Immunopeptidomics-based Development of Next-Generation Bacterial mRNA Vaccines

Informazioni relative al progetto

BAXERNA 2.0

ID dell’accordo di sovvenzione: 101080544

DOI

10.3030/101080544

Data della firma CE 12 Aprile 2023

Data di avvio 1 Luglio 2023

Data di completamento 30 Giugno 2028

Finanziato da

• Health

Costo totale

€ 9 458 801,25

Contributo UE

€ 9 458 801,25

Coordinato da

VIB VZW
Belgium

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

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.

Pubblicazioni

Peer reviewed articles (28)

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

Autori: 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
Pubblicato in: Nature Communications, Numero 15, 2024, ISSN 2041-1723
Editore: 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

Autori: 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
Pubblicato in: Journal of Proteome Research, 2025, ISSN 1535-3893
Editore: 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

Autori: 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
Pubblicato in: Theranostics, Numero 13, 2023, ISSN 1838-7640
Editore: Ivyspring International Publisher
DOI: 10.7150/THNO.85106

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

Autori: 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
Pubblicato in: Journal of Controlled Release, Numero 370, 2025, ISSN 0168-3659
Editore: Elsevier BV
DOI: 10.1016/j.jconrel.2024.04.052

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

Autori: Simon Hackl, Caroline Jachmann, Mathias Witte Paz, Theresa Anisja Harbig, Lennart Martens, Kay Nieselt
Pubblicato in: Journal of Proteome Research, Numero 24, 2025, ISSN 1535-3893
Editore: 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

Autori: 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
Pubblicato in: Molecular Therapy Methods & Clinical Development, Numero 33, 2025, ISSN 2329-0501
Editore: Elsevier BV
DOI: 10.1016/J.OMTM.2025.101493

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

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

MHCquant2 refines immunopeptidomics tumor antigen discovery

Autori: 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
Pubblicato in: Genome Biology, Numero 26, 2025, ISSN 1474-760X
Editore: Springer Science and Business Media LLC
DOI: 10.1186/S13059-025-03763-8

Immunopeptidomics Mapping of Listeria monocytogenes T Cell Epitopes in Mice

Autori: 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
Pubblicato in: Molecular & Cellular Proteomics, Numero 23, 2024, ISSN 1535-9476
Editore: Elsevier BV
DOI: 10.1016/j.mcpro.2024.100829

Target acquired: Lock-on bacterial immunopeptides

Autori: Patrick Willems, Lyudmila Kovalchuke, Francis Impens
Pubblicato in: Journal of Experimental Medicine, Numero 222, 2025, ISSN 0022-1007
Editore: 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

Autori: 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
Pubblicato in: Frontiers in Immunology, Numero 16, 2025, ISSN 1664-3224
Editore: Frontiers Media SA
DOI: 10.3389/FIMMU.2025.1641997

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

Autori: Tim Van Den Bossche, Denis Beslic, Sam van Puyenbroeck, Tomi Suomi, Tanja Holstein, Lennart Martens, Laura L. Elo, Thilo Muth
Pubblicato in: PROTEOMICS, Numero 25, 2025, ISSN 1615-9853
Editore: Wiley
DOI: 10.1002/PMIC.202400321

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

Autori: Julian Pipart, Tanja Holstein, Lennart Martens, Thilo Muth
Pubblicato in: Journal of Proteome Research, Numero 24, 2025, ISSN 1535-3893
Editore: 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

Autori: 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
Pubblicato in: Nature Communications, Numero 17, 2026, ISSN 2041-1723
Editore: Springer Science and Business Media LLC
DOI: 10.1038/S41467-026-68981-5

mRNA Galsomes Vaccine Protects Budgerigars Against Virulent Chlamydia psittaci Challenge

