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Practical Course HP-F11: Tumor Heterogeneity and Proteomics

Type: Practical Course with Student Seminars

Date: 19. June - 7. July 2023

pause: 4.-5. July

Hosts/Supervisors: Stefan Pusch (responsible organizer contact:; Rocio Sotillo (; Sevin Turcan (; Jeroen Krijgsveld (

Topics and Content:

Part of Rocio Sotillo: "Tumor heterogeneity and mouse models" (5 days: 17.-21. June 2024; DKFZ Main Building, INF 280, 3rd floor division labs):

Chromosome instability has been shown to lead to tumor heterogeneity and poor therapeutic response. Using in vivo animal models as well as 3-dimentional culture systems we were able to identify aneuploidy and the continuous missegregation of chromosomes as a cause of tumor diversity. The students will study time lapse video-microscopy of tumor cells to identify missegregating events both in 2-dimensional and 3-dimensional cultures. In addition they will learn how to phenotypically characterize mouse models of human cancer by using histological (sample preparation, embedding, immunohistochemistry, immunofluorescence) and molecular biology methods (PCR and RT-PCR, Western blotting). Generation of lung and breast cancer orthotopic models will be performed.


Part of Sevin Turcan: "Cancer epigenetics" (4 days: 24.-27. June 2024; NCT, INF 460, 2nd floor, 02.120):

Cancer phenotypes are driven by genetic and epigenetic alterations. In gliomas, recurrent hotspot mutations in isocitrate dehydrogenase (IDH1) cause widespread epigenetic alterations, leading to global DNA hypermethylation and altered histone marks. Understanding the interplay between epigenetics and genetics will shed light on processes involved in tumorigenesis and guide the design of better therapeutic approaches. This course will cover cancer epigenetics (with a particular focus on IDH mutations) and next-generation sequencing based approaches to study epigenomics. Students will be introduced to patient-derived glioma tumorsphere models and gain hands-on experience on chromatin immunoprecipitation (ChIP), ChIP-qPCR and its analysis.


Part of Stefan Pusch: "Generation and analysis of mutant proteins" (4 days: 28. June – 3. July 2024; DKFZ Main building, INF 280, 6th floor, H1.06.048):

The main causes of cancer are mutations in the coding regions of genes. These mutations lead to changes in the amino acid composition of these proteins and thereby often to changes in their functionality. This change in functionality is then most often the trigger to cause cancer. One such mutation, which is common in glioma, is the IDH1R132H mutation. In the past years we were able to establish several diagnostic assays to detect this mutation and also develop a drug against this mutation, which is currently in clinical trials. The practical course will provide inside how the process from mutation identification to final drug development works. Therefore the students will generate mutations and purify mutant protein for analysis. Furthermore, proteins will be used in functional assays and secondary assays will be applied on cells to confirm the mutation and drug response.


Part of Jeroen Krijgsveld: "Proteomics" (2 days: 8.-9. July 2024; TP4, INF 581, S0.226 ground floor):

Mass spectrometry-based proteomics has become an established technology to identify and quantify proteins in cells and tissues. When performed at a proteome-wide scale, this provides a global view on cellular processes that underlie a particular cellular treatment or stress condition, or that may help explain a disease state. In addition, mass spectrometry can identify protein interactions or modifications, thereby unraveling layers of regulation that are not apparent from e.g. gene/RNA sequencing technologies. This practical will provide training in the basic principles of proteomics, including sample preparation, mass spectrometric data acquisition, and protein identification using computational methods with a focus on its use to identify mutated proteins.

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