Practical Course HP-F9: Cancer Genomics, Proteomics and Murine Tumor Models

plus 3 planning days ahead in March/April (to be arranged with the participants)

Functional genomics research collects quantitative genomic as well as proteomic data and links this to functional and phenotypic measurements. This practical presents an overview of genomic, proteomic and functional analysis methods in cancer research, in vitro and in vivo. Main learning objectives of this course are to enable students to work in a team to plan a small project based on previous data, to conduct and explain selected functional genomics methods and mouse models and to interpret their data with respect to the initial research question.

Module 1 (3 days planning in March/April + 7 days lab work in 8. April – 10. May)

Functional characterization of activating promoter mutations in cancer

Supervisors: Cindy Körner, Janina Müller, Dominic Helm, Luisa Schwarzmüller, Veronica Rodrigues de Melo Costa, Stefan Wiemann

During a pre-meeting (date will be arranged with the participants), we will present background on breast cancer as well as on a scientific observation of the division. This will serve as basis for generating research questions and hypotheses to be addressed during the course both theoretically and experimentally. Prior to the course (in March/April, dates to be determined), together with the supervisors, all students will spend 3 days (potentially virtual/hybrid channels) to give their seminar presentations and to develop in groups of four a complete project plan to be followed in the second part of this module (7 days lab work in total, time windows to be arranged). They will conduct selected experiments to test their hypotheses. Data will be interpreted together with the supervisors in the context of the initial hypothesis. Methods may include CRISPR editing, CRISPRa, TaqMan qRT-PCR, transfections and functional analyses (e.g. cell cycle, proliferation, apoptosis, drug sensitivity). Further, the participants will be introduced to mass spectrometry based proteomics workflows (LC-MS/MS) for creating an unbiased picture of their cellular system; they will also gain insights into different resources of publicly available patient datasets and how to exploit them (e.g. using R) in order to establish translational relevance to their in vitro hypotheses.

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Module 2 (5 days – group 1: 6.-10. May; group 2: 13.-17. May)

Gene expression analysis in mouse models of human tumors

Supervisors: Haikun Liu, Xian Li, Yuling Chen @TP4

Using advanced genetically engineered mouse models of glioblastoma, the students will learn how to isolate mouse brain tumors, prepare sections, and perform immunohistochemistry experiments followed with microscopic analysis. Alterations of key signalling pathways like PI3K/AKT or MAPK pathway will be analysed in this in vivo material. Basic principles of mouse models of human cancer will be introduced.