Practical Course HP-F1: Molecular, Genetic, Cellular and Bioinformatic Approaches in Cancer Research

Type: Practical Course with Student Seminars

Date: 28. October - 15. November 2019

Introduction, delivery of script/literature: date and time t.b.a. (DKFZ Main Building, INF 280, 2. floor, H2.02.073)

Hosts/Supervisors: Karin Müller-Decker (responsible organizer contact:; Maïwen Caudron-Herger, Sven Diederichs; Friederike Herbst



  1. Analysis of mass spectrometry data on protein-RNA interactions using a major bioinformatic tool
  2. Understanding molecular and functional heterogeneity of patient derived tumor models to improve treatment strategies
  3. The role of pro-inflammatory COX-2 in cancer: Analysis of genetically engineered mouse tumor models



  1. The analysis of a mass spectrometry dataset linked to protein-RNA interactions will serve as basis to introduce simple programming notions in R ranging from reading a file to the production of graphics. The results of the proteomic analysis and their meaning will be discussed. 
  2. Patient specific tumor cultures are used to characterize the role of critical and deregulated factors, which lead to metastasis formation or therapy resistance with the overall aim to improve clinical treatment strategies. Therefore, lentiviral vectors encoding for identified candidate genes will be generated and used for genetic engineering of primary cultures. These cultures will be used to gain mechanistic insights by analyzing functional properties like ATP level, mitochondrial activity or cell adhesion and migration.
    Moreover, depending on the tumoral genetic makeup, the toxicity of individual substances will be investigated to predict patient specific treatment options and outcome.
  3. Transgenic mice as tumour models. Analysis of oncogene Ki-Ras and COX-2 expression/activities. Protein enrichment from various tissues by immunoprecipitation, pull-down assays, immunoblot analysis, in situ protein detection by multi-colour immunofluorescence; lipid extractions, reverse-phase-chromatography of lipids, enzyme-immuno-assay of lipids.


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