Autori: Anne De Meyst, Joeri Van Mieghem, Koen Chiers, Koen Raemdonck, Rein Verbeke, Ine Lentacker, Daisy Vanrompay
Pubblicato in: Vaccines, Numero 13, 2025, ISSN 2076-393X
Editore: MDPI AG
DOI: 10.3390/VACCINES13020206

Challenges and opportunities in mRNA vaccine development against bacteria

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

Recent Advances Using Genetic Therapies Against Infectious Diseases and for Vaccination

Autori: Anne Galy, Ben Berkhout, Karine Breckpot, Chantal Pichon, Kristie Bloom, Hans-Peter Kiem, Michael D Mühlebach, Joseph M McCune
Pubblicato in: Human Gene Therapy, ISSN 1043-0342
Editore: 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

Autori: 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
Pubblicato in: Journal of Proteome Research, Numero 25, 2026, ISSN 1535-3893
Editore: 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

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

Collisional Cross-Section Prediction for Multiconformational Peptide Ions with IM2Deep

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

Data-Independent Immunopeptidomics Discovery of Low-Abundant Bacterial Epitopes

Autori: Patrick Willems, An Staes, Laia Miret-Casals, Vadim Demichev, Simon Devos, Francis Impens
Pubblicato in: Journal of Proteome Research, Numero 24, 2025, ISSN 1535-3893
Editore: 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

Autori: Stijn Vandenbulcke, Christophe Vanderaa, Oliver Crook, Lennart Martens, Lieven Clement
Pubblicato in: Molecular &amp; Cellular Proteomics, Numero 24, 2025, ISSN 1535-9476
Editore: 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

Autori: Arthur Esprit, Dorien Autaers, Ilke Aernout, Ine Lentacker, Steve Pascolo, Kris Thielemans, Karine Breckpot, Lorenzo Franceschini
Pubblicato in: Molecular Therapy Nucleic Acids, Numero 36, 2026, ISSN 2162-2531
Editore: Elsevier BV
DOI: 10.1016/J.OMTN.2025.102591

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

Autori: 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
Pubblicato in: Journal of Molecular Biology, ISSN 0022-2836
Editore: Academic Press
DOI: 10.1016/J.JMB.2023.168385

Open-Source and FAIR Research Software for Proteomics

Autori: 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
Pubblicato in: Journal of Proteome Research, Numero 24, 2025, ISSN 1535-3893
Editore: American Chemical Society (ACS)
DOI: 10.1021/ACS.JPROTEOME.4C01079

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

Autori: 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
Pubblicato in: Journal of Proteome Research, Numero 24, 2025, ISSN 1535-3893
Editore: 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

Autori: 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
Pubblicato in: Analytical Chemistry, 2026, ISSN 0003-2700
Editore: American Chemical Society (ACS)
DOI: 10.1021/ACS.ANALCHEM.6C01359

Paneth cell TNF signaling induces gut bacterial translocation and sepsis

Autori: 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
Pubblicato in: Cell Host &amp; Microbe, Numero 32, 2025, ISSN 1931-3128
Editore: Elsevier BV
DOI: 10.1016/J.CHOM.2024.08.007

Other (4)

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

Autori: 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
Pubblicato in: 2024
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2024.11.22.624860

Collisional cross-section prediction for multiconformational peptide ions with IM2Deep

Autori: Robbe Devreese, Alireza Nameni, Arthur Declercq, Emmy Terryn, Ralf Gabriels, Francis Impens, Kris Gevaert, Lennart Martens, Robbin Bouwmeester
Pubblicato in: 2025
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.02.18.638865

MHCquant2 refines immunopeptidomics tumor antigen discovery

Autori: 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
Pubblicato in: 2024
Editore: Springer Science and Business Media LLC
DOI: 10.21203/rs.3.rs-5560023/v1

Open-source and FAIR Research Software for Proteomics

Autori: 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
Pubblicato in: 2024
Editore: American Chemical Society (ACS)
DOI: 10.26434/CHEMRXIV-2024-WF6DW