Single Cell Metabolic Analysis at High Speed and Scale

In a groundbreaking development, a team of scientists from the European Molecular Biology Laboratory (EMBL) and the German Cancer Research Center (DKFZ) have developed a new method called SpaceM. This innovative approach allows for the analysis of metabolite profiles of individual cells, combining fluorescence microscopy and a specific form of mass spectrometry called MALDI-imaging.

The new method, published in the prestigious journal Nature Methods (DOI: 10.1038/s41592-021-01198-0), offers novel capacities for spatial single-cell metabolomics and is cost-efficient, using existing instrumentation. According to Theodore Alexandrov from EMBL, SpaceM is set to democratize single-cell metabolomics worldwide, answering a variety of pressing biomedical questions.

The analysis of metabolite profiles has become a focus of interest in many research disciplines, as individual cells in organs or tissues do not have a uniform metabolite profile, but often exhibit pronounced heterogeneity. This heterogeneity is crucial for understanding the condition of an organ or tissue, and the localization of individual cells within the tissue network is of particular importance.

The team behind SpaceM studied nearly 30,000 individual cells, of which a quarter showed a distinctly altered lipid profile indicating an inflammatory change known as steatosis. They validated the method by studying a population of human liver cells stimulated with fatty acids and pro-inflammatory cytokines as an in vitro model of Non-Alcoholic Fatty Liver Disease and Non-Alcoholic Steatohepatitis.

The DKFZ, a member of the Helmholtz Association of German Research Centers, is the largest biomedical research institution in Germany, employing over 3,000 people. More than 1,300 scientists at the DKFZ focus on cancer research, including the study of cancer development, identification of risk factors, and the development of new strategies for cancer prevention and treatment.

The DKFZ is a member of the German Consortium for Translational Cancer Research (DKTK), which operates at seven university partner locations. It also operates the National Center for Tumor Diseases (NCT) in Heidelberg and Dresden, and the Hopp Children's Tumour Center KiTZ in Heidelberg, jointly with partners from university hospitals. The DKFZ is 90 percent financed by the Federal Ministry of Education and Research and 10 percent by the state of Baden-Württemberg.

In addition to its research activities, the DKFZ's Cancer Information Service (KID) provides individual answers to all questions on cancer for patients, interested citizens, and experts. The KID is a valuable resource for those seeking information about cancer and its treatment options.

With SpaceM, the team expects to make significant strides in understanding the complexities of single-cell metabolomics, ultimately leading to more precise tumor diagnosis and successful cancer treatment. The method and open-source algorithms are set to revolutionize the field and open up a wealth of new research opportunities.