Immunopeptidomics-based Development of Next-Generation Bacterial mRNA Vaccines

Informations projet

BAXERNA 2.0

N° de convention de subvention: 101080544

DOI

10.3030/101080544

Date de signature de la CE 12 Avril 2023

Date de début 1 Juillet 2023

Date de fin 30 Juin 2028

Financé au titre de

• Health

Coût total

€ 9 458 801,25

Contribution de l’UE

€ 9 458 801,25

Coordonné par

VIB VZW
Belgium

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Documents, reports (11)

Data management plan in place

Report on the creation of the initial version of the project's data management plan, describing the intended data to be generated, the storage and handling of this data with an eye to IP and ethics constraints, and it's long-term archival and/or (where appropriate and possible) public dissemination approach.

Report on epitopes and antigens identified for MTB and BCG

Description of the performance of a miniaturized and automated procedure for immunopeptidomics sample preparation, including MHC Class I and II peptide complex immunoprecipitation in 96-wells using a positive pressure liquid handling device.

Report on the application of SaaS on immunopeptidomics results

Description of the utility of applying the Search All, Select Subset statistical approach for false discovery rate estimation on (small) subsets of identifications coming from mass spectrometry based proteomics approaches, on immunopeptidomics data sets.

Report on a miniaturized and (semi-)automated pipeline for immunopeptidomics sample preparation

Description of the performance of a miniaturized and automated procedure for immunopeptidomics sample preparation, including MHC Class I and II peptide complex immunoprecipitation in 96-wells using a positive pressure liquid handling device.

Dissemination and exploitation plan

The plan describes the planned measures to maximize the impact of the project, including the dissemination and exploitation measures that are planned, and the target group(s) addressed. Regarding communication measures and public engagement strategy, the aim is to inform and reach out to society and show the activities performed, and the use and the benefits the project will have for citizens.

Report on improved immunopeptide separation ionization and fragmentation

Assessment of peptide TMT derivatization to improve ionization and fragmentation of MHC Class I and II immunopeptides along with EThcD fragmentation. Evaluation of peptide pre-fractionation to reduce sample complexity, and novel nanoLC columns that should increase the number of identified immunopeptides.

Policy briefing 1

At the end of the 1st reporting period, a report (policy briefing) will be shared with the policy makers.

Report on a new version of MS²Rescore with an EThcD-TMT model and DeepLC

Description of a new version of the MSRescore immunopeptidomics mass spectrometry data analysis algorithm, implementing DeepLC retention time prediction, and an updated prediction algorithm for the prediction of fragmentation spectra for peptides carrying TMT tags, and fragmented using the EThcD method.

Setup of a project website and logo

Report on the availability of a project website and a logo for the project.

Report on immuno-ionbot, a version of ionbot capable of performing open modification searches on immunopeptidomics data

Description of an updated verison of the ionbot algorithm, which will be fitted with the capability to handle non-tryptic peptides (including immunopeptides), alongside the use of immunopeptide fragmentation and retention time predictions coming from the MS²PIP and DeepLC predictors, respectively.

IP management plan in place

Report on the IP management plan as described in the project's Grant Agreement, including conflict resolution approaches.

Publications

Peer reviewed articles (28)

Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model

Auteurs: David Gomez-Zepeda, Danielle Arnold-Schild, Julian Beyrle, Arthur Declercq, Ralf Gabriels, Elena Kumm, Annica Preikschat, Mateusz Krzysztof Łącki, Aurélie Hirschler, Jeewan Babu Rijal, Christine Carapito, Lennart Martens, Ute Distler, Hansjörg Schild, Stefan Tenzer
Publié dans: Nature Communications, Numéro 15, 2024, ISSN 2041-1723
Éditeur: Springer Science and Business Media LLC
DOI: 10.1038/S41467-024-46380-Y

TIMS²Rescore: A Data Dependent Acquisition-Parallel Accumulation and Serial Fragmentation-Optimized Data-Driven Rescoring Pipeline Based on MS²Rescore

