Functional Genomics Center Zurich

New FGCZ outstations at the UZH Schlieren and ETH Hönggerberg campuses Bringing state-of-the-art multi-omics technologies directly to where research happens at both UZH Schlieren and ETH Hönggerberg! Here is what is new and available across our outstations: 📍 New Outstation: UZH Schlieren Campus Hosted by the UZH Flow ➡️ Cytometry Facility (Wagistrasse 12, 5th Floor), our Genomics unit is opening a dedicated hub starting this October: ➡️Single-Cell Transcriptomics: Walk-in access to 10x Genomics Chromium X and BD Rhapsody Express workflows. ➡️Sample Prep & QC: Walk-in access for library preparation and quality control, including an Agilent TapeStation. ➡️On-Site Sequencing: Walk-in access to an Illumina MiSeq i100 sequencer. ➡️Proteomics & Metabolomics Support: Regular on-site Help Desks offering free consultations on experimental design, sample preparation, and multi-omics data integration. Questions or upcoming projects? Reach out directly at sequencing@fgcz.ethz.ch. 📍 Expanded Presence: ETH Hönggerberg Campus We are continuing to broaden our long-standing support for the Hönggerberg research community: ➡️Genomics (HPL Building, G Floor): Full walk-in access to QC instrumentation (Qubit, TapeStation 4200), Illumina NextSeq 2000 sequencing, and single-cell workflows (10x Genomics and BD/Waters). ➡️Proteomics: A newly established outstation at the Institute of Biochemistry featuring an on-site mass spectrometer and expert FGCZ staff support, with more capabilities coming soon. ➡️Help Desks: Ongoing monthly Proteomics and Metabolomics consultation sessions. Check the FGCZ website for upcoming Help Desk schedules, walk-in training, and booking details. #LifeSciences #Genomics #Proteomics #Metabolomics #SingleCell #ETHZurich #UZH #Biotechnology #ResearchInfrastructure

Climate change is reshaping our forests. But forests are not passive. Trees respond. They adjust. They carry a history. Could a tree’s past help it cope with today’s climate? And if so, how long does it remember? In our recent study, we explored these questions in Scots pine: https://lnkd.in/e3y8xHzB I am grateful to all my coauthors and to institutional supports from Swiss Federal Institute for Forest, Snow and Landscape Research WSL; Functional Genomics Center Zurich, Epigenetics lab of University of Zurich, Epigenetics lab of NIBIO Norwegian Institute of Bioeconomy Research and Metabolomics lab of Albert-Ludwigs-Universität Freiburg (Albert Ludwig University of Freiburg)

Swiss Metabolomics Society Annual Meeting 2026 : 23 October 2026, Geneva ! A friendly reminder: the deadline for registration and poster abstract submissions is fast approaching! We are also delighted to announce that the full scientific programme is now available online: https://lnkd.in/e648a7ty The meeting will feature keynote lectures by Gunda Köllensperger from the University of Vienna and Tim Ebbels from Imperial College London, together with presentations showcasing the latest advances in metabolomics from researchers across Switzerland and beyond. There is still time to contribute and present your research during the poster session. If you have not yet submitted your abstract or completed your registration, we warmly encourage you to do so before the deadline (September 18, 2026). We look forward to welcoming you to Geneva for an inspiring day of scientific exchange, new ideas and networking! #Metabolomics #SwissMetabolomicsSociety #SMS2026 #Geneva #ScientificMeeting #Research #Networking

Superbugs🦠are getting tougher, but predatory bacteria like B. bacteriovorus can hunt them down! We show that model bacterium E.coli can escape these ‘living antibiotic’ by evolution, mainly through OmpF-porin loss. However, this comes at a cost ⚡ . Our newly accepted manuscript provides insights into this intricate bacterial predator-prey interaction. Link here: https://lnkd.in/e_zKK3UV Many thanks to my co-corresponding and first author Subham Mridha as well as Rolf Kümmerli for the collaboration on this extensive study at Universität Zürich | University of Zurich. This work was additionally supported by three great Master students Sarah L., Ove Christopher Mattmann, and Saskia Isele, as well as Bernd Roschitzki from Functional Genomics Center Zurich. This project nucleated based on FAN funding from the UZH Alumni Foundation and Ernst Göhner Stiftung. Completion of the study was enabled by Kurt and Senta Herrmann-Stiftung, as well as the Schweizerischer Nationalfonds SNF. #AMR, #Bacteria, #PredatoryBacteria, #Evolution

