Single amino acid fingerprinting of the human antibody repertoire with high density peptide arrays.
The antibody species that patrol in a patient's blood are an invaluable part of the immune system. While most of them shield us from life-threatening infections, some of them do harm in autoimmune diseases. If we knew exactly all the antigens that elicited all the antibody species within a group of patients, we could learn which ones correlate with immune protection, are irrelevant, or do harm. Here, we demonstrate an approach to this question: First, we use a plethora of phage-displayed peptides to identify many different serum antibody binding peptides. Next, we synthesize identified peptides in the array format and rescreen the serum used for phage panning to validate antibody binding peptides. Finally, we systematically vary the sequence of validated antibody binding peptides to identify those amino acids within the peptides that are crucial for binding "their" antibody species. The resulting immune fingerprints can then be used to trace them back to potential antigens. We investigated the serum of an individual in this pipeline, which led to the identification of 73 antibody fingerprints. Some fingerprints could be traced back to their most likely antigen, for example the immunodominant capsid protein VP1 of enteroviruses, most likely elicited by the ubiquitous poliovirus vaccination. Thus, with our approach, it is possible, to pinpoint those antibody species that correlate with a certain antigen, without any pre-information. This can help to unravel hitherto enigmatic diseases.
Karlsruhe Institute of Technology, Institute of Microstructure Technology (IMT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
Laura K
LK
Weber
Karlsruhe Institute of Technology, Institute of Microstructure Technology (IMT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
Andrea
A
Palermo
Yumab GmbH, Rebenring 33, 38106 Braunschweig, Germany.
Jonas
J
Kügler
Karlsruhe Institute of Technology, Institute of Toxicology and Genetics (ITG), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
Olivier
O
Armant
Karlsruhe Institute of Technology, Institute of Microstructure Technology (IMT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
Awale
A
Isse
Karlsruhe Institute of Technology, Institute of Microstructure Technology (IMT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
Simone
S
Rentschler
Heidelberg University Hospital, Department for Infectious Diseases, Parasitology Unit, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany; German Centre for Infection Research (DZIF), partner site Heidelberg, Germany; HEiKA - Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Germany.
Thomas
T
Jaenisch
Karlsruhe Institute of Technology, Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Engler-Bunte Ring 3, 76131 Karlsruhe, Germany.
Jürgen
J
Hubbuch
Technische Universität Braunschweig, Department of Biotechnology, Institute for Biochemistry and Biotechnology, Spielmannstr. 7, 38106 Braunschweig, Germany.
Stefan
S
Dübel
Karlsruhe Institute of Technology, Institute of Microstructure Technology (IMT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. Electronic address: alexander.nesterov-mueller@kit.edu.
Alexander
A
Nesterov-Mueller
Karlsruhe Institute of Technology, Institute of Microstructure Technology (IMT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. Electronic address: frank.breitling@kit.edu.
Frank
F
Breitling
Karlsruhe Institute of Technology, Institute of Microstructure Technology (IMT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; HEiKA - Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Germany; Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Am Mühlenberg 1, 14476 Potsdam, Germany. Electronic address: felix.loeffler@mpikg.mpg.de.
Felix F
FF
Loeffler
D000595:Amino Acid Sequence; D000906:Antibodies / Q000097:blood / Q000276:immunology*; D000914:Antibodies, Viral / Q000097:blood / Q000276:immunology; D000918:Antibody Specificity; D000941:Antigens / Q000097:blood / Q000737:chemistry* / Q000235:genetics / Q000276:immunology*; D001666:Binding Sites, Antibody; D036022:Capsid Proteins / Q000276:immunology; D061505:Cell Surface Display Techniques; D019295:Computational Biology; D004770:Enterovirus / Q000276:immunology; D057166:High-Throughput Screening Assays; D006801:Humans; D056724:Immunity, Humoral; D010449:Peptide Mapping / Q000379:methods*; D023321:Poliovirus Vaccines / Q000008:administration & dosage / Q000276:immunology; D012698:Serologic Tests; D014611:Vaccination
D000906:Antibodies; D000914:Antibodies, Viral; D000941:Antigens; D036022:Capsid Proteins; D023321:Poliovirus Vaccines
Humoral immune system; Next generation sequencing; Phage display; Serology; Substitution analysis