Immunopeptidomics Platform
Dr. David Gomez-Zepeda
Aim
The High-throughput immunopeptidomics (HTIP) platform aims to identify cancer-specific immunopeptides (MHC-ligands), antigens that can trigger the immune response, and potential targets for immunotherapy. MHC ligand peptides are valuable targets for vaccines or personalized immunotherapies since tumor antigens can elicit the immune response and the elimination of cancer cells. Moreover, neoantigens resulting directly or indirectly from tumor-derived mutations constitute highly-specific targets. However, specific changes in the immunopeptidome in cancer and tumors are unique to each patient and can vary during disease progression and as a response to treatments. Liquid chromatography-mass spectrometry (LC-MS)-based immunopeptidomics is the gold standard for directly identifying MHC ligands in biological samples. However, most workflows are not adapted to the throughput and response times required for clinical studies or patient monitoring. To meet these needs, we are developing high-throughput immunopeptidomics workflows by optimizing parallelized sample preparation, high-sensitivity LC-MS methods, and streamlined data analysis pipelines.
Immunopeptidomics Platform
Dr. David Gomez-Zepeda
privat
[2021 - 2023] Head of the lmmunopeptidomics Platform (HI-TRON), Germany
[2021 - 2023] Junior team leader, Immunoproteomics Unit, Helmholtz Institute for Translational Oncology Mainz (HI-TRON), Germany
[2020 - 2021] Senior postdoctoral research scientist, Mass Spectrometry Facility, Institute of Immunology, University Medical Center Mainz, Germany
[2017 - 2019] Postdoctoral fellow research scientist, Mass Spectrometry Facility, National Laboratory of Genomics for Biodiversity (LANGEBIO – CINVESTAV), Mexico
[2013 - 2016] Doctoral scientist, Ph.D. student, INSERM UMR-S 1144, Paris Descartes University, Response Variability to Psychotropics, France
[2018 - 2022] Member of the National System of Researchers (SNI), Mexico
[2017 - 2019] Postdoctoral fellowship, National Council for Science and Technology (CONACYT), Mexico
HI-TRON Mainz DKFZ
Immunopeptidomics Platform
Obere Zahlbacherstr. 63
Building 911
55131 Mainz
Team
DKFZ
Prof. Dr. Stefan Tenzer
Scientific advisor
Collaborations
We have strong collaborations with scientists from the German Cancer Research Center (DKFZ), the Johannes Gutenberg University Mainz (JGU), the Research Institute for Translational Oncology (TRON, gGmbH) at the UMM, the University Medical Center Mainz (UMM), and the Charité University Medicine Berlin.
Selected publications of D.Gomez-Zepeda
- Gomez‐Zepeda D, Arnold-Schild D, Beyrle J, Kumm J, Distler U, Schild H, Tenzer S. Thunder-DDA-PASEF enables high-coverage immunopeptidomics and identifies HLA class-I presented SarsCov-2 spike protein epitopes. Preprint, 2023.
- Gomez-Zepeda D, Perrière N, Glacial F, Taghi M, Chhuon C, Scherrmann J, Sergen tP, Moreau A, Denizot C, Parmentier Y, Cisternino S, Decleves X, Menet M. Functional and targeted proteomics characterization of a human primary endothelial cell model of the blood-brain barrier (BBB) for drug permeability studies. Toxicol. Appl. Pharmacol. 2023; 465 (116456).
- Gomez-Zepeda D, Taghi M, Scherrmann J, Decleves X, Menet MC. ABC Transporters at the Blood–Brain Interfaces, Their Study Models, and Drug Delivery Implications in Gliomas. Pharmaceutics. 2019;12 20.
- Gomez-Zepeda D, Taghi M, Smirnova M, Sergent P, Liu W, Chhuon C, Vidal M, Picard M, Thioulouse E, Broutin I, Guerrera I, Scherrmann J, Parmentier Y, Decleves X, Menet M. LC–MS/MS-based quantification of efflux transporter proteins at the BBB. J. Pharm. Biomedical Analysis. 2019; 164: 496–508.
Platform News
12/2023: The new Bruker timsTOF Ultra mass spectrometer arrives.