Auteurs: Arthur Declercq, Robbe Devreese, Jonas Scheid, Caroline Jachmann, Tim Van Den Bossche, Annica Preikschat, David Gomez-Zepeda, Jeewan Babu Rijal, Aurélie Hirschler, Jonathan R Krieger, Tharan Srikumar, George Rosenberger, Claudia Martelli, Dennis Trede, Christine Carapito, Stefan Tenzer, Juliane S Walz, Sven Degroeve, Robbin Bouwmeester, Lennart Martens, Ralf Gabriels
Publié dans: Journal of Proteome Research, 2025, ISSN 1535-3893
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPROTEOME.4C00609

Nanobody-mediated SPECT/CT imaging reveals the spatiotemporal expression of programmed death-ligand 1 in response to a CD8⁺ T cell and iNKT cell activating mRNA vaccine

Auteurs: Thomas Ertveldt, Sofie Meulewaeter, Yannick De Vlaeminck, Oscar Olarte, Katrijn Broos, Serge Van Calenbergh, Stephanie Bourgeois, Joke Deprez, Yves Heremans, Cleo Goyvaerts, Willem Staels, Stefaan De Smedt, Heleen Dewitte, Nick Devoogdt, Marleen Keyaerts, Rein Verbeke, Kurt Barbé, Ine Lentacker, Karine Breckpot
Publié dans: Theranostics, Numéro 13, 2023, ISSN 1838-7640
Éditeur: Ivyspring International Publisher
DOI: 10.7150/THNO.85106

Alpha-galactosylceramide improves the potency of mRNA LNP vaccines against cancer and intracellular bacteria

Auteurs: Sofie Meulewaeter, Ilke Aernout, Joke Deprez, Yanou Engelen, Margo De Velder, Lorenzo Franceschini, Karine Breckpot, Serge Van Calenbergh, Caroline Asselman, Katie Boucher, Francis Impens, Stefaan C. De Smedt, Rein Verbeke, Ine Lentacker
Publié dans: Journal of Controlled Release, Numéro 370, 2025, ISSN 0168-3659
Éditeur: Elsevier BV
DOI: 10.1016/j.jconrel.2024.04.052

PTMVision: An Interactive Visualization Webserver for Post-translational Modifications of Proteins

Auteurs: Simon Hackl, Caroline Jachmann, Mathias Witte Paz, Theresa Anisja Harbig, Lennart Martens, Kay Nieselt
Publié dans: Journal of Proteome Research, Numéro 24, 2025, ISSN 1535-3893
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/acs.jproteome.4c00679

Preclinical toxicological assessment of an α-galactosylceramide-adjuvanted mRNA cancer vaccine in Wistar Han rats and domestic pigs

Auteurs: Sofie Meulewaeter, Margo De Velder, Diethard Reckelbus, Kevin Mwangi, Thomas Ehouarne, Ilke Aernout, Yanou Engelen, Fellanza Halimi, Isis Van herteryck, Lobke De Bels, Valerie Redant, Louise De la Mane, Joline Ingels, Bo Coppens, Serge Van Calenbergh, Pieter Cornillie, Gabriële Holtappels, Benedicte Descamps, Daisy Vanrompay, Stefaan C. De Smedt, Wim Van den Broeck, Bart Vandekerckhove, Mathias Devreese, Rein Verbeke, Ine Lentacker
Publié dans: Molecular Therapy Methods & Clinical Development, Numéro 33, 2025, ISSN 2329-0501
Éditeur: Elsevier BV
DOI: 10.1016/J.OMTM.2025.101493

Continuous freeze-drying of messenger RNA lipid nanoparticles enables storage at higher temperatures

Auteurs: Sofie Meulewaeter, Gust Nuytten, Miffy H.Y. Cheng, Stefaan C. De Smedt, Pieter R. Cullis, Thomas De Beer, Ine Lentacker, Rein Verbeke
Publié dans: Journal of Controlled Release, Numéro 357, 2023, ISSN 0168-3659
Éditeur: Elsevier BV
DOI: 10.1016/J.JCONREL.2023.03.039

MHCquant2 refines immunopeptidomics tumor antigen discovery

Auteurs: Jonas Scheid, Steffen Lemke, Naomi Hoenisch-Gravel, Anna Dengler, Timo Sachsenberg, Arthur Declerq, Ralf Gabriels, Jens Bauer, Marcel Wacker, Leon Bichmann, Lennart Martens, Marissa L. Dubbelaar, Sven Nahnsen, Juliane S. Walz
Publié dans: Genome Biology, Numéro 26, 2025, ISSN 1474-760X
Éditeur: Springer Science and Business Media LLC
DOI: 10.1186/S13059-025-03763-8

Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice

Auteurs: Adillah Gul, Lecia L. Pewe, Patrick Willems, Rupert Mayer, Fabien Thery, Caroline Asselman, Ilke Aernout, Rein Verbeke, Denzel Eggermont, Laura Van Moortel, Ellen Upton, Yifeng Zhang, Katie Boucher, Laia Miret-Casals, Hans Demol, Stefaan C. De Smedt, Ine Lentacker, Lilliana Radoshevich, John T. Harty, Francis Impens
Publié dans: Molecular & Cellular Proteomics, Numéro 23, 2024, ISSN 1535-9476
Éditeur: Elsevier BV
DOI: 10.1016/j.mcpro.2024.100829

Target acquired: Lock-on bacterial immunopeptides

Auteurs: Patrick Willems, Lyudmila Kovalchuke, Francis Impens
Publié dans: Journal of Experimental Medicine, Numéro 222, 2025, ISSN 0022-1007
Éditeur: Rockefeller University Press
DOI: 10.1084/JEM.20251232

Humoral response induced after intranasal vaccination with heat inactivated Acinetobacter baumannii protects immunodeficient mice against hypervirulent LAC-4 strain

Auteurs: Thomas Rouma, Emeline Barbieux, Lorenzo Bossi, Katy Poncin, Sébastien Denanglaire, Yohannes Tafesse, David Vermijlen, Sandrine Delbauve, Véronique Flamand, Juliette Van Buylaere, Charles Van der Henst, Xavier De Bolle, Fabienne Andris, Eric Muraille
Publié dans: Frontiers in Immunology, Numéro 16, 2025, ISSN 1664-3224
Éditeur: Frontiers Media SA
DOI: 10.3389/FIMMU.2025.1641997

Metaproteomics Beyond Databases: Addressing the Challenges and Potentials of De Novo Sequencing

Auteurs: Tim Van Den Bossche, Denis Beslic, Sam van Puyenbroeck, Tomi Suomi, Tanja Holstein, Lennart Martens, Laura L. Elo, Thilo Muth
Publié dans: PROTEOMICS, Numéro 25, 2025, ISSN 1615-9853
Éditeur: Wiley
DOI: 10.1002/PMIC.202400321

MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics

Auteurs: Julian Pipart, Tanja Holstein, Lennart Martens, Thilo Muth
Publié dans: Journal of Proteome Research, Numéro 24, 2025, ISSN 1535-3893
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPROTEOME.4C00901

Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setups

Auteurs: Robbin Bouwmeester, Alireza Nameni, Arthur Declercq, Robbe Devreese, Kevin Velghe, Vladimir Gorshkov, Pelayo A. Penanes, Frank Kjeldsen, Magali Rompais, Christine Carapito, Ralf Gabriels, Lennart Martens
Publié dans: Nature Communications, Numéro 17, 2026, ISSN 2041-1723
Éditeur: Springer Science and Business Media LLC
DOI: 10.1038/S41467-026-68981-5

mRNA Galsomes Vaccine Protects Budgerigars Against Virulent Chlamydia psittaci Challenge

Auteurs: Anne De Meyst, Joeri Van Mieghem, Koen Chiers, Koen Raemdonck, Rein Verbeke, Ine Lentacker, Daisy Vanrompay
Publié dans: Vaccines, Numéro 13, 2025, ISSN 2076-393X
Éditeur: MDPI AG
DOI: 10.3390/VACCINES13020206

Challenges and opportunities in mRNA vaccine development against bacteria

Auteurs: Ilke Aernout, Rein Verbeke, Fabien Thery, Patrick Willems, Uri Elia, Stefaan C. De Smedt, Rino Rappuoli, Dan Peer, Francis Impens, Ine Lentacker
Publié dans: Nature Microbiology, Numéro 10, 2025, ISSN 2058-5276
Éditeur: Springer Science and Business Media LLC
DOI: 10.1038/S41564-025-02070-Z

Recent Advances Using Genetic Therapies Against Infectious Diseases and for Vaccination

