Practical Course HP-F2: Molecular Neurobiology, Applied Tumor Immunity, and Bioinformatics

Type: Practical Course with Student Seminars

part I: Stem cells vs. Cancer stem cells

Date: 11.-15. November 2019

Introduction: date/time t.b.a., TP4 left, 3rd floor

Location: Molecular Neurobiology Labs, TP4 left, 3rd floor

Hosts/Supervisors: Ana Martin-Villalba, Susanne Kleber, and members of the group (contact: or; Annarita Patrizi (


The recognition that within the tumour, there is a cell population that shares common features with their normal stem cell counterparts has opened a new window to look at neoplasia. This cancer stem cell-like population, also known as tumour-initiating cells, represents the most therapy-resistant cell population within a tumour and has therefore become a major focus in the development of future therapeutic strategies. Neural cancer stem cells (NCSCs) have been identified in GBM, medulloblastoma and ependymoma. These NCSCs share common signalling pathways for self renewal, proliferation and differentiation with normal NSCs. Understanding the pathways that are common to both normal and cancer stem cells and may be dysregulated in the latter will facilitate the discovery of new targets for gene therapy.


  • culturing glioma cancer stem cells and neural stem cells
  • orthotopic injections of glioma cells in immunosuppressed mice
  • characterization of cancer stem cells by FACS-analysis
  • investigating the signaling pathways of glioma cancer stem cells and neural stem cells
  • proximity ligation assay in glioma cancer stem cells upon different stimuli

part II: Analysis of differential expression using RNA-seq data

Date: 25.-29. November 2019

Location: IPMB (Institute of Pharmacy and Molecular Biotechnology) INF 364, 5th floor, CIP-Pool: Room 542 (t.b.c.)

Hosts/Supervisors: Matthias Schlesner ( & Cihan Erkut (


High-throughput technologies have become essential tools in almost every biomedical research field. These techniques allow to perform a large number of measurements simultaneously, and thus enable the profiling of biological systems at unprecedented speed and resolution.
One example is gene expression profiling, where the expression levels of thousands of genes are determined in parallel to create a global picture of the cellular state. The comparison of expression profiles to determine differential expression between healthy and diseased cells can reveal detailed insights into the biology of the disease.


  • Experimental design
  • Processing of RNA-seq data
  • Statistical considerations
  • Diagnostic plots and result visualization
  • Annotation and downstream analysis


part III: CARTs & AAVLPs: immunologic weapons against cancer

Date: 2.-6. December 2019

Location: DKFZ Teaching Lab

Hosts/Supervisors: Silke Uhrig-Schmidt, Patrick Schmidt (contacts:,


In recent years, immunotherapy has become of great interest to researchers, clinicians and pharmaceutical companies, particularly in its promise to treat various forms of cancer. By activating a patient’s own immune system, especially CAR T cell therapy achieved success in specifically eradicating tumor cells of hematologic malignancies. However, CAR T cells are sharp weapons that may overshoot or miss their target which often leads to life-threatening consequences. Thus, in order to offer a safe and efficient immunotherapy, CAR T cells need to be precisely controlled. One way to do so is the development of AAV-based virus-like particles (AAVLPs) that structurally mimic the cellular target of a CAR. The specific CAR-AAVLP interaction leads to temporal unavailability of the CAR on the T cell surface which is directly linked to reduced cytotoxic activity of the T cell. Likewise, a control of undesired cross-reactivity of CAR T cells by designer AAVLPs could be anticipated for future use in cancer immunotherapy.


• Isolation, sorting and activation of T cells from whole blood by Ficoll gradient
• Lentiviral transduction of T cells with CARs, expression analysis (FACS) and assessment of killing activity by xcelligence assay
• Small scale AAVLP production, characterization by western blot and Dynabead-assay (FACS analysis)
• Medium scale AAVLP purification by density gradient ultracentrifugation and titration by ELISA
• AAVLP-competition assay with CAR+ T cell line (Transduction followed by FACS analysis)

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