Skip to main content

Cancer cells on a slippery slope

Sep 10, 2021 // How cellular adaptations can complicate tumor treatments

A tumor consists of numerous cell types with different characteristics. The differences between individual cancer cells determine the development of the disease, but also the effect of targeted therapies. A research team from the Charité - Universitätsmedizin Berlin, the IRI Life Sciences and the German Cancer Consortium has now succeeded in tracing the life paths of colorectal cancer cells. The researchers were able to observe how the individual cells react to therapy and sometimes adopt a resistant state after cancer treatment. As they describe in the scientific journal EMBO Molecular Medicine, weak points of current therapeutic interventions can be recognised in this way and improved in the future.

Single cell sequencing unveils the development of colorectal cancer

A technique known as single cell sequencing enables researchers to study gene expression – the activity of individual genes – across thousands of individual cells at the same time. Tumors consists of subpopulations of cells which, in addition  to having different characteristics, continually adapt to changes in their microenvironment. Using single cell sequencing, a team of researchers led by PD Dr. Markus Morkel and Prof. Dr. Nils Blüthgen from Charité’s Institute of Pathology and at the IRI Life Sciences studied the inherent heterogeneity of tumor tissues in order to gain a clearer picture of the colorectal cancer development process.

Using a trick helped to determine the current state of each cell and what the gene activity looked like before

The researchers started by comparing human colorectal cancer cells with cells found in healthy gut tissue. By collecting data on a total of more than 100,000 individual cells, they were able to define cell characteristics which were universal across individual patients. Conventional sequencing methods only provide a picture of gene activity at a specific moment in time.

In order to recreate and observe the dynamic changes taking place in tissues at the cellular level, the researchers had to create three-dimensional cultures of human colorectal cancer cells. “Using these ‘organoids’ as they are called, we were able to trace the cells’ developmental trajectory,” explains PD Dr. Morkel, adding: “Thanks to a clever laboratory technique, we were able to label the cells’ RNA at a specific point in time. In addition to determining the current status of activity for each individual cell, this technique also provided us with a picture of gene transcription from a few hours earlier.”

The research team then examined the way in which the cancer cells within these organoids adapted to clinically important therapies with targeted inhibitors. Not all of the cancer cells responded in the same way. While some cells were extinguished by this treatment, others took what might be best described as ‘a wrong turn’. Deviating from their normal developmental trajectories, they entered a new state which rendered them resistant to the recently administered drugs.

Machine learning is crucial to analyse data and better understand the processes in cells

“These types of single cell experiments with cancer tissues represent a huge logistical and technical challenge. They involve collaborations between specialists across multiple facilities – ranging from surgical specialists to database experts,” explains PD Dr. Morkel, who also serves as the main point of contact at the Berlin Institute of Health at Charité’s Bioportal Single Cells, a core facility which aims to enable the fast and efficient incorporation of single cell technologies in near-patient translational research.

One obvious challenge is addressed by Prof. Blüthgen: “Measuring the activity of thousands of genes in hundreds of thousands of cells produces very large volumes of data,” he explains, adding: “It is mainly due to advances in the field of machine learning that we are now in a position to analyse these data in an efficient way. This enables us to gain a better understanding of the essential cellular processes during tumor development and resistance formation to  improve colectoral cancer treatments for the benefit of patients.”

Original publication

Uhlitz F et al. Mitogen-activated protein kinase activity drives cell trajectories in colorectal cancer. EMBO Mol Med (2021), DOI: 10.15252/emmm.202114123


Dr. Markus Morkel
Institute of Pathology and BIH Bioportal Single Cells
Charité – Universitätsmedizin Berlin
email: markus.morkel(at)

Prof. Dr. Nils Blüthgen
IRI Life Sciences and Institute of Pathology
Charité – Universitätsmedizin Berlin        
email: nils.bluethgen(at)