CompCancer Seminar 02.06.2021 - Bernd Bodenmiller

The upcoming CompCancer Seminar will be hosted by Bettina Schmidt. Find the invitation below. The link is available from compcancer at charite dot de.

Dear PI's and fellow students,

in our next CompCancer seminar on Wednesday, 2nd of June at 10 AM, please welcome Bernd Bodenmiller, who will talk about his newly published paper (19.5.21, Cell Systems) on drug-sensitivity prediction based on signaling pathways in breast cancer.

It is interesting for you if you work on

#signaling pathways  #CyTOF  #drug-sensitivity prediction #bigdata #MANOVA #precision medicine

and I'm sure many different things that I did not capture. Feel free to forward this information to people who could be interested


One goal of precision medicine is to tailor effective treatments to patients’ specific molecular markers of disease. Here, we used mass cytometry to characterize the single-cell signaling landscapes of 62 breast cancer cell lines and five lines from healthy tissue. We quantified 34 markers in each cell line upon stimulation by the growth factor EGF in the presence or absence of five kinase inhibitors. These data—on more than 80 million single cells from 4,000 conditions—were used to fit mechanistic signaling network models that provide insight into how cancer cells process information. Our dynamic single-cell-based models accurately predicted drug sensitivity and identified genomic features associated with drug sensitivity, including a missense mutation in DDIT3 predictive of PI3K-inhibition sensitivity. We observed similar trends in genotype-drug sensitivity associations in patient-derived xenograft mouse models. This work provides proof of principle that patient-specific single-cell measurements and modeling could inform effective precision medicine strategies.

See you then,


Life after PhD Seminar - with Bastian Gastl

We would like to announce our upcoming Life after PhD (LAP) seminar, which will take place on Tuesday, 11.5.2021 at 4:30 pm on Zoom (the link is available from compcancer at charite dot de).

Our guest will be Dr. Bastian Gastl, who will share insights into his career path and current occupation as a Medical Science Liaison at Novocure. After having worked at a bank for a short time, he decided to switch gears entirely and did his Bachelor’s degree in Biology at the Ludwigs-Maximilians Universität in Munich. Following up on this, Bastian pursued his Master’s degree at Charité in Molecular Medicine. He extended his stay at Charité by doing his PhD in the group for Molecular Tumorpathology, focusing on effects of reduced DNA replication efficiency in KRAS-mutatant colorectal cancer cell models. When looking for interesting positions outside of academia after finishing his PhD, he first took up work as a Digital Business Consultant, before changing for his current job at Novocure.

Join us to find out about Bastian’s experiences on this way and get tips and hints for perspectives after completing your PhD!

Best wishes,

Wiebke (IRTG2403), Juliane (IRTG2290), and Pamela (CompCancer/ RTG2424)

For more information about this series, visit the IRTG 2403 website:

CompCancer Seminar 05.05.2021 - Adriana Salcedo

The upcoming CompCancer Seminar will be hosted by Louisa Krützfeldt from the Schulte group. Find the invitation below. The link is available from compcancer at charite dot de.

Dear all,

I would like to announce next week's CompCancer seminar on May 5th at 4 pm (CET). Adriana Salcedo from the Ontario Institute for Cancer Research will present her paper "A community effort to create standards for evaluating tumor subclonal reconstruction".

I invite you to read this interesting publication and collect your questions. Please feel free to share the information with anyone who might be interested in.

Please note that the Journal Club will be at 4 pm, not at 10 am as usual!

Best regards,


CompCancer Seminar 31.03.2021 - Samantha Praktiknjo

The upcoming CompCancer Seminar will be hosted by Clemens Messerschmidt from the Leser group. Find the invitation below. The link is available from compcancer at charite dot de.

Dear compcancer members,

Next Wednesday (2021-03-31) at 10:00, Samantha Praktiknjo will join us for our seminar to present her paper

"Tracing tumorigenesis in a solid tumor model at single-cell resolution".

The publication describes work done as a senior scientist in Nikolaus Rajewsky's group at the BIMSB.

Recently, she has joined the the newly established Single-Cell Research Focus Area as an Associate Group Leader at the BIH, Charité and MDC .

For this reason, they are eager to learn what others in Berlin are doing in the field, and are looking forward to identifying potentially interesting collaboration opportunities.

Best regards and hope to see you next week,


Wanja Kassuhn published his work on Classification of High-Grade Serous Ovarian Cancer

Classification of Molecular Subtypes of High-Grade Serous Ovarian Cancer by MALDI-Imaging

Wanja Kassuhn, Oliver Klein, Silvia Darb-Esfahani, Hedwig Lammert, Sylwia Handzik, Eliane T. Taube, Wolfgang D. Schmitt, Carlotta Keunecke, David Horst, Felix Dreher, Joshy George, David D. Bowtell, Oliver Dorigo, Michael Hummel, Jalid Sehouli, Nils Blüthgen, Hagen Kulbe, and Elena I. Braicu

Cancers, 2021

High-grade serous ovarian cancer (HGSOC) accounts for 70% of ovarian carcinomas with sobering survival rates. The mechanisms mediating treatment efficacy are still poorly understood with no adequate biomarkers of response to treatment and risk assessment. This variability of treatment response might be due to its molecular heterogeneity. Therefore, identification of biomarkers or molecular signatures to stratify patients and offer personalized treatment is of utmost priority. Currently, comprehensive gene expression profiling is time- and cost-extensive and limited by tissue heterogeneity. Thus, it has not been implemented into clinical practice. This study demonstrates for the first time a spatially resolved, time- and cost-effective approach to stratifying HGSOC patients by combining novel matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) technology with machine-learning algorithms. Eventually, MALDI-derived predictive signatures for treatment efficacy, recurrent risk, or, as demonstrated here, molecular subtypes mightbe utilized for emerging clinical challenges to ultimately improve patient outcomes.

1 2 3 4 5 6 7 >


The research training group CompCancer (RTG2424) is a DFG funded PhD programme in Berlin, focussing on computational aspects of cancer research.

Contact: compcancer at charite dot de