How do mammals keep their body temperature stable? It turns out they use more tricks than we thought. Did you know that the constant making and breaking of lipids can actually generate heat? After many unexpected twists and turns, we uncovered a hidden thermogenic role for futile lipid cycling in mice, highlighting the remarkable flexibility of adipocyte metabolism in regulating core body temperature. Huge thanks to my amazing postdoctoral mentor, great collaborators, and all co-authors. Christian Wolfrum Radhika Khandelwal ETH Zürich Cell Metabolism by Cell Press In addition to colleagues from Wolfrum lab, Jelena Zurkovic, PhD, Christoph Thiele, Alaa Othman, Chandramohan (Mohan) Chitraju, Ph.D. Robert Farese, Jr. Tobias Walther, and Miroslav Balaz were instrumental. #thermogenesis #lipid_Metabolism #Cell_Metabolism #futile_cycle #non_shivering_thermogenesis https://lnkd.in/gRrSgrZz

I am excited to share our latest research on apolipoprotein E (apoE), the primary genetic risk factor for Alzheimer’s disease. Our study shows that apoE is not a universal lipoprotein particle. Rather, apoE-containing particles are complex structures that carry distinct combinations of proteins and lipids. Importantly, we found that their molecular composition is determined by the cell of origin. In other words, apoE particles produced by different brain cell types have distinct molecular signatures, which may explain why apoE has divers and sometimes opposing functions in the brain. Huge BRAVOS to Evelina Voloviceva who led this project brilliantly from start to finish! Your dedication and hard work made this study possible. Thank you also to our collaborators at ETH Zurich and the University of Zurich for their invaluable contributions and support throughout this project, Sandra Goetze Arnold von Eckardstein Annika Jagels Alaa Othman and last but not least Stephy for the technical support. A special thank you to the Demenz Forschung Schweiz - Stiftung Synapsis for believing in this project and providing the necessary funding.

🧬 Our paper is now published in Cell Reports: 𝗦𝘁𝗿𝗲𝘀𝘀 𝗴𝗿𝗮𝗻𝘂𝗹𝗲𝘀 𝗮𝗿𝗲𝗻'𝘁 𝗷𝘂𝘀𝘁 𝘀𝘁𝗼𝗿𝗮𝗴𝗲 𝗹𝗼𝗰𝗸𝗲𝗿𝘀 𝗳𝗼𝗿 𝗺𝗥𝗡𝗔. 𝗧𝗵𝗲𝘆'𝗿𝗲 𝗮𝗰𝘁𝗶𝘃𝗲𝗹𝘆 𝗿𝗲𝗺𝗼𝗱𝗲𝗹𝗲𝗱 𝘁𝗼 𝘁𝘂𝗻𝗲 𝗺𝗲𝘁𝗮𝗯𝗼𝗹𝗶𝘀𝗺 𝗱𝗼𝘄𝗻, 𝗮𝗻𝗱 𝗯𝗮𝗰𝗸 𝘂𝗽 𝗮𝗴𝗮𝗶𝗻. 🔑 Key findings: 👉 Stress granules (SGs) — the membraneless condensates cells form under stress — 𝗺𝗮𝘁𝘂𝗿𝗲 𝘁𝗵𝗿𝗼𝘂𝗴𝗵 𝗽𝗵𝗼𝘀𝗽𝗵𝗼𝗿𝘆𝗹𝗮𝘁𝗶𝗼𝗻 by protein kinase A (PKA) in S. cerevisiae 👉 Catalytic PKA subunits condense into SGs during stationary phase, where 𝗦𝗚-𝗹𝗼𝗰𝗮𝗹𝗶𝘇𝗲𝗱 𝗣𝗞𝗔 𝗮𝗰𝘁𝗶𝘃𝗶𝘁𝘆 is selectively maintained 👉 Inhibiting PKA during long-term stationary phase blocks SG maturation, prevents metabolic shutdown, and delays the ordered restart of cell growth 👉 Together, this reveals a SG maturation mechanism selectively activated during chronic stress that 𝗽𝗿𝗲𝘀𝗲𝗿𝘃𝗲𝘀 𝗦𝗚 𝗶𝗻𝘁𝗲𝗴𝗿𝗶𝘁𝘆 and promotes cell recovery from prolonged starvation 💡 These findings reshape our understanding of stress granules — not as static "storage" compartments, but as dynamically regulated structures with their own maturation program and purpose. This raises the question of whether similar mechanisms could be conserved in mammalian cells, particularly given that SG protein deposition into insoluble aggregates is a hallmark of neurodegenerative pathologies. 📄 Read the full paper: https://lnkd.in/eZnppBKB 👥 Huge thanks to the team and collaborators from Raffaele Mezzenga lab (ETH Zurich) and the Functional Genomics Center Zurich #StressGranules #PKA #Maturation #PhaseSeparation #PhaseTransition #Metabolism #Starvation #Neurodegeneration #CellReports

