulators by impinging on the LNK/JAK2 pathway.
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Affiliation(s)
- Jing Jiang
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104-4318, USA
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16
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Bersenev A, Wu C, Balcerek J, Jing J, Kundu M, Blobel GA, Chikwava KR, Tong W. Lnk constrains myeloproliferative diseases in mice. J Clin Invest 2010; 120:2058-69. [PMID: 20458146 PMCID: PMC2877957 DOI: 10.1172/jci42032] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [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: 12/14/2009] [Accepted: 03/31/2010] [Indexed: 12/24/2022] Open
Abstract
Hematopoietic stem and progenitor cell (HSPC) expansion is regulated by intrinsic signaling pathways activated by cytokines. The intracellular kinase JAK2 plays an essential role in cytokine signaling, and activating mutations in JAK2 are found in a number of hematologic malignancies. We previously demonstrated that lymphocyte adaptor protein (Lnk, also known as Sh2b3) binds JAK2 and attenuates its activity, thereby limiting HSPC expansion. Here we show that loss of Lnk accelerates and exacerbates oncogenic JAK2-induced myeloproliferative diseases (MPDs) in mice. Specifically, Lnk deficiency enhanced cytokine-independent JAK/STAT signaling and augmented the ability of oncogenic JAK2 to expand myeloid progenitors in vitro and in vivo. An activated form of JAK2, unable to bind Lnk, caused greater myeloid expansion than activated JAK2 alone and accelerated myelofibrosis, indicating that Lnk directly inhibits oncogenic JAK2 in constraining MPD development. In addition, Lnk deficiency cooperated with the BCR/ABL oncogene, the product of which does not directly interact with or depend on JAK2 or Lnk, in chronic myeloid leukemia (CML) development, suggesting that Lnk also acts through endogenous pathways to constrain HSPCs. Consistent with this idea, aged Lnk-/- mice spontaneously developed a CML-like MPD. Taken together, our data establish Lnk as a bona fide suppressor of MPD in mice and raise the possibility that Lnk dysfunction contributes to the development of hematologic malignancies in humans.
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Affiliation(s)
- Alexey Bersenev
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
Department of Pathology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Chao Wu
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
Department of Pathology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joanna Balcerek
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
Department of Pathology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jiang Jing
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
Department of Pathology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Mondira Kundu
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
Department of Pathology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Gerd A. Blobel
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
Department of Pathology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kudakwashe R. Chikwava
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
Department of Pathology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wei Tong
- Division of Hematology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA.
Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA.
Department of Pathology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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Bersenev A, Wu C, Balcerek J, Tong W. Lnk controls mouse hematopoietic stem cell self-renewal and quiescence through direct interactions with JAK2. J Clin Invest 2008; 118:2832-44. [PMID: 18618018 DOI: 10.1172/jci35808] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2008] [Accepted: 05/27/2008] [Indexed: 12/22/2022] Open
Abstract
In addition to its role in megakaryocyte production, signaling initiated by thrombopoietin (TPO) activation of its receptor, myeloproliferative leukemia virus protooncogene (c-Mpl, or Mpl), controls HSC homeostasis and self-renewal. Under steady-state conditions, mice lacking the inhibitory adaptor protein Lnk harbor an expanded HSC pool with enhanced self-renewal. We found that HSCs from Lnk-/- mice have an increased quiescent fraction, decelerated cell cycle kinetics, and enhanced resistance to repeat treatments with cytoablative 5-fluorouracil in vivo compared with WT HSCs. We further provide genetic evidence demonstrating that Lnk controls HSC quiescence and self-renewal, predominantly through Mpl. Consistent with this observation, Lnk-/- HSCs displayed potentiated activation of JAK2 specifically in response to TPO. Biochemical experiments revealed that Lnk directly binds to phosphorylated tyrosine residues in JAK2 following TPO stimulation. Of note, the JAK2 V617F mutant, found at high frequencies in myeloproliferative diseases, retains the ability to bind Lnk. Therefore, we identified Lnk as a physiological negative regulator of JAK2 in stem cells and TPO/Mpl/JAK2/Lnk as a major regulatory pathway in controlling stem cell self-renewal and quiescence.
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Affiliation(s)
- Alexey Bersenev
- Division of Hematology, Children's Hospital of Philadelphia, Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104-4318, USA
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