Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response

Yariv Wine, Daniel R. Boutz, Jason J. Lavinder, Aleksandr E. Miklos, Randall A. Hughes, Kam Hon Hoi, Sang Taek Jung, Andrew P. Horton, Ellen M. Murrin, Andrew D. Ellington, Edward M. Marcotte, George Georgiou

Research output: Contribution to journalArticle

79 Citations (Scopus)

Abstract

We have developed and validated a methodology for determining the antibody composition of the polyclonal serum response after immunization. Pepsin-digested serum IgGs were subjected to standard antigen-affinity chromatography, and resulting elution, wash, and flow-through fractions were analyzed by bottom-up, liquid chromatography-high-resolution tandem mass spectrometry. Identification of individual monoclonal antibodies required the generation of a database of IgG variable gene (V-gene) sequences constructed by NextGen sequencing of mature B cells. Antibody V-gene sequences are characterized by short complementarity determining regions (CDRs) of high diversity adjacent to framework regions shared across thousands of IgGs, greatly complicating the identification of antigen-specific IgGs from proteomically observed peptides. By mapping peptides marking unique VH CDRH3 sequences, we identified a set of V-genes heavily enriched in the affinity chromatography elution, constituting the serum polyclonal response. After booster immunization in a rabbit, we find that the antigenspecific serum immune response is oligoclonal, comprising antibodies encoding 34 different CDRH3s that group into 30 distinct antibody VH clonotypes. Of these 34 CDRH3s, 12 account for ∼60% of the antigen-specific CDRH3 peptide mass spectral counts. For comparison, antibodies with 18 different CDRH3s (12 clonotypes) were represented in the antigen-specific IgG fraction from an unimmunized rabbit that fortuitously displayed a moderate titer for BSA. Proteomically identified antibodies were synthesized and shown to display subnanomolar affinities. The ability to deconvolute the polyclonal serum response is likely to be of key importance for analyzing antibody responses after vaccination and for more completely understanding adaptive immune responses in health and disease.

Original languageEnglish
Pages (from-to)2993-2998
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume110
Issue number8
DOIs
Publication statusPublished - 2013 Feb 19
Externally publishedYes

Fingerprint

Monoclonal Antibodies
Antibodies
Serum
Antigens
Affinity Chromatography
Immunoglobulin G
Genes
Rabbits
Complementarity Determining Regions
Secondary Immunization
Peptides
Peptide Mapping
Pepsin A
Adaptive Immunity
Tandem Mass Spectrometry
Liquid Chromatography
Antibody Formation
Immune Sera
Immunization
Vaccination

Keywords

  • Antibody proteomics
  • Antibody repertoire
  • B-cell response
  • Humoral response
  • Serum immunoprofiling

ASJC Scopus subject areas

  • General

Cite this

Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response. / Wine, Yariv; Boutz, Daniel R.; Lavinder, Jason J.; Miklos, Aleksandr E.; Hughes, Randall A.; Hoi, Kam Hon; Jung, Sang Taek; Horton, Andrew P.; Murrin, Ellen M.; Ellington, Andrew D.; Marcotte, Edward M.; Georgiou, George.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 110, No. 8, 19.02.2013, p. 2993-2998.

Research output: Contribution to journalArticle

Wine, Y, Boutz, DR, Lavinder, JJ, Miklos, AE, Hughes, RA, Hoi, KH, Jung, ST, Horton, AP, Murrin, EM, Ellington, AD, Marcotte, EM & Georgiou, G 2013, 'Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response', Proceedings of the National Academy of Sciences of the United States of America, vol. 110, no. 8, pp. 2993-2998. https://doi.org/10.1073/pnas.1213737110
Wine, Yariv ; Boutz, Daniel R. ; Lavinder, Jason J. ; Miklos, Aleksandr E. ; Hughes, Randall A. ; Hoi, Kam Hon ; Jung, Sang Taek ; Horton, Andrew P. ; Murrin, Ellen M. ; Ellington, Andrew D. ; Marcotte, Edward M. ; Georgiou, George. / Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response. In: Proceedings of the National Academy of Sciences of the United States of America. 2013 ; Vol. 110, No. 8. pp. 2993-2998.
@article{92dbba81921a4cc09eeb2c2fd9d04a4c,
title = "Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response",
abstract = "We have developed and validated a methodology for determining the antibody composition of the polyclonal serum response after immunization. Pepsin-digested serum IgGs were subjected to standard antigen-affinity chromatography, and resulting elution, wash, and flow-through fractions were analyzed by bottom-up, liquid chromatography-high-resolution tandem mass spectrometry. Identification of individual monoclonal antibodies required the generation of a database of IgG variable gene (V-gene) sequences constructed by NextGen sequencing of mature B cells. Antibody V-gene sequences are characterized by short complementarity determining regions (CDRs) of high diversity adjacent to framework regions shared across thousands of IgGs, greatly complicating the identification of antigen-specific IgGs from proteomically observed peptides. By mapping peptides marking unique VH CDRH3 sequences, we identified a set of V-genes heavily enriched in the affinity chromatography elution, constituting the serum polyclonal response. After booster immunization in a rabbit, we find that the antigenspecific serum immune response is oligoclonal, comprising antibodies encoding 34 different CDRH3s that group into 30 distinct antibody VH clonotypes. Of these 34 CDRH3s, 12 account for ∼60{\%} of the antigen-specific CDRH3 peptide mass spectral counts. For comparison, antibodies with 18 different CDRH3s (12 clonotypes) were represented in the antigen-specific IgG fraction from an unimmunized rabbit that fortuitously displayed a moderate titer for BSA. Proteomically identified antibodies were synthesized and shown to display subnanomolar affinities. The ability to deconvolute the polyclonal serum response is likely to be of key importance for analyzing antibody responses after vaccination and for more completely understanding adaptive immune responses in health and disease.",
keywords = "Antibody proteomics, Antibody repertoire, B-cell response, Humoral response, Serum immunoprofiling",
author = "Yariv Wine and Boutz, {Daniel R.} and Lavinder, {Jason J.} and Miklos, {Aleksandr E.} and Hughes, {Randall A.} and Hoi, {Kam Hon} and Jung, {Sang Taek} and Horton, {Andrew P.} and Murrin, {Ellen M.} and Ellington, {Andrew D.} and Marcotte, {Edward M.} and George Georgiou",
year = "2013",
month = "2",
day = "19",
doi = "10.1073/pnas.1213737110",
language = "English",
volume = "110",
pages = "2993--2998",
journal = "Proceedings of the National Academy of Sciences of the United States of America",
issn = "0027-8424",
number = "8",