Thrilled to share a new important study from the lab, published today in Nature, showing how cohesin mediates efficient replication fork plasticity and stress response, using its loop extrusion activity to promote 3D contacts on replicating DNA: https://lnkd.in/e57mD9E9 Combining a new MicroC-based method to map 3D-genome interactions at replicating DNA with genetic tools to inactivate cohesin functions, we show that cohesin accumulates at stressed replication forks and uses loop extrusion to modulate 3D interactions among sister forks and neighboring replicons. Such fork tethering enables coordinated slowdown of DNA synthesis by preventing PRIMPOL engagement and driving fork reversal. While protecting the genome from replication stress, this may support cancer cell resistance to genotoxic treatments and be targeted or defective in cohesin-mutated tumours. Mechanistically, our work supports the emerging role of 3D genome organization in genome maintenance and a novel view of the replication stress response that goes beyond local responses to stress and lesions, instead integrating throughout the nucleus via nuclear architecture and organization. This work largely reflects the creativity, technical skills & impressive resilience of Daniel G. Acosta, outstanding postdoc in our lab, currently transitioning towards independence. Dani is clearly a rising star in our field and deserves by far the largest credit for this work. This was truly a joint effort with Ana Losada, Daniel Giménez Llorente and Ana Cuadrado at CNIO - Spanish National Cancer Research Centre, providing essential expertise in 3D genome organization and analysis. More help from Melani Martins Rodrigues and Moses Aouami in our lab, and proteomic analyses from Javier Munoz and Orhi Barroso Gomila. We are grateful to the Swiss National Science Foundation SNSF for the generous support to this project, and to EMBO and Novartis Foundation for their direct support to Daniel’s work in our lab. Thanks also to the Functional Genomics Center Zurich for excellent technical support.

A full room for the Zurich Trace Tutorial Afternoon 🎉 More than 75 registrations and a full room: On 9 September, researchers and clinicians from Zurich, from other parts of Switzerland, and from Germany joined us at the FGCZ for an afternoon on stable isotope tracing, from the fundamentals to in vivo studies and clinical applications. Thank you to our speakers: 🔹 Nicola Zamboni (ETH Zurich) – The good, the bad, and the ugly of stable isotope tracing 🔹 Raphael J. Morscher (University Children's Hospital Zurich) – In vivo tracing 🔹 Thorsten Hornemann (University Hospital Zurich) – Tracing sphingolipids 🔹 Sean Froese (University Children's Hospital Zurich) – Tracing in inherited metabolic disorders 🔹 Laurent Bigler (University of Zurich) – Tracing and structure elucidation with MS and NMR 🔹 Alaa Othman (FGCZ) – Cases from the platform The questions kept coming through the coffee break and well into the apéro – exactly what we hoped for!! Zurich Trace is a clinical platform for stable isotope tracing, built jointly by the University Hospital Zurich, the University Children's Hospital Zurich, the University of Zurich, ETH Zurich and the Functional Genomics Center Zurich: from assay design and standardized pre-analytics to analysis pipelines and interpretation. Planning a tracing experiment, or sitting on data you would like to discuss? Get in touch with us, or visit zurichtrace.ch. In case you missed it in the meantime, you can also now visit Zurich Trace B-Fabric at https://lnkd.in/e2dztRwF. Thanks to Can Türker and his team for the great efforts at Zurich Trace. Thanks to everyone who came, and to the FGCZ team who made the afternoon run smoothly ( especially Alaa Othman, Annika Jagels, Martina Zanella). #StableIsotopeTracing #Metabolomics #Fluxomics #MassSpectrometry #ZurichTrace #FGCZ #UMZH University of Zurich ETH Zürich Universitätsspital Zürich Kinderspital Zürich Functional Genomics Center Zurich Thorsten Hornemann, Raphael J. Morscher, Martin Poms, Sean Froese, Matthias Baumgartner, Martin Hersberger, Nicola Zamboni, Laurent Bigler, Alaa Othman, Can Türker, Ralph Schlapbach

Where Does a Protein Really Begin? Proteins often undergo extensive processing after their synthesis. They can be cleaved by proteases as part of their biological function or partially degraded during purification and storage. As a result, identifying the authentic N-terminus of a protein is not always straightforward. At FGCZ, our proteomics experts, Dr. Peter Gehrig, Simone Wüthrich, Dr. Serge Chesnov, and Dr. Paolo Nanni, have systematically investigated different reagents and workflows for the confident characterization of protein N-termini. Their work provides valuable guidance in selecting the most suitable approach for a wide range of protein samples and experimental questions. For further details, please refer to the publication below. https://lnkd.in/eqsiF8rZ