Auteurs: Anne Galy, Ben Berkhout, Karine Breckpot, Chantal Pichon, Kristie Bloom, Hans-Peter Kiem, Michael D Mühlebach, Joseph M McCune
Publié dans: Human Gene Therapy, ISSN 1043-0342
Éditeur: Mary Ann Liebert Inc.
DOI: 10.1089/HUM.2023.123

The <i>Escherichia coli</i> PeptideAtlas Build: Characterizing the Observed <i>Escherichia coli</i> Pan-Proteome and Its Post-Translational Modifications

Auteurs: Caroline Jachmann, Zhi Sun, Kevin Velghe, Florence Arsène-Ploetze, Aurélie Hirschler, Jasper Zuallaert, Christine Carapito, Robbin Bouwmeester, Kay Nieselt, Eric W. Deutsch, Lennart Martens, Ralf Gabriels, Tim Van Den Bossche
Publié dans: Journal of Proteome Research, Numéro 25, 2026, ISSN 1535-3893
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPROTEOME.5C00902

MS²Rescore 3.0 Is a Modular, Flexible, and User-Friendly Platform to Boost Peptide Identifications, as Showcased with MS Amanda 3.0

Auteurs: Louise M. Buur, Arthur Declercq, Marina Strobl, Robbin Bouwmeester, Sven Degroeve, Lennart Martens, Viktoria Dorfer, Ralf Gabriels
Publié dans: Journal of Proteome Research, Numéro 23, 2024, ISSN 1535-3893
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPROTEOME.3C00785

Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2Deep

Auteurs: Robbe Devreese, Alireza Nameni, Arthur Declercq, Emmy Terryn, Ralf Gabriels, Francis Impens, Kris Gevaert, Lennart Martens, Robbin Bouwmeester
Publié dans: Analytical Chemistry, Numéro 97, 2025, ISSN 0003-2700
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.ANALCHEM.5C01142

Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes

Auteurs: Patrick Willems, An Staes, Laia Miret-Casals, Vadim Demichev, Simon Devos, Francis Impens
Publié dans: Journal of Proteome Research, Numéro 24, 2025, ISSN 1535-3893
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPROTEOME.5C00449

msqrob2TMT: Robust Linear Mixed Models for Inferring Differential Abundant Proteins in Labeled Experiments With Arbitrarily Complex Design

Auteurs: Stijn Vandenbulcke, Christophe Vanderaa, Oliver Crook, Lennart Martens, Lieven Clement
Publié dans: Molecular &amp; Cellular Proteomics, Numéro 24, 2025, ISSN 1535-9476
Éditeur: Elsevier BV
DOI: 10.1016/J.MCPRO.2025.101002

Sequence simplification of antigen coding IVT mRNA allows accelerated synthetic DNA template generation and epitope immunogenicity validation

Auteurs: Arthur Esprit, Dorien Autaers, Ilke Aernout, Ine Lentacker, Steve Pascolo, Kris Thielemans, Karine Breckpot, Lorenzo Franceschini
Publié dans: Molecular Therapy Nucleic Acids, Numéro 36, 2026, ISSN 2162-2531
Éditeur: Elsevier BV
DOI: 10.1016/J.OMTN.2025.102591

Considerations on the Design of Lipid-based mRNA Vaccines Against Cancer

Auteurs: Sofie Meulewaeter, Yao Zhang, Abishek Wadhwa, Kevin Fox, Ine Lentacker, Kenneth W. Harder, Pieter R. Cullis, Stefaan C. De Smedt, Miffy H.Y. Cheng, Rein Verbeke
Publié dans: Journal of Molecular Biology, ISSN 0022-2836
Éditeur: Academic Press
DOI: 10.1016/J.JMB.2023.168385

Open-Source and FAIR Research Software for Proteomics

Auteurs: Yasset Perez-Riverol, Wout Bittremieux, William S. Noble, Lennart Martens, Aivett Bilbao, Michael R. Lazear, Bjorn Grüning, Daniel S. Katz, Michael J. MacCoss, Chengxin Dai, Jimmy K. Eng, Robbin Bouwmeester, Michael R. Shortreed, Enrique Audain, Timo Sachsenberg, Jeroen Van Goey, Georg Wallmann, Bo Wen, Lukas Käll, William E. Fondrie
Publié dans: Journal of Proteome Research, Numéro 24, 2025, ISSN 1535-3893
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPROTEOME.4C01079