}

TY - JOUR

T1 - Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response

AU - Wine, Yariv

AU - Boutz, Daniel R.

AU - Lavinder, Jason J.

AU - Miklos, Aleksandr E.

AU - Hughes, Randall A.

AU - Hoi, Kam Hon

AU - Jung, Sang Taek

AU - Horton, Andrew P.

AU - Murrin, Ellen M.

AU - Ellington, Andrew D.

AU - Marcotte, Edward M.

AU - Georgiou, George

PY - 2013/2/19

Y1 - 2013/2/19

N2 - We have developed and validated a methodology for determining the antibody composition of the polyclonal serum response after immunization. Pepsin-digested serum IgGs were subjected to standard antigen-affinity chromatography, and resulting elution, wash, and flow-through fractions were analyzed by bottom-up, liquid chromatography-high-resolution tandem mass spectrometry. Identification of individual monoclonal antibodies required the generation of a database of IgG variable gene (V-gene) sequences constructed by NextGen sequencing of mature B cells. Antibody V-gene sequences are characterized by short complementarity determining regions (CDRs) of high diversity adjacent to framework regions shared across thousands of IgGs, greatly complicating the identification of antigen-specific IgGs from proteomically observed peptides. By mapping peptides marking unique VH CDRH3 sequences, we identified a set of V-genes heavily enriched in the affinity chromatography elution, constituting the serum polyclonal response. After booster immunization in a rabbit, we find that the antigenspecific serum immune response is oligoclonal, comprising antibodies encoding 34 different CDRH3s that group into 30 distinct antibody VH clonotypes. Of these 34 CDRH3s, 12 account for ∼60% of the antigen-specific CDRH3 peptide mass spectral counts. For comparison, antibodies with 18 different CDRH3s (12 clonotypes) were represented in the antigen-specific IgG fraction from an unimmunized rabbit that fortuitously displayed a moderate titer for BSA. Proteomically identified antibodies were synthesized and shown to display subnanomolar affinities. The ability to deconvolute the polyclonal serum response is likely to be of key importance for analyzing antibody responses after vaccination and for more completely understanding adaptive immune responses in health and disease.

AB - We have developed and validated a methodology for determining the antibody composition of the polyclonal serum response after immunization. Pepsin-digested serum IgGs were subjected to standard antigen-affinity chromatography, and resulting elution, wash, and flow-through fractions were analyzed by bottom-up, liquid chromatography-high-resolution tandem mass spectrometry. Identification of individual monoclonal antibodies required the generation of a database of IgG variable gene (V-gene) sequences constructed by NextGen sequencing of mature B cells. Antibody V-gene sequences are characterized by short complementarity determining regions (CDRs) of high diversity adjacent to framework regions shared across thousands of IgGs, greatly complicating the identification of antigen-specific IgGs from proteomically observed peptides. By mapping peptides marking unique VH CDRH3 sequences, we identified a set of V-genes heavily enriched in the affinity chromatography elution, constituting the serum polyclonal response. After booster immunization in a rabbit, we find that the antigenspecific serum immune response is oligoclonal, comprising antibodies encoding 34 different CDRH3s that group into 30 distinct antibody VH clonotypes. Of these 34 CDRH3s, 12 account for ∼60% of the antigen-specific CDRH3 peptide mass spectral counts. For comparison, antibodies with 18 different CDRH3s (12 clonotypes) were represented in the antigen-specific IgG fraction from an unimmunized rabbit that fortuitously displayed a moderate titer for BSA. Proteomically identified antibodies were synthesized and shown to display subnanomolar affinities. The ability to deconvolute the polyclonal serum response is likely to be of key importance for analyzing antibody responses after vaccination and for more completely understanding adaptive immune responses in health and disease.

KW - Antibody proteomics

KW - Antibody repertoire

KW - B-cell response

KW - Humoral response

KW - Serum immunoprofiling

UR - http://www.scopus.com/inward/record.url?scp=84874223925&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84874223925&partnerID=8YFLogxK

U2 - 10.1073/pnas.1213737110

DO - 10.1073/pnas.1213737110

M3 - Article

VL - 110

SP - 2993

EP - 2998

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

SN - 0027-8424

IS - 8

ER -