Immunopeptidomics-based Development of Next-Generation Bacterial mRNA Vaccines

Información del proyecto

BAXERNA 2.0

Identificador del acuerdo de subvención: 101080544

DOI

10.3030/101080544

Fecha de la firma de la CE 12 Abril 2023

Fecha de inicio 1 Julio 2023

Fecha de finalización 30 Junio 2028

Financiado con arreglo a

• Health

Coste total

€ 9 458 801,25

Aportación de la UE

€ 9 458 801,25

Coordinado por

VIB VZW
Belgium

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

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.

Publicaciones

Peer reviewed articles (28)

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

Autores: 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
Publicado en: Nature Communications, Edición 15, 2024, ISSN 2041-1723
Editor: 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

Autores: 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
Publicado en: Journal of Proteome Research, 2025, ISSN 1535-3893
Editor: 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

Autores: 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
Publicado en: Theranostics, Edición 13, 2023, ISSN 1838-7640
Editor: Ivyspring International Publisher
DOI: 10.7150/THNO.85106

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

Autores: 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
Publicado en: Journal of Controlled Release, Edición 370, 2025, ISSN 0168-3659
Editor: Elsevier BV
DOI: 10.1016/j.jconrel.2024.04.052

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

Autores: Simon Hackl, Caroline Jachmann, Mathias Witte Paz, Theresa Anisja Harbig, Lennart Martens, Kay Nieselt
Publicado en: Journal of Proteome Research, Edición 24, 2025, ISSN 1535-3893
Editor: 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

Autores: 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
Publicado en: Molecular Therapy Methods & Clinical Development, Edición 33, 2025, ISSN 2329-0501
Editor: Elsevier BV
DOI: 10.1016/J.OMTM.2025.101493

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

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

MHCquant2 refines immunopeptidomics tumor antigen discovery

Autores: 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
Publicado en: Genome Biology, Edición 26, 2025, ISSN 1474-760X
Editor: Springer Science and Business Media LLC
DOI: 10.1186/S13059-025-03763-8

Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice

Autores: 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
Publicado en: Molecular & Cellular Proteomics, Edición 23, 2024, ISSN 1535-9476
Editor: Elsevier BV
DOI: 10.1016/j.mcpro.2024.100829

Target acquired: Lock-on bacterial immunopeptides

Autores: Patrick Willems, Lyudmila Kovalchuke, Francis Impens
Publicado en: Journal of Experimental Medicine, Edición 222, 2025, ISSN 0022-1007
Editor: 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

Autores: 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
Publicado en: Frontiers in Immunology, Edición 16, 2025, ISSN 1664-3224
Editor: Frontiers Media SA
DOI: 10.3389/FIMMU.2025.1641997

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

Autores: Tim Van Den Bossche, Denis Beslic, Sam van Puyenbroeck, Tomi Suomi, Tanja Holstein, Lennart Martens, Laura L. Elo, Thilo Muth
Publicado en: PROTEOMICS, Edición 25, 2025, ISSN 1615-9853
Editor: Wiley
DOI: 10.1002/PMIC.202400321

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

Autores: Julian Pipart, Tanja Holstein, Lennart Martens, Thilo Muth
Publicado en: Journal of Proteome Research, Edición 24, 2025, ISSN 1535-3893
Editor: 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

Autores: 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
Publicado en: Nature Communications, Edición 17, 2026, ISSN 2041-1723
Editor: Springer Science and Business Media LLC
DOI: 10.1038/S41467-026-68981-5

mRNA Galsomes Vaccine Protects Budgerigars Against Virulent Chlamydia psittaci Challenge

Autores: Anne De Meyst, Joeri Van Mieghem, Koen Chiers, Koen Raemdonck, Rein Verbeke, Ine Lentacker, Daisy Vanrompay
Publicado en: Vaccines, Edición 13, 2025, ISSN 2076-393X
Editor: MDPI AG
DOI: 10.3390/VACCINES13020206

Challenges and opportunities in mRNA vaccine development against bacteria

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

Recent Advances Using Genetic Therapies Against Infectious Diseases and for Vaccination

Autores: Anne Galy, Ben Berkhout, Karine Breckpot, Chantal Pichon, Kristie Bloom, Hans-Peter Kiem, Michael D Mühlebach, Joseph M McCune
Publicado en: Human Gene Therapy, ISSN 1043-0342
Editor: 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

Autores: 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
Publicado en: Journal of Proteome Research, Edición 25, 2026, ISSN 1535-3893
Editor: 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

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

Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2Deep

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

Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes

Autores: Patrick Willems, An Staes, Laia Miret-Casals, Vadim Demichev, Simon Devos, Francis Impens
Publicado en: Journal of Proteome Research, Edición 24, 2025, ISSN 1535-3893
Editor: 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

Autores: Stijn Vandenbulcke, Christophe Vanderaa, Oliver Crook, Lennart Martens, Lieven Clement
Publicado en: Molecular &amp; Cellular Proteomics, Edición 24, 2025, ISSN 1535-9476
Editor: 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

Autores: Arthur Esprit, Dorien Autaers, Ilke Aernout, Ine Lentacker, Steve Pascolo, Kris Thielemans, Karine Breckpot, Lorenzo Franceschini
Publicado en: Molecular Therapy Nucleic Acids, Edición 36, 2026, ISSN 2162-2531
Editor: Elsevier BV
DOI: 10.1016/J.OMTN.2025.102591

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

Autores: 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
Publicado en: Journal of Molecular Biology, ISSN 0022-2836
Editor: Academic Press
DOI: 10.1016/J.JMB.2023.168385

Open-Source and FAIR Research Software for Proteomics

Autores: 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
Publicado en: Journal of Proteome Research, Edición 24, 2025, ISSN 1535-3893
Editor: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPROTEOME.4C01079

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

Autores: 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
Publicado en: Journal of Proteome Research, Edición 24, 2025, ISSN 1535-3893
Editor: 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

Autores: 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
Publicado en: Analytical Chemistry, 2026, ISSN 0003-2700
Editor: American Chemical Society (ACS)
DOI: 10.1021/ACS.ANALCHEM.6C01359

Paneth cell TNF signaling induces gut bacterial translocation and sepsis

Autores: 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
Publicado en: Cell Host &amp; Microbe, Edición 32, 2025, ISSN 1931-3128
Editor: Elsevier BV
DOI: 10.1016/J.CHOM.2024.08.007

Other (4)

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

Autores: 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
Publicado en: 2024
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.22.624860

Collisional cross-section prediction for multiconformational peptide ions with IM2Deep

Autores: Robbe Devreese, Alireza Nameni, Arthur Declercq, Emmy Terryn, Ralf Gabriels, Francis Impens, Kris Gevaert, Lennart Martens, Robbin Bouwmeester
Publicado en: 2025
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.18.638865

MHCquant2 refines immunopeptidomics tumor antigen discovery

Autores: 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
Publicado en: 2024
Editor: Springer Science and Business Media LLC
DOI: 10.21203/rs.3.rs-5560023/v1

Open-source and FAIR Research Software for Proteomics

Autores: 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
Publicado en: 2024
Editor: American Chemical Society (ACS)
DOI: 10.26434/CHEMRXIV-2024-WF6DW