Cookie Settings

We use cookies to optimize our website. These include cookies that are necessary for the operation of the site, as well as those that are only used for anonymous statistic. You can decide for yourself which categories you want to allow. Further information can be found in our data privacy protection .


These cookies are necessary to run the core functionalities of this website and cannot be disabled.

Name Webedition CMS
Purpose This cookie is required by the CMS (Content Management System) Webedition for the system to function correctly. Typically, this cookie is deleted when the browser is closed.
Name econda
Purpose Session cookie emos_jcsid for the web analysis software econda. This runs in the “anonymized measurement” mode. There is no personal reference. As soon as the user leaves the site, tracking is ended and all data in the browser are automatically deleted.

These cookies help us understand how visitors interact with our website by collecting and analyzing information anonymously. Depending on the tool, one or more cookies are set by the provider.

Name econda
Purpose Statistics
External media

Content from external media platforms is blocked by default. If cookies from external media are accepted, access to this content no longer requires manual consent.

Name YouTube
Purpose Show YouTube content
Name Twitter
Purpose activate Twitter Feeds

HP-F3: Epitranscriptomics, Crystallography, and Organoid Cancer Models

Type: Practical Course with Student Seminars


Part 1: Crystallography


Date: 30. October – 3. November 2023 (no course on 1. Nov.)

Location: DKFZ Teaching Lab and D160 Division Labs (DKFZ Main Building, 7th floor)

Hosts/Supervisors: Erec Stebbins, Johan Zeelen, Alex Hempelmann, and Monica Chandra (contacts:,



Crystallography: A tool to understand protein-protein interactions and drug discovery 



  • Practical introduction to crystallography
  • Crystallography and cancer research
  • Crystallization of a protein
  • Solving the structure of a protein

Part 2: Epitranscriptomics: RNA editing and its therapeutic application

Date: 13.-17. November 2023

Location: DKFZ Teaching Lab, D150 Division Labs and Flow Cytometry Facility (DKFZ Main Building, 7th floor)

Hosts/Supervisors: Nina Papavasiliou, Riccardo Pecori, Beatrice Casati, Annette Arnold (contacts:,



Epitranscriptomics: RNA editing and its therapeutic application



RNA editing is the most abundant epitranscriptomic modification in Metazoans. It has several essential biological functions in many organisms and humans. RNA editing is the result of the deamination of adenosine-to-inosine (A-to-I) or cytosine-to-uracil (C-to-U) leading to a base change within the RNA molecule. In this module, we explore the biological functions of RNA editing and RNA editors and how ADAR1 (one A-to-I RNA editor) can be used to manipulate genetic information for therapeutic purposes.

Functional assays to assess RNA editing activity (including tissue culture and flow cytometer approaches)


Part 3: Creating cancer models using organoids and CRISPR/Cas9 base editors

Date: 4.-8. December 2023

Location: DKFZ Teaching Lab

Host/Supervisors: Jens Puschhof, Lena Schorr, Kyanna Ouyang, Kamil Moskal, Sahana Asokan, Aurelia Saftien (contact:



Adult stem cells (ASCs) reside in most organs of the mammalian body, where they constantly renew tissue or replenish lost cells upon injury. This process is based on the stem cells' ability to self-renew and give rise to differentiated daughter cells. One of the most active ASCs is located at the bottom of the crypts in the intestine, from where it continuously replenishes all cell types of the epithelium every 5 days. In 2009, it was first shown that ASCs from the mouse small intestine can perform their functions in vitro as well. Upon embedding the intestinal stem cells in a gel of extracellular matrix proteins and providing them with medium containing the essential niche components, they started to self-renew, differentiate and organize into 3D structures which are referred to as organoids. These models can be propagated indefinitely, contain both ASCs and differentiated cell types and resemble the structure and function of the original organ. Organoids models are rapidly becoming a central workhorse of cancer research to study the cellular heterogeneity of tumors, test patient-specific drug efficacy, recapitulate the mutational processes active in a tumor and assess tumor-microenvironment interactions.



In this practical, organoids will be derived from mouse biopsies and engineered using CRISPR/Cas9 base editing techniques to recapitulate key mutations found in colorectal cancer. To achieve these goals, several key aspects of organoid experimentation will be introduced, including media preparation, passaging and plating of organoids, live imaging, electroporation, clonal expansion, DNA extraction and sanger sequencing to validate CRISPR success.

to top
powered by webEdition CMS