A new imaging approach is shedding light on one of cell biology’s most elusive questions: how lipids are organized and sorted within membranes.
Cell membranes are far from simple barriers. They are highly organized landscapes made up of tiny patches called nanodomains, where lipids (fats) and proteins cluster together to carry out essential tasks such as communication, cargo sorting, and material transport. These nanoscale regions act like busy hubs, directing molecular traffic and helping cells respond to their environment.
Researchers have mapped protein behavior in these domains in detail, but lipids have remained much harder to pin down. Unlike proteins, lipids move extremely quickly within membranes, making them difficult to track. Traditional imaging tools often blur their positions, leaving major gaps in understanding how these molecules are arranged and how they contribute to cellular function.
Tracking Elusive Lipids
To overcome this challenge, scientists developed “bifunctional lipid probes.” These specially designed molecules closely resemble natural lipids but carry subtle chemical features that allow them to be tracked.
Once inside living cells, the probes can be “locked” in place using light (photo-crosslinking), effectively freezing lipid movement at a specific moment in time. Researchers then attach fluorescent tags through click chemistry, making it possible to visualize where individual lipid types were located without significantly disturbing the cell.
Combining Imaging Techniques
Even with these probes, standard light microscopy cannot reveal the fine structure of cell membranes. Electron microscopy offers much higher resolution, but it lacks the ability to track specific molecules.
Correlative light and electron microscopy (CLEM) combines both approaches, linking molecular labeling with detailed structural images. When paired with lipid probes, this method, called Lipid-CLEM, shows both where lipids are located and how membranes are organized at a microscopic level.
Earlier versions of CLEM had important limitations. Some damaged delicate membrane structures, others only worked at the cell surface, and many could not distinguish between different lipid types. To overcome these issues, Mathilda Lennartz and colleagues from the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, Germany, and the Weizmann Institute of Science in Rehovot, Israel, developed an improved technique known as Lipid-CLEM.
Novel 3D imaging of lipids
Mathilda Lennartz, co-corresponding and lead author of the study, explains, “To study lipid sorting in early endosomes – a key sorting station inside the cell – cells must be rapidly frozen to stop lipids in their tracks and to preserve the membrane of the cells. Later, these lipids can be labeled on very thin slices of the sample, termed “sections,” of cells using click chemistry. These sections are what we then image using the Lipid-CLEM approach.”
“With Lipid-CLEM, we observed that a specific lipid called sphingomyelin is more common in small vesicles inside the endosome and less common in tubular membrane domains. This separation has already been observed for some proteins,” says Mathilda. “What we concluded from this is that at least some lipids, just like proteins, must also be sorted in the endosome. Interestingly, in our study, sphingomyelin and a protein cargo arrive at the same time in the early endosome but separate into different domains, indicating that lipid and protein trafficking routes can diverge during this sorting.”
The power of team work
Ori Avinoam’s team at the Weizmann Institute contributed expertise in correlative light and electron microscopy. Ori says, “This study highlights how essential collaborations are for driving research forward. Bringing together complementary expertise allowed us to establish a method that made it possible to uncover fundamental principles of lipid sorting that were previously inaccessible.”
André Nadler, corresponding author, summarizes, “Our Lipid-CLEM workflow enables 3D visualization of lipid densities in membrane nanodomains, offering a new way to study lipid organization in complex cellular structures. We finally can look at lipid sorting in membranes with the resolution we need. We believe that our new method Lipid-CLEM will help us to better understand how lipids work in cells, as it allows us to study both lipids and proteins together during membrane organization and function. This may also contribute to a better understanding of membrane dysfunction-related diseases.”
Reference: “Visualizing suborganellar lipid distribution using correlative light and electron microscopy” by H. Mathilda Lennartz, Suman Khan, Weihua Leng, Kristin Böhlig, Gunar Fabig, Yannick Kieswald, Falk Elsner, Nadav Scher, Michaela Wilsch-Bräuninger, Ori Avinoam and André Nadler, 20 March 2026, Nature Cell Biology.
DOI: 10.1038/s41556-026-01915-x
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