Maximizing Immunopeptidomics-Based Bacterial Epitope Discovery by Multiple Search Engines and Rescoring

Auteurs: Patrick Willems, Fabien Thery, Laura Van Moortel, Margaux De Meyer, An Staes, Adillah Gul, Lyudmila Kovalchuke, Arthur Declercq, Robbe Devreese, Robbin Bouwmeester, Ralf Gabriels, Lennart Martens, Francis Impens
Publié dans: Journal of Proteome Research, Numéro 24, 2025, ISSN 1535-3893
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPROTEOME.4C00864

High-Throughput Quantification of Spike Protein Expression by LC–MS for mRNA-LNP Evaluation and Immune Response Profiling

Auteurs: Ruben Almey, Kevin Mwangi, Amélie De Maesschalck, Thomas Ehouarne, Sieglinde de Cae, Pathmanaban Ramasamy, Marijn Van Hulle, Ine Lentacker, Bert Schepens, Dieter Deforce, Geert Martens, Pieter Ramaut, Johannes P.C. Vissers, Xavier Saelens, Rein Verbeke, Maarten Dhaenens, Bart Van Puyvelde
Publié dans: Analytical Chemistry, 2026, ISSN 0003-2700
Éditeur: American Chemical Society (ACS)
DOI: 10.1021/ACS.ANALCHEM.6C01359

Paneth cell TNF signaling induces gut bacterial translocation and sepsis

Auteurs: Charlotte Wallaeys, Natalia Garcia-Gonzalez, Steven Timmermans, Jolien Vandewalle, Tineke Vanderhaeghen, Somara De Beul, Hester Dufoor, Melanie Eggermont, Elise Moens, Victor Bosteels, Riet De Rycke, Fabien Thery, Francis Impens, Serge Verbanck, Stefan Lienenklaus, Sophie Janssens, Richard S. Blumberg, Takao Iwawaki, Claude Libert
Publié dans: Cell Host &amp; Microbe, Numéro 32, 2025, ISSN 1931-3128
Éditeur: Elsevier BV
DOI: 10.1016/J.CHOM.2024.08.007

Other (4)

Maximizing immunopeptidomics-based bacterial epitope discovery by multiple search engines and rescoring

Auteurs: Patrick Willems, Fabien Thery, Laura Van Moortel, Margaux De Meyer, An Staes, Adillah Gul, Lyudmila Kovalchuke, Arthur Declercq, Robbe Devreese, Robbin Bouwmeester, Ralf Gabriels, Lennart Martens, Francis Impens
Publié dans: 2024
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.22.624860

Collisional cross-section prediction for multiconformational peptide ions with IM2Deep

Auteurs: Robbe Devreese, Alireza Nameni, Arthur Declercq, Emmy Terryn, Ralf Gabriels, Francis Impens, Kris Gevaert, Lennart Martens, Robbin Bouwmeester
Publié dans: 2025
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.18.638865

MHCquant2 refines immunopeptidomics tumor antigen discovery

Auteurs: Jonas Scheid, Steffen Lemke, Naomi Hoenisch-Gravel, Anna Dengler, Timo Sachsenberg, Arthur Declerq, Ralf Gabriels, Jens Bauer, Marcel Wacker, Leon Bichmann, Lennart Martens, Marissa L. Dubbelaar, Sven Nahnsen, Juliane S. Walz
Publié dans: 2024
Éditeur: Springer Science and Business Media LLC
DOI: 10.21203/rs.3.rs-5560023/v1

Open-source and FAIR Research Software for Proteomics

Auteurs: Yasset Perez-Riverol, Wout Bittremieux, William S. Noble, Lennart Martens, Aivett Bilbao, Michael R. Lazear, Bjorn Grüning, Daniel S. Katz, Michael J. MacCoss, Chengxin Dai, Jimmy K. Eng, Robbin Bouwmeester, Michael Robert Shortreed, Enrique Audain, Timo Sachsenberg, Jeroen Van Goey, Georg Wallmann, Bo Wen, Lukas Käll, William E. Fondrie
Publié dans: 2024
Éditeur: American Chemical Society (ACS)
DOI: 10.26434/CHEMRXIV-2024-WF6DW