Jonas D. Förster - German Cancer Research Center

Scientific CV


Dec 2023 - Apr 2024	Postdoctoral Scientist, Immunotherapy and Immunoprevention, DKFZ, Heidelberg
2018 - 2023	PhD student, Immunotherapy and Immunoprevention, DKFZ, Heidelberg
2017 - 2018	Research assistant, Junior Research Group Biological Information Processing, BioQuant, Heidelberg
2011 - 2017	MSc Molecular Biosciences, Ruprecht-Karls-University, Heidelberg
2008 - 2011	BSc Molecular Cell Biology, Ruprecht-Karls-University, Heidelberg

Research Project

Mass spectrometry-based identification of HPV16 target epitopes for therapeutic vaccine design

The overall aim of the group is to develop a therapeutic vaccine against malignancies and precursor lesions caused by high-risk types of human papillomavirus (HPV). Identification of T-cell epitopes which are presented to the immune system on the surface of transformed cells is essential for rational vaccine development. A highly sensitive targeted nano-flow liquid chromatography mass spectrometry (nanoLC-MS) methodology has been developed in our group for the detection of low-abundant viral epitopes.

The first aim of this PhD project was to establish and implement a standardized pipeline to facilitate the analysis of proteomics data by specialized software, including storage, transfer and statistical analysis. To do so, further development of existing computing strategies for epitope detection, and building of new software packages was performed. The second aim was to identify novel HPV16 epitopes for the major human leukocyte antigen (HLA) types, namely HLA-A2, HLA-A3/A11, HLA-A24, HLA-B7 and HLA-B15/A1, which together cover >95 % of the world’s population. To this end, the immunoprecipitation and sample preparation for epitope purification and detection was adapted to allow for flexible targeting of peptides relevant to any assayed cell line. This necessitated the development of software assisting the selection of peptides, identification of optimal LC-MS acquisition parameters specific to each peptide and the evaluation of peptide detection. The resulting validated HPV16 epitopes will facilitate future immunotherapy design.

Resulting Publications

Mol Cell Proteomics. 2024.

optiPRM: A Targeted Immunopeptidomics LC-MS Workflow With Ultra-High Sensitivity for the Detection of Mutation-Derived Tumor Neoepitopes From Limited Input Material.

Salek M, Förster JD, Becker JP, Meyer M, Charoentong P, Lyu Y, Lindner K, Lotsch C, Volkmar M, Momburg F, Poschke I, Fröhling S, Schmitz M, Offringa R, Platten M, Jäger D, Zörnig I, Riemer AB.

Sci Transl Med. 2023.

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.

Pathogens. 2023.

Development of an Orthotopic HPV16-Dependent Base of Tongue Tumor Model in MHC-Humanized Mice.

Schifflers C, Zottnick S, Förster JD, Kruse S, Yang R, Wiethoff H, Bozza M, Hoppe-Seyler K, Heikenwälder M, Harbottle RP, Michiels C, Riemer AB.

Front Immunol. 2022.

Effects of hypoxia on antigen presentation and T cell-based immune recognition of HPV16-transformed cells.

Mohan N, Wellach K, Özerdem C, Veits N, Förster JD, Foehr S, Bonsack M, Riemer AB.

Anal Bioanal Chem. 2022.

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.