Abstract
Dissecting the evolution of memory B cells (MBCs) against SARS-CoV-2 is critical for understanding antibody recall upon secondary exposure. Here, we used single-cell sequencing to profile SARS-CoV-2-reactive B cells in 38 COVID-19 patients. Using oligo-tagged antigen baits, we isolated B cells specific to the SARS-CoV-2 spike, nucleoprotein (NP), open reading frame 8 (ORF8), and endemic human coronavirus (HCoV) spike proteins. SARS-CoV-2 spike-specific cells were enriched in the memory compartment of acutely infected and convalescent patients several months post symptom onset. With severe acute infection, substantial populations of endemic HCoV-reactive antibody-secreting cells were identified and possessed highly mutated variable genes, signifying preexisting immunity. Finally, MBCs exhibited pronounced maturation to NP and ORF8 over time, especially in older patients. Monoclonal antibodies against these targets were non-neutralizing and non-protective in vivo. These findings reveal antibody adaptation to non-neutralizing intracellular antigens during infection, emphasizing the importance of vaccination for inducing neutralizing spike-specific MBCs.
| Original language | English |
|---|---|
| Pages (from-to) | 1290-1303.e7 |
| Journal | Immunity |
| Volume | 54 |
| Issue number | 6 |
| DOIs | |
| State | Published - Jun 8 2021 |
Keywords
- COVID-19
- ORF8
- RNA sequencing
- SARS-CoV-2
- antibody
- immunodominance
- memory B cell
- nucleoprotein
- preexisting immunity
- spike
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In: Immunity, Vol. 54, No. 6, 08.06.2021, p. 1290-1303.e7.
Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - Profiling B cell immunodominance after SARS-CoV-2 infection reveals antibody evolution to non-neutralizing viral targets
AU - Dugan, Haley L.
AU - Stamper, Christopher T.
AU - Li, Lei
AU - Changrob, Siriruk
AU - Asby, Nicholas W.
AU - Halfmann, Peter J.
AU - Zheng, Nai Ying
AU - Huang, Min
AU - Shaw, Dustin G.
AU - Cobb, Mari S.
AU - Erickson, Steven A.
AU - Guthmiller, Jenna J.
AU - Stovicek, Olivia
AU - Wang, Jiaolong
AU - Winkler, Emma S.
AU - Madariaga, Maria Lucia
AU - Shanmugarajah, Kumaran
AU - Jansen, Maud O.
AU - Amanat, Fatima
AU - Stewart, Isabelle
AU - Utset, Henry A.
AU - Huang, Jun
AU - Nelson, Christopher A.
AU - Dai, Ya Nan
AU - Hall, Paige D.
AU - Jedrzejczak, Robert P.
AU - Joachimiak, Andrzej
AU - Krammer, Florian
AU - Diamond, Michael S.
AU - Fremont, Daved H.
AU - Kawaoka, Yoshihiro
AU - Wilson, Patrick C.
N1 - Funding Information: The University of Chicago has filed a patent application relating to anti-SARS-CoV-2 antibodies generated in this work, with P.C.W., H.L.D., and C.T.S. as co-inventors. Several antibodies generated from this work are being used by Now Diagnostics (Springdale, Arkansas) for the development of a diagnostic test. M.S.D. is a consultant for Inbios, Vir Biotechnology, NGM Biopharmaceuticals, and Carnival Corporation and is on the scientific advisory boards of Moderna and Immunome. The Diamond laboratory has received funding support in sponsored research agreements from Moderna, Vir Biotechnology, and Emergent BioSolutions. The Icahn School of Medicine at Mount Sinai has filed patent applications relating to SARS-CoV-2 serological assays and NDV-based SARS-CoV-2 vaccines that list F.K. as co-inventor. Mount Sinai has spun out a company, Kantaro, to market serological tests for SARS-CoV-2. F.K. has consulted for Merck and Pfizer (before 2020) and is currently consulting for Pfizer, Seqirus, and Avimex. The Krammer laboratory is also collaborating with Pfizer on animal models of SARS-CoV-2. Funding Information: This project was funded in part by the National Institute of Allergy and Infectious Diseases (NIAID); National Institutes of Health (NIH) grant numbers U19AI082724 (P.C.W.), U19AI109946 (P.C.W.), and U19AI057266 (P.C.W.); and NIAID Centers of Excellence for Influenza Research and Surveillance (CEIRS) grant HHSN272201400005C (P.C.W.). N.W.A. was supported by the Multi-disciplinary Training program in Cancer Research (MTCR) (NIH grant T32 CA009594). A.J. and R.P.J. were supported by federal funds from NIAID, NIH, and the U.S. Department of Health and Human Services under contract HHSN272201700060C. F.K. and F.A. were funded by NIAID CEIRS contract HHSN272201400008C and Collaborative Influenza Vaccine Innovation Centers (CIVIC) contract 75N93019C00051 and the generous support of the JPB Foundation, the Open Philanthropy Project (2020-215611), and other philanthropic donations. Y.K. and P.J.H. were funded by the Research Program on Emerging and Re-emerging Infectious Disease grant (JP19fk0108113) and the Japan Program for Infectious Diseases Research and Infrastructure (JP20fk0108272) of the Japan Agency for Medical Research and Development (AMED), NIAID CEIRS contract HHSN272201400008C, and CIVIC contract 75N93019C00051. D.H.F. C.A.N. Y.