Human plasma IgG1 repertoires are simple, unique, and dynamic
Bondt, Albert; Hoek, Max; Tamara, Sem; de Graaf, Bastiaan; Peng, Weiwei; Schulte, Douwe; van Rijswijck, Danique M H; den Boer, Maurits A; Greisch, Jean-François; Varkila, Meri R J; Snijder, Joost; Cremer, Olaf L; Bonten, Marc J M; Heck, Albert J R
(2021) Cell Systems, volume 12, issue 12, pp. 1131 - 1143.e5
(Article)
Abstract
Although humans can produce billions of IgG1 variants through recombination and hypermutation, the diversity of IgG1 clones circulating in human blood plasma has largely eluded direct characterization. Here, we combined several mass-spectrometry-based approaches to reveal that the circulating IgG1 repertoire in human plasma is dominated by a limited number of
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clones in healthy donors and septic patients. We observe that each individual donor exhibits a unique serological IgG1 repertoire, which remains stable over time but can adapt rapidly to changes in physiology. We introduce an integrative protein- and peptide-centric approach to obtain and validate a full sequence of an individual plasma IgG1 clone de novo. This IgG1 clone emerged at the onset of a septic episode and exhibited a high mutation rate (13%) compared with the closest matching germline DNA sequence, highlighting the importance of de novo sequencing at the protein level. A record of this paper's transparent peer review process is included in the supplemental information.
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Keywords: Fab profiling, IgG, LC-MS, antibodies, de novo sequencing, immunoglobulins, mass spectrometry, sepsis, serology, top-down proteomics, Pathology and Forensic Medicine, Histology, Cell Biology
ISSN: 2405-4712
Publisher: Cell Press
Note: Funding Information: This research received funding through the Netherlands Organization for Scientific Research ( NWO ) through the ENPPS.LIFT.019.001 project (A.J.R.H. and J.F.G.), the NACTAR project 16442 (A.J.R.H. and M.A.d.B.), Gravitation Subgrant 00022 from the Institute for Chemical Immunology (A.B., D.M.H.v.R., W.P., D.S., and J.S.), and the Spinoza award SPI.2017.028 to A.J.R.H. This project received additional funding from the European Union’s Horizon 2020 research and innovation program under the grant agreement 686547 (EPIC-XS) for A.J.R.H. We kindly acknowledge the teams of Janine Schuurman, Frank Beurskens, and Boris Bleijlevens (Genmab, Utrecht, NL) for continuous support over the years, stimulating discussions, financial co-support for A.B. and S.T., and the generation of the recombinant clone based on the sequence of the plasma clone 24.4 1 47,359.4 . We thank Dietmar Reusch and Markus Haberger (Roche, Penzberg) for the kind donation of trastuzumab. Funding Information: This research received funding through the Netherlands Organization for Scientific Research (NWO) through the ENPPS.LIFT.019.001 project (A.J.R.H. and J.F.G.), the NACTAR project 16442 (A.J.R.H. and M.A.d.B.), Gravitation Subgrant 00022 from the Institute for Chemical Immunology (A.B. D.M.H.v.R. W.P. D.S. and J.S.), and the Spinoza award SPI.2017.028 to A.J.R.H. This project received additional funding from the European Union's Horizon 2020 research and innovation program under the grant agreement 686547 (EPIC-XS) for A.J.R.H. We kindly acknowledge the teams of Janine Schuurman, Frank Beurskens, and Boris Bleijlevens (Genmab, Utrecht, NL) for continuous support over the years, stimulating discussions, financial co-support for A.B. and S.T. and the generation of the recombinant clone based on the sequence of the plasma clone 24.4 1 47,359.4. We thank Dietmar Reusch and Markus Haberger (Roche, Penzberg) for the kind donation of trastuzumab. A.J.R.H. conceived the idea for this study. A.B. S.T. and A.J.R.H. designed the research, planned the experiments, and supervised the project. A.B. M.H. M.A.d.B. and D.M.H.v.R. performed the IgG capture from serum and subsequent generation of Fabs, subsequently analyzed by intact LC-MS. M.H. developed the repertoire profiling bioinformatics workflow. S.T. performed the middle-down MS/MS analysis of the clones and generated the bioinformatics workflow to analyze the data. W.P. M.H. D.S. and J.S. performed all bottom-up proteomics experiments and subsequent data analysis. J.-F.G. and B.d.G. contributed to study design and data analysis. M.V. M.J.M.B. and O.L.C. provided the MARS cohort samples and selected the patient population used in this study. A.B. M.H. S.T. and A.J.R.H. wrote the original draft, which was read, improved, and approved by all co-authors. The authors declare no competing interests. Publisher Copyright: © 2021 The Author(s)
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