1
|
Jappe EC, Garde C, Ramarathinam SH, Passantino E, Illing PT, Mifsud NA, Trolle T, Kringelum JV, Croft NP, Purcell AW. Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and aid for immunotherapy design. Nat Commun 2020; 11:6305. [PMID: 33298915 PMCID: PMC7726561 DOI: 10.1038/s41467-020-20166-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
The features of peptide antigens that contribute to their immunogenicity are not well understood. Although the stability of peptide-MHC (pMHC) is known to be important, current assays assess this interaction only for peptides in isolation and not in the context of natural antigen processing and presentation. Here, we present a method that provides a comprehensive and unbiased measure of pMHC stability for thousands of individual ligands detected simultaneously by mass spectrometry (MS). The method allows rapid assessment of intra-allelic and inter-allelic differences in pMHC stability and reveals profiles of stability that are broader than previously appreciated. The additional dimensionality of the data facilitated the training of a model which improves the prediction of peptide immunogenicity, specifically of cancer neoepitopes. This assay can be applied to any cells bearing MHC or MHC-like molecules, offering insight into not only the endogenous immunopeptidome, but also that of neoepitopes and pathogen-derived sequences.
Collapse
Affiliation(s)
- Emma C Jappe
- Evaxion Biotech, Bredgade 34E, 1260, Copenhagen, Denmark
- Department of Health Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | | | - Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ethan Passantino
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Patricia T Illing
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Nicole A Mifsud
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Thomas Trolle
- Evaxion Biotech, Bredgade 34E, 1260, Copenhagen, Denmark
| | | | - Nathan P Croft
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
| |
Collapse
|
2
|
Garde C, Ramarathinam SH, Jappe EC, Nielsen M, Kringelum JV, Trolle T, Purcell AW. Improved peptide-MHC class II interaction prediction through integration of eluted ligand and peptide affinity data. Immunogenetics 2019; 71:445-454. [PMID: 31183519 DOI: 10.1007/s00251-019-01122-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 04/12/2019] [Accepted: 05/31/2019] [Indexed: 01/17/2023]
Abstract
Major histocompatibility complex (MHC) class II antigen presentation is a key component in eliciting a CD4+ T cell response. Precise prediction of peptide-MHC (pMHC) interactions has thus become a cornerstone in defining epitope candidates for rational vaccine design. Current pMHC prediction tools have, so far, primarily focused on inference from in vitro binding affinity. In the current study, we collate a large set of MHC class II eluted ligands generated by mass spectrometry to guide the prediction of MHC class II antigen presentation. We demonstrate that models developed on eluted ligands outperform those developed on pMHC binding affinity data. The predictive performance can be further enhanced by combining the eluted ligand and pMHC affinity data in a single prediction model. Furthermore, by including ligand data, the peptide length preference of MHC class II can be accurately learned by the prediction model. Finally, we demonstrate that our model significantly outperforms the current state-of-the-art prediction method, NetMHCIIpan, on an external dataset of eluted ligands and appears superior in identifying CD4+ T cell epitopes.
Collapse
Affiliation(s)
- Christian Garde
- Evaxion Biotech, Bredgade 34E, DK-1260, Copenhagen, Denmark.
| | - Sri H Ramarathinam
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Emma C Jappe
- Evaxion Biotech, Bredgade 34E, DK-1260, Copenhagen, Denmark.,Department of Bio and Health Informatics, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, DK-2800, Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | | | - Thomas Trolle
- Evaxion Biotech, Bredgade 34E, DK-1260, Copenhagen, Denmark
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology & Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia.
| |
Collapse
|
3
|
Engmark M, Andersen MR, Laustsen AH, Patel J, Sullivan E, de Masi F, Hansen CS, Kringelum JV, Lomonte B, Gutiérrez JM, Lund O. High-throughput immuno-profiling of mamba (Dendroaspis) venom toxin epitopes using high-density peptide microarrays. Sci Rep 2016; 6:36629. [PMID: 27824133 PMCID: PMC5100549 DOI: 10.1038/srep36629] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [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: 08/01/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022] Open
Abstract
Snakebite envenoming is a serious condition requiring medical attention and administration of antivenom. Current antivenoms are antibody preparations obtained from the plasma of animals immunised with whole venom(s) and contain antibodies against snake venom toxins, but also against other antigens. In order to better understand the molecular interactions between antivenom antibodies and epitopes on snake venom toxins, a high-throughput immuno-profiling study on all manually curated toxins from Dendroaspis species and selected African Naja species was performed based on custom-made high-density peptide microarrays displaying linear toxin fragments. By detection of binding for three different antivenoms and performing an alanine scan, linear elements of epitopes and the positions important for binding were identified. A strong tendency of antivenom antibodies recognizing and binding to epitopes at the functional sites of toxins was observed. With these results, high-density peptide microarray technology is for the first time introduced in the field of toxinology and molecular details of the evolution of antibody-toxin interactions based on molecular recognition of distinctive toxic motifs are elucidated.
