Literature DB >> 31611696

Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes.

Julien Racle1,2, Justine Michaux1,3, Georg Alexander Rockinger1, Marion Arnaud1,3, Sara Bobisse1,3, Chloe Chong1,3, Philippe Guillaume1,3, George Coukos1,3, Alexandre Harari1,3, Camilla Jandus1, Michal Bassani-Sternberg4,5, David Gfeller6,7.   

Abstract

Predictions of epitopes presented by class II human leukocyte antigen molecules (HLA-II) have limited accuracy, restricting vaccine and therapy design. Here we combined unbiased mass spectrometry with a motif deconvolution algorithm to profile and analyze a total of 99,265 unique peptides eluted from HLA-II molecules. We then trained an epitope prediction algorithm with these data and improved prediction of pathogen and tumor-associated class II neoepitopes.

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Year:  2019        PMID： 31611696     DOI： 10.1038/s41587-019-0289-6

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN： 1087-0156            Impact factor:   54.908


  42 in total

Review 1.  Towards a systems understanding of MHC class I and MHC class II antigen presentation.

Authors:  Jacques Neefjes; Marlieke L M Jongsma; Petra Paul; Oddmund Bakke
Journal:  Nat Rev Immunol       Date:  2011-11-11       Impact factor: 53.106

2.  Mutant MHC class II epitopes drive therapeutic immune responses to cancer.

Authors:  Sebastian Kreiter; Mathias Vormehr; Niels van de Roemer; Mustafa Diken; Martin Löwer; Jan Diekmann; Sebastian Boegel; Barbara Schrörs; Fulvia Vascotto; John C Castle; Arbel D Tadmor; Stephen P Schoenberger; Christoph Huber; Özlem Türeci; Ugur Sahin
Journal:  Nature       Date:  2015-04-22       Impact factor: 49.962

3.  Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide-HLA Interactions.

Authors:  Michal Bassani-Sternberg; David Gfeller
Journal:  J Immunol       Date:  2016-08-10       Impact factor: 5.422

4.  An automated benchmarking platform for MHC class II binding prediction methods.

Authors:  Massimo Andreatta; Thomas Trolle; Zhen Yan; Jason A Greenbaum; Bjoern Peters; Morten Nielsen
Journal:  Bioinformatics       Date:  2018-05-01       Impact factor: 6.937

5.  Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification.

Authors:  Massimo Andreatta; Edita Karosiene; Michael Rasmussen; Anette Stryhn; Søren Buus; Morten Nielsen
Journal:  Immunogenetics       Date:  2015-09-29       Impact factor: 2.846

6.  High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma.

Authors:  Carsten Linnemann; Marit M van Buuren; Laura Bies; Els M E Verdegaal; Remko Schotte; Jorg J A Calis; Sam Behjati; Arno Velds; Henk Hilkmann; Dris El Atmioui; Marten Visser; Michael R Stratton; John B A G Haanen; Hergen Spits; Sjoerd H van der Burg; Ton N M Schumacher
Journal:  Nat Med       Date:  2014-12-22       Impact factor: 53.440

7.  Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry.

Authors:  Michal Bassani-Sternberg; Eva Bräunlein; Richard Klar; Thomas Engleitner; Pavel Sinitcyn; Stefan Audehm; Melanie Straub; Julia Weber; Julia Slotta-Huspenina; Katja Specht; Marc E Martignoni; Angelika Werner; Rüdiger Hein; Dirk H Busch; Christian Peschel; Roland Rad; Jürgen Cox; Matthias Mann; Angela M Krackhardt
Journal:  Nat Commun       Date:  2016-11-21       Impact factor: 14.919

8.  Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity.

Authors:  Michal Bassani-Sternberg; Chloé Chong; Philippe Guillaume; Marthe Solleder; HuiSong Pak; Philippe O Gannon; Lana E Kandalaft; George Coukos; David Gfeller
Journal:  PLoS Comput Biol       Date:  2017-08-23       Impact factor: 4.475

9.  Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens.

Authors:  Michael S Khodadoust; Niclas Olsson; Lisa E Wagar; Ole A W Haabeth; Binbin Chen; Kavya Swaminathan; Keith Rawson; Chih Long Liu; David Steiner; Peder Lund; Samhita Rao; Lichao Zhang; Caleb Marceau; Henning Stehr; Aaron M Newman; Debra K Czerwinski; Victoria E H Carlton; Martin Moorhead; Malek Faham; Holbrook E Kohrt; Jan Carette; Michael R Green; Mark M Davis; Ronald Levy; Joshua E Elias; Ash A Alizadeh
Journal:  Nature       Date:  2017-03-22       Impact factor: 49.962

10.  High-throughput and Sensitive Immunopeptidomics Platform Reveals Profound Interferonγ-Mediated Remodeling of the Human Leukocyte Antigen (HLA) Ligandome.

