Mogjib Salek, PhD

2017 - 2021
Postdoctoral scientist, Immunotherapy and Immunoprevention, DKFZ, Heidelberg

2013 - 2016
Scientist, Large Scale Biology (EDyP, BGE), Biosciences and Biotechnology Institute of Grenoble (BIG), France

2012 - 2013
Consultant in Proteomics, Toulouse, France

2006 - 2011                    
Research fellow, T Cell Signaling Group, Sir William Dunn School of Pathology, University of Oxford, UK

2004 - 2006
Postdoctoral fellow, Institute of European Oncology – FIRC Institute of Molecular Oncology Foundation (IEO-IFOM), Milan, Italy

2001 - 2004                    
PhD student, Central Spectroscopy Unit (Prof. Lehmann), DKFZ, Heidelberg

Mass spectrometry-based identification of mutation-derived tumor neoepitopes

To differentiate tumor cells from normal cells, the immune system needs to recognize structures that are tumor-specific. Altered proteins resulting from tumor-specific mutations – so-called neoantigens - fulfil this requirement, and are thus attractive targets for immunotherapy approaches. However, it is not yet clear which epitopes derived from neoantigens (i.e. "neoepitopes") are actually presented to the immune system on the tumor cell surface, as they mostly are of low abundance and therefore difficult to detect. But only presented neoepitopes represent meaningful targets for epitope-specific vaccines or adoptive transfer of T cells with transgenic T cell receptors.
A targeted mass spectrometry (MS) approach has been developed in the lab to detect low abundance epitopes. It has successfully been applied to detect neoepitopes. This research project aimed at establishing a high-throughput neoepitope detection workflow using the most recent mass spectrometry technology and advanced bioinformatics. The developed workflow is applicable for every tumor for which the tumor-specific mutations have been identified by genome sequencing, and for which samples are available for MS analysis. The analysis provides a rational basis for the development of immunotherapies by providing validated target neoepitopes.

Transcriptome-based identification of tumor-reactive and bystander CD8+ T cell receptor clonotypes in human pancreatic cancer.
Meng Z*, Rodriguez Ehrenfried A*, Tan CL*, Steffens LK, Kehm H, Zens S, Lauenstein C, Paul A, Schwab M, Förster JD, Salek M, Riemer AB, Wu H, Eckert C, Leonhardt CS, Strobel O, Volkmar M, Poschke I, Offringa R. * Equal contributors.
International Journal of Molecular Sciences. 2023; 15(722):eadh9562.

Light contamination in stable isotope-labelled internal peptide standards is frequent and a potential source of false discovery and quantitation error in proteomics.
Salek M*, Förster JD*, Lehmann WD, Riemer AB. * Equal contributors.
Analytical and Bioanalytical Chemistry 2022, 414(8): 2545-2552.

A targeted LC-MS strategy for low-abundant HLA class-I-presented peptide detection identifies novel human papillomavirus T-cell epitopes.
Blatnik R*, Mohan N*, Bonsack M*, Falkenby LG, Hoppe S, Josef K, Steinbach A, Becker S, Nadler WM, Rucevic M, Larsen MR, Salek M, Riemer AB. * Equal contributors.
Proteomics 2018, 18(11): e1700390.