-N.D. and P.D.H. were supported by NIAID contracts HHSN272201700060C and 75N93019C00062. M.S.D. and E.S.W. were supported by NIH grants R01 AI157155 and F30 AI152327, respectively. We kindly thank the University of Chicago CAT Facility (RRID: SCR_017760) for their assistance and allowing us to use their facilities. We thank Dr. Nicholas Chevrier for allowing us to use the Pritzker School of Molecular Engineering's sequencing facility. We are thankful to the University of Chicago Genomics Facility (RRID: SCR_019196) for their assistance with sequencing several samples. We thank John Bivona and the staff of the Howard Taylor Ricketts Laboratory for prompt training in BSL-3 practices and procedures and for use of their facilities for severe acute infected sample collection. Last, we are appreciative of the patients who donated samples for our research purposes. The Graphical abstract was created with Biorender.com. H.L.D. and C.T.S. collected samples, designed and performed experiments; generated VDJ, 5? transcriptome, and feature libraries; performed Illumina sequencing; analyzed the data; and wrote the manuscript. L.L. performed computational analyses of single-cell data and wrote the manuscript. S.C. collected samples, performed the sorting of severe acute infected subjects and Illumina sequencing, performed ELISAs, and expressed recombinant SARS-CoV-2 proteins. N.W.A. generated VDJ, 5? transcriptome, and feature libraries and performed Illumina sequencing. P.J.H. performed virus neutralization and in vivo protection assays with mAbs. N.-Y.Z. collected samples, expressed recombinant SARS-CoV-2 proteins, and generated mAbs. M.H. performed mAb cloning. D.G.S. and M.S.C. collected severe acute infected samples. S.A.E. performed sorting of severe acute infected subjects. J.J.G. collected samples, performed serum ELISAs, and generated the infection severity scoring system. O.S. and J.W. performed serum ELISAs. J.W. assisted in mAb generation. E.S.W. performed ORF8 mAb protection studies in mice. M.L.M. K.S. and M.O.J. coordinated the convalescent COVID-19 clinical study and collected patient samples. I.S. performed ELISAs. H.A.U. collected samples and expressed recombinant SARS-CoV-2 proteins. J.H. provided funding and resources for N.W.A. to perform sequencing. F.A. C.A.N. Y.-N.D. P.D.H. D.H.F. R.P.J. A.J. and F.K. provided recombinant SARS-CoV-2 proteins. E.S.W. M.S.D. and Y.K. performed and analyzed mAb neutralization and in vivo protection data. P.C.W. supervised the work, analyzed the data, and wrote the manuscript. The University of Chicago has filed a patent application relating to anti-SARS-CoV-2 antibodies generated in this work, with P.C.W. H.L.D. and C.T.S. as co-inventors. Several antibodies generated from this work are being used by Now Diagnostics (Springdale, Arkansas) for the development of a diagnostic test. M.S.D. is a consultant for Inbios, Vir Biotechnology, NGM Biopharmaceuticals, and Carnival Corporation and is on the scientific advisory boards of Moderna and Immunome. The Diamond laboratory has received funding support in sponsored research agreements from Moderna, Vir Biotechnology, and Emergent BioSolutions. The Icahn School of Medicine at Mount Sinai has filed patent applications relating to SARS-CoV-2 serological assays and NDV-based SARS-CoV-2 vaccines that list F.K. as co-inventor. Mount Sinai has spun out a company, Kantaro, to market serological tests for SARS-CoV-2. F.K. has consulted for Merck and Pfizer (before 2020) and is currently consulting for Pfizer, Seqirus, and Avimex. The Krammer laboratory is also collaborating with Pfizer on animal models of SARS-CoV-2. Funding Information: This project was funded in part by the National Institute of Allergy and Infectious Diseases (NIAID); National Institutes of Health (NIH) grant numbers U19AI082724 (P.C.W.), U19AI109946 (P.C.W.), and U19AI057266 (P.C.W.); and NIAID Centers of Excellence for Influenza Research and Surveillance (CEIRS) grant HHSN272201400005C (P.C.W.). N.W.A. was supported by the Multi-disciplinary Training program in Cancer Research (MTCR) ( NIH grant T32 CA009594 ). A.J. and R.P.J. were supported by federal funds from NIAID, NIH , and the U.S. Department of Health and Human Services under contract HHSN272201700060C . F.K. and F.A. were funded by NIAID CEIRS contract HHSN272201400008C and Collaborative Influenza Vaccine Innovation Centers (CIVIC) contract 75N93019C00051 and the generous support of the JPB Foundation , the Open Philanthropy Project ( 2020-215611 ), and other philanthropic donations. Y.K. and P.J.H. were funded by the Research Program on Emerging and Re-emerging Infectious Disease grant ( JP19fk0108113 ) and the Japan Program for Infectious Diseases Research and Infrastructure ( JP20fk0108272 ) of the Japan Agency for Medical Research and Development (AMED), NIAID CEIRS contract HHSN272201400008C , and CIVIC contract 75N93019C00051 . D.H.F., C.A.N., Y.-N.D., and P.D.H. were supported by NIAID contracts HHSN272201700060C and 75N93019C00062 . M.S.D. and E.S.W. were supported by NIH grants R01 AI157155 and F30 AI152327 , respectively. We kindly thank the University of Chicago CAT Facility (RRID: SCR_017760 ) for their assistance and allowing us to use their facilities. We thank Dr. Nicholas Chevrier for allowing us to use the Pritzker School of Molecular Engineering’s sequencing facility. We are thankful to the University of Chicago Genomics Facility (RRID: SCR_019196 ) for their assistance with sequencing several samples. We thank John Bivona and the staff of the Howard Taylor Ricketts Laboratory for prompt training in BSL-3 practices and procedures and for use of their facilities for severe acute infected sample collection. Last, we are appreciative of the patients who donated samples for our research purposes. The Graphical abstract was created with Biorender.com . Publisher Copyright: © 2021 Elsevier Inc.
PY - 2021/6/8
Y1 - 2021/6/8
N2 - Dissecting the evolution of memory B cells (MBCs) against SARS-CoV-2 is critical for understanding antibody recall upon secondary exposure. Here, we used single-cell sequencing to profile SARS-CoV-2-reactive B cells in 38 COVID-19 patients. Using oligo-tagged antigen baits, we isolated B cells specific to the SARS-CoV-2 spike, nucleoprotein (NP), open reading frame 8 (ORF8), and endemic human coronavirus (HCoV) spike proteins. SARS-CoV-2 spike-specific cells were enriched in the memory compartment of acutely infected and convalescent patients several months post symptom onset. With severe acute infection, substantial populations of endemic HCoV-reactive antibody-secreting cells were identified and possessed highly mutated variable genes, signifying preexisting immunity. Finally, MBCs exhibited pronounced maturation to NP and ORF8 over time, especially in older patients. Monoclonal antibodies against these targets were non-neutralizing and non-protective in vivo. These findings reveal antibody adaptation to non-neutralizing intracellular antigens during infection, emphasizing the importance of vaccination for inducing neutralizing spike-specific MBCs.
AB - Dissecting the evolution of memory B cells (MBCs) against SARS-CoV-2 is critical for understanding antibody recall upon secondary exposure. Here, we used single-cell sequencing to profile SARS-CoV-2-reactive B cells in 38 COVID-19 patients. Using oligo-tagged antigen baits, we isolated B cells specific to the SARS-CoV-2 spike, nucleoprotein (NP), open reading frame 8 (ORF8), and endemic human coronavirus (HCoV) spike proteins. SARS-CoV-2 spike-specific cells were enriched in the memory compartment of acutely infected and convalescent patients several months post symptom onset. With severe acute infection, substantial populations of endemic HCoV-reactive antibody-secreting cells were identified and possessed highly mutated variable genes, signifying preexisting immunity. Finally, MBCs exhibited pronounced maturation to NP and ORF8 over time, especially in older patients. Monoclonal antibodies against these targets were non-neutralizing and non-protective in vivo. These findings reveal antibody adaptation to non-neutralizing intracellular antigens during infection, emphasizing the importance of vaccination for inducing neutralizing spike-specific MBCs.
KW - COVID-19
KW - ORF8
KW - RNA sequencing
KW - SARS-CoV-2
KW - antibody
KW - immunodominance
KW - memory B cell
KW - nucleoprotein
KW - preexisting immunity
KW - spike
UR - http://www.scopus.com/inward/record.url?scp=85106533643&partnerID=8YFLogxK
U2 - 10.1016/j.immuni.2021.05.001
DO - 10.1016/j.immuni.2021.05.001
M3 - Article
C2 - 34022127
AN - SCOPUS:85106533643
SN - 1074-7613
VL - 54
SP - 1290-1303.e7
JO - Immunity
JF - Immunity
IS - 6
ER -