Authors:  Chloe Chong; Fabio Marino; HuiSong Pak; Julien Racle; Roy T Daniel; Markus Müller; David Gfeller; George Coukos; Michal Bassani-Sternberg
Journal:  Mol Cell Proteomics       Date:  2017-12-14       Impact factor: 5.911
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  63 in total

Review 1.  Antitumour dendritic cell vaccination in a priming and boosting approach.

Authors:  Alexandre Harari; Michele Graciotti; Michal Bassani-Sternberg; Lana E Kandalaft
Journal:  Nat Rev Drug Discov       Date:  2020-08-06       Impact factor: 84.694

Review 2.  Beyond Sequencing: Prioritizing and Delivering Neoantigens for Cancer Vaccines.

Authors:  Alexander S Roesler; Karen S Anderson
Journal:  Methods Mol Biol       Date:  2022

3.  Detecting Tumor Antigen-Specific T Cells via Interaction-Dependent Fucosyl-Biotinylation.

Authors:  Zilei Liu; Jie P Li; Mingkuan Chen; Mengyao Wu; Yujie Shi; Wei Li; John R Teijaro; Peng Wu
Journal:  Cell       Date:  2020-10-22       Impact factor: 41.582

4.  HLA Class II Specificity Assessed by High-Density Peptide Microarray Interactions.

Authors:  Thomas Osterbye; Morten Nielsen; Nadine L Dudek; Sri H Ramarathinam; Anthony W Purcell; Claus Schafer-Nielsen; Soren Buus
Journal:  J Immunol       Date:  2020-06-01       Impact factor: 5.422

Review 5.  Overcoming malignant cell-based mechanisms of resistance to immune checkpoint blockade antibodies.

Authors:  Reham Ajina; David J Zahavi; Yong-Wei Zhang; Louis M Weiner
Journal:  Semin Cancer Biol       Date:  2019-12-19       Impact factor: 15.707

6.  Integral Use of Immunopeptidomics and Immunoinformatics for the Characterization of Antigen Presentation and Rational Identification of BoLA-DR-Presented Peptides and Epitopes.

Authors:  Andressa Fisch; Birkir Reynisson; Lindert Benedictus; Annalisa Nicastri; Deepali Vasoya; Ivan Morrison; Søren Buus; Beatriz Rossetti Ferreira; Isabel Kinney Ferreira de Miranda Santos; Nicola Ternette; Tim Connelley; Morten Nielsen
Journal:  J Immunol       Date:  2021-03-31       Impact factor: 5.422

Review 7.  Promises and challenges of adoptive T-cell therapies for solid tumours.

Authors:  Matteo Morotti; Ashwag Albukhari; Abdulkhaliq Alsaadi; Mara Artibani; James D Brenton; Stuart M Curbishley; Tao Dong; Michael L Dustin; Zhiyuan Hu; Nicholas McGranahan; Martin L Miller; Laura Santana-Gonzalez; Leonard W Seymour; Tingyan Shi; Peter Van Loo; Christopher Yau; Helen White; Nina Wietek; David N Church; David C Wedge; Ahmed A Ahmed
Journal:  Br J Cancer       Date:  2021-03-29       Impact factor: 7.640

8.  Implications of antibody-dependent enhancement of infection for SARS-CoV-2 countermeasures.

Authors:  Nikolai Eroshenko; Taylor Gill; Marianna K Keaveney; George M Church; Jose M Trevejo; Hannu Rajaniemi
Journal:  Nat Biotechnol       Date:  2020-07       Impact factor: 54.908

9.  Improved prediction of HLA antigen presentation hotspots: Applications for immunogenicity risk assessment of therapeutic proteins.

Authors:  Anders Steenholdt Attermann; Carolina Barra; Birkir Reynisson; Heidi Schiøler Schultz; Ulrike Leurs; Kasper Lamberth; Morten Nielsen
Journal:  Immunology       Date:  2020-10-19       Impact factor: 7.397

10.  Challenges targeting cancer neoantigens in 2021: a systematic literature review.

Authors:  Ina Chen; Michael Y Chen; S Peter Goedegebuure; William E Gillanders
Journal:  Expert Rev Vaccines       Date:  2021-06-09       Impact factor: 5.683
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