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Fighting off pathogens is a tour de force that must happen with speed and precision. A team of researchers at CeMM and MedUni Vienna led by Christoph Bock and Matthias Farlik has investigated how macrophages—immune cells that are the body’s first responders—master this challenge. Their study, published in Cell Systems (DOI: 10.1016/j.cels.2025.101346), offers a time-resolved analysis of the molecular processes that unfold when these cells encounter various pathogens. They developed a new method that combines gene editing and machine learning, which identified key regulators of macrophage immune responses.

With this prestigious recognition, EMBO honors Christoph Bock for his scientific contributions at the interface of biotechnology, bioinformatics, and molecular medicine. His research combines experimental immunology and cancer biology with computational methods, including machine learning and artificial intelligence. “We develop technologies to help understand human diseases in all their complexity, and we aim to program immune cells as molecular therapies,” Christoph Bock says, describing the main focus of his work.

The artificial intelligence (AI) model GPT-4, known from its application in ChatGPT, shows impressive capabilities in biomedical research and can be used in many ways for simulations. A simulator developed at MedUni Vienna and CeMM and based on GPT-4 shows increased accuracy in classifying the importance of genes in cancer cells, as well as in the prognosis of cancer patients. The results of the study were published in the journal Computers in Biology and Medicine.

When pathogens invade the body, the immune system must react immediately to prevent or contain an infection. But how do our defence cells stay ready when no attacker is in sight? Scientists from Vienna have found a surprising explanation: They are constantly stimulated by healthy tissue. This keeps them active and ready to respond to pathogens. Based on this insight, future medications could be devised to selectively enhance our immune system’s attention. The study has been published in the journal Nature Immunology.

Bacillus Calmette-Guérin (BCG) is one of the world’s oldest and most widely used vaccines. It was developed in the early 20th century to provide protection from tuberculosis. Surprisingly, this vaccine protects not only against tuberculosis but also reduces the risk for various other infections, through a mechanism called trained immunity. A new study led by Christoph Bock and Mihai Netea found that epigenetic cell states predict whether or not an individual profits from the “wake-up call” to the innate immune system that is provided by the BCG vaccine. This discovery contributes to the development of future therapeutics that induce protective trained immunity.

Granulomas are an accumulation of immune cells in the tissue, often the result of an overactive immune response. Granulomas contribute to several inflammatory systemic diseases such as sarcoidosis, berylliosis, and rheumatoid arthritis. For the first time, scientists at CeMM, the Medical University of Vienna and the Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases have thoroughly characterized granulomas in the skin in immense detail. The results provide numerous insights into the composition, structure and signaling pathways of granulomas, providing clues for new therapeutic approaches. The study was published in the journal Immunity.

Christoph Bock’s team at the CeMM established a catalog of DNA methylation across 580 animal species. These data enabled a detailed dissection of the evolution of epigenetic regulation and the epigenome. The new study, published in Nature Communications, shows that the characteristic DNA methylation signatures of animal genomes are evolutionarily very old, having emerged long before the first mammals. Surprisingly, DNA methylation in starfish and sharks follows a very similar “code” as in orangutans or humans. This epigenetic code may even help protect against cancer – as indicated by DNA methylation patterns in birds, which rarely develop cancer.

CeMM congratulates Principal Investigator Christoph Bock on being awarded the Erwin Schrödinger Award of the Austrian Academy of Sciences (ÖAW) for his pioneering achievements in the field of single-cell sequencing and epigenetics. The Erwin Schrödinger Award together with the Wilhelm Hartel Prize are the highest prizes awarded annually by the ÖAW.

Molecular analysis of single cells provides an important basis for precision medicine. Five years ago, scientists around the world came together to pursue the “Human Cell Atlas” project, with the aim of cataloging all cells in the human body. These data have helped, for example, to identify those cell types that the coronavirus can infect particularly well. To accelerate and improve the creation of such cell catalogs, Paul Datlinger and André F. Rendeiro from Christoph Bock’s research group at CeMM developed a new method that enables single-cell RNA sequencing in a very large number of individual cells at the same time.

A new study exploits the characteristic epigenetic signatures of childhood tumors to detect, classify and monitor the disease. The scientists analyzed short fragments of tumor DNA that are circulating in the blood. These "liquid biopsy" analyses exploit the unique epigenetic landscape of bone tumors and do not depend on any genetic alterations, which are rare in childhood cancers. This approach promises to improve personalized diagnostics and, possibly, future therapies of childhood tumors such as Ewing sarcoma. The study has been published in Nature Communications.