Collapse
Affiliation(s)
- Mikael Engmark
- Technical University of Denmark, Department of Bio and Health Informatics, Kgs. Lyngby, 2800, Denmark.,Technical University of Denmark, Department of Biotechnology and Biomedicine, Kgs. Lyngby, 2800, Denmark
| | - Mikael R Andersen
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Kgs. Lyngby, 2800, Denmark
| | - Andreas H Laustsen
- Technical University of Denmark, Department of Biotechnology and Biomedicine, Kgs. Lyngby, 2800, Denmark.,University of Copenhagen, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, Copenhagen East, 2100, Denmark
| | - Jigar Patel
- Roche NimbleGen, Madison, Wisconsin 53719, USA
| | | | - Federico de Masi
- Technical University of Denmark, Department of Bio and Health Informatics, Kgs. Lyngby, 2800, Denmark
| | - Christian S Hansen
- Technical University of Denmark, Department of Bio and Health Informatics, Kgs. Lyngby, 2800, Denmark
| | - Jens V Kringelum
- Technical University of Denmark, Department of Bio and Health Informatics, Kgs. Lyngby, 2800, Denmark
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica
| | - José María Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501, Costa Rica
| | - Ole Lund
- Technical University of Denmark, Department of Bio and Health Informatics, Kgs. Lyngby, 2800, Denmark
| |
Collapse
|
4
|
Sun H, Y.K. Yue P, Wang SR, Huo L, Zhao Y, Xie S, V. Kringelum J, Lund O, Taboureau O, Zhou J, N. S. Wong R, Fang WS. Synthesis and Biological Evaluations of Cytotoxic and Antiangiogenic Triterpenoids-Jacaranone Conjugates. Med Chem 2016; 12:775-785. [DOI: 10.2174/1573406412666160502153930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 03/29/2016] [Accepted: 04/27/2016] [Indexed: 11/22/2022]
|
5
|
Christiansen A, Kringelum JV, Hansen CS, Bøgh KL, Sullivan E, Patel J, Rigby NM, Eiwegger T, Szépfalusi Z, de Masi F, Nielsen M, Lund O, Dufva M. High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum. Sci Rep 2015; 5:12913. [PMID: 26246327 PMCID: PMC4650709 DOI: 10.1038/srep12913] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [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: 03/16/2015] [Accepted: 07/08/2015] [Indexed: 12/13/2022] Open
Abstract
Phage display is a prominent screening technique with a multitude of applications including therapeutic antibody development and mapping of antigen epitopes. In this study, phages were selected based on their interaction with patient serum and exhaustively characterised by high-throughput sequencing. A bioinformatics approach was developed in order to identify peptide motifs of interest based on clustering and contrasting to control samples. Comparison of patient and control samples confirmed a major issue in phage display, namely the selection of unspecific peptides. The potential of the bioinformatic approach was demonstrated by identifying epitopes of a prominent peanut allergen, Ara h 1, in sera from patients with severe peanut allergy. The identified epitopes were confirmed by high-density peptide micro-arrays. The present study demonstrates that high-throughput sequencing can empower phage display by (i) enabling the analysis of complex biological samples, (ii) circumventing the traditional laborious picking and functional testing of individual phage clones and (iii) reducing the number of selection rounds.
Collapse
Affiliation(s)
- Anders Christiansen
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jens V Kringelum
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christian S Hansen
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Katrine L Bøgh
- National Food Institute, Technical University of Denmark, Søborg, Denmark
| | - Eric Sullivan
- Roche NimbleGen, Madison, Wisconsin, the United States of America
| | - Jigar Patel
- Roche NimbleGen, Madison, Wisconsin, the United States of America
| | - Neil M Rigby
- Institute of Food Research, Norwich, United Kingdom
| | - Thomas Eiwegger
- Department of Paediatrics, Medical University of Vienna, Vienna, Austria
| | - Zsolt Szépfalusi
- Department of Paediatrics, Medical University of Vienna, Vienna, Austria
| | - Federico de Masi
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Morten Nielsen
- 1] Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark [2] Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Ole Lund
- Center for Biological Sequence Analysis, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Martin Dufva
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|