Four times as much information per cell
Scientists from the BIH at Charité and the MDC have teamed up with U.S. and Japanese researchers to take single-cell analysis to a new level. They combined methods for determining mRNA levels and DNA accessibility with those used for detecting proteins and mutations in mitochondrial DNA, thus allowing them to simultaneously profile all this information from thousands of individual cells. The researchers have now published their findings in the journal Nature Biotechnology and one of the lead authors recently joined the joint Focus Area “Single Cell Approaches for Personalized Medicine,” which is jointly run by the BIH at Charité and was co-founded with the MDC and Charité – Universitätsmedizin Berlin.
These days single-cell analysis is primarily associated with determining the messenger RNA (mRNA) profile of individual cells. These messenger molecules transmit information from the genome in the cell nucleus – the DNA – into the cytoplasm, where the mRNA is translated into protein. The amount and composition of mRNA may thereby vary across different types of cells. For example, cells of the nervous system require different proteins than liver cells, meaning they also read (or transcribe) different genes from DNA into mRNA.
“However, a picture of a cell based on its mRNA profile alone is incomplete,” explains Dr. Leif S. Ludwig, head of the Emmy Noether Junior Research Group “Stem Cell Dynamics and Mitochondrial Genomics” at the BIH and the MDC. “Not all mRNA molecules are necessarily translated 1:1 into proteins, and the amount of mRNA cannot be readily measured for every gene,” explains Leif S. Ludwig. “The ability to simultaneously quantify proteins provides a more comprehensive picture of what is happening in the cell.”
In collaboration with colleagues from the United States and Japan, the scientists determined not only the mRNA and protein profiles but also the “accessibility” of the DNA in individual cells. This is because the genetic material of the cell is tightly packed into a complex structure called chromatin: sites where the chromatin is less tightly packed can be more easily transcribed into mRNA, while very tightly packed sites are hardly ever used for transcription. “This enables us to assess how the DNA structure is related to the amount of mRNA, and as a result we can better understand why some genes are transcribed more often than others,” says Leif S. Ludwig, a trained biochemist and physician.
With his group, which is based at the Berlin Institute of Medical Systems Biology (BIMSB) of the MDC, he is also studying the DNA of mitochondria – the “power plants” of the cell – which have their own genome. They are, for example, investigating how changes in mitochondrial DNA contribute to human diseases. “So it made sense for us to include mitochondrial DNA in the single-cell analysis,” explains Leif S. Ludwig. This enabled the scientists to be the first in the world to examine four modalities simultaneously at the single cell level. This ability is also of uttermost importance from a medical perspective. “For example, the more comprehensively we can analyze cancer cells, the better we can understand what goes wrong inside these cells – which will in turn facilitate the precise tailoring of treatment strategies,” he says.
Dr. Ludwig is pursuing the clinical application of his findings together with his clinical partners, Professors Lars Bullinger and Ulrich Keller, the Directors of the Department of Hematology, Oncology and Tumor Immunology at Charité Campus Virchow-Klinikum (CVK) and Charité Campus Benjamin Franklin (CBF), respectively.
Publication: Nature Biotechnology “Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells,” E. P. Mimitou, …. Leif S. Ludwig, Vijay G. Sankaran, Aviv Regev and Peter Smibert https://doi.org/10.1038/s41587-021-00927-2