1. Identification of novel markers to predict response to anti-PD-1 immunotherapy in melanoma applying proteomics
- serum glycoproteomics, serum depletion to enrich low abundant proteins using baseline serum samples (biobank USZ Prof. Levesque, samples of department of dermatology, MUW) of responder and non-responder to anti-PD-1 immunotherapy
- application of high sensitive mass spectrometry (i.e. timsTOF) and different bioinformatic tools
- quantification by selected reaction monitoring
- functional assays and exosomal enrichment
- clinical validation
2. Identification of drug resistance mechanisms to targeted and immune therapy by proteome characterisation of drug sensitive and resistant melanoma tumor cells or tissue
- identification of a resistance signature
- correlation of proteomics and RNAseq data
- functional and clinical validation of the signature
3. Comprehensive analysis of proteomics, metabolomics and lipidomics in blood plasma of patients treated with Extracorporeal Photopheresis (ECP)
- shotgun proteomics, metabolomics and lipidomics of serum samples before and after photopheresis for the evaluation of the acting mechanism
- functional assays with different immune cells
4. Tumor Microenvironment
- characterization of tumor associated fibroblasts and endothelial cells
Project in planning: Metabolomics and MS fingerprints of melanoma patients
Mass spectrometry:
Department of Analytical Chemistry , University Vienna, Prof Christopher Gerner anchem.univie.ac.at and Joint Metabolome Facility (JMEF)
Institute of Molecular Systems Biology, ETH Zurich, Prof Ruedi Aebersold