Visualizing suborganellar lipid distribution using correlative light and electron microscopy

H. Mathilda Lennartz; Suman Khan; Weihua Leng; Kristin Böhlig; Gunar Fabig; Yannick Kieswald; Falk Elsner; Nadav Scher; Michaela Wilsch-Bräuninger; Ori Avinoam; André Nadler

doi:10.1038/s41556-026-01915-x

Visualizing suborganellar lipid distribution using correlative light and electron microscopy

H. Mathilda Lennartz^*
, Suman Khan
, Weihua Leng
, Kristin Böhlig
, Gunar Fabig
, Yannick Kieswald
, Falk Elsner
, Nadav Scher
, Michaela Wilsch-Bräuninger
, Ori Avinoam
, André Nadler^*

^*Corresponding author for this work

Department of Biomolecular Sciences

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

Abstract

Lipids and proteins compartmentalize biological membranes into nanoscale domains, which are crucial for signalling, intracellular trafficking and many other cellular processes. Studying nanodomain function requires the ability to measure protein and lipid localization at the nanoscale. Current methods for visualizing lipid localization do not meet this requirement. Here we introduce a correlative light and electron microscopy workflow to image lipids (Lipid-CLEM), combining near-native lipid probes and on-section labelling by click chemistry. This approach enables the quantification of relative lipid densities in membrane nanodomains. We find differential partitioning of sphingomyelin into intraluminal vesicles, recycling tubules and the boundary membrane of the early endosome, representing a degree of nanoscale organization previously observed only for proteins. We anticipate that our Lipid-CLEM workflow will greatly facilitate the mechanistic analysis of lipid functions in cell biology, allowing for the simultaneous investigation of proteins and lipids during membrane nanodomain assembly and function.

Original language	English
Journal	Nature Cell Biology
DOIs	https://doi.org/10.1038/s41556-026-01915-x
Publication status	Published - 20 Mar 2026

Funding

A.N. gratefully acknowledges financial support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement nos. GA 758334 ASYMMEM and AURORA). A.N. acknowledges financial support by the Deutsche Forschungsgemeinschaft (DFG) via the TRR83 consortium. This research was supported by an Allen Distinguished Investigator Award, a Paul G. Allen Frontiers Group advised grant of the Paul G. Allen Family Foundation to A.N. O.A. gratefully acknowledges financial support by the Israel Science Foundation (grant no. 3729/20), the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 851080), the Henry Chanoch Krenter Institute for Biomedical Imaging and Genomics and support given by the Heineman Foundation through Minerva. O.A. is the incumbent of the Miriam Berman presidential development chair. G.F. thanks the support by the Simons Foundation (CCBx programme, no. 1157392). We thank the following services and facilities at MPI-CBG Dresden for their support: the Electron Microscopy Facility, the Light Microscopy Facility, the Genome Engineering Facility, the Scientific Computing Facility and the Organoid and Stem Cell Facility. We thank J. Peychl, B. Schroth-Diez and T. Fürstenhaupt for their outstanding support and expert advice. We thank the Core Facility Cellular Imaging at the Faculty of Medicine Carl Gustav Carus at TU Dresden for technical support. We thank P. Ronchi and A. von Appen for expert advice during the development of the CLEM workflow and V. Oorschot for advising on immunogold labellin

All Science Journal Classification (ASJC) codes

Cell Biology

Access to Document

10.1038/s41556-026-01915-xLicence: CC BY

Cite this

@article{78fc3321fe2242adab5dc8d9634d7ea2,

title = "Visualizing suborganellar lipid distribution using correlative light and electron microscopy",

abstract = "Lipids and proteins compartmentalize biological membranes into nanoscale domains, which are crucial for signalling, intracellular trafficking and many other cellular processes. Studying nanodomain function requires the ability to measure protein and lipid localization at the nanoscale. Current methods for visualizing lipid localization do not meet this requirement. Here we introduce a correlative light and electron microscopy workflow to image lipids (Lipid-CLEM), combining near-native lipid probes and on-section labelling by click chemistry. This approach enables the quantification of relative lipid densities in membrane nanodomains. We find differential partitioning of sphingomyelin into intraluminal vesicles, recycling tubules and the boundary membrane of the early endosome, representing a degree of nanoscale organization previously observed only for proteins. We anticipate that our Lipid-CLEM workflow will greatly facilitate the mechanistic analysis of lipid functions in cell biology, allowing for the simultaneous investigation of proteins and lipids during membrane nanodomain assembly and function.",

author = "Lennartz, \{H. Mathilda\} and Suman Khan and Weihua Leng and Kristin B{\"o}hlig and Gunar Fabig and Yannick Kieswald and Falk Elsner and Nadav Scher and Michaela Wilsch-Br{\"a}uninger and Ori Avinoam and Andr{\'e} Nadler",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2026.",

year = "2026",

month = mar,

day = "20",

doi = "10.1038/s41556-026-01915-x",

language = "English",

journal = "Nature Cell Biology",

issn = "1465-7392",

publisher = "Nature Research",

}

TY - JOUR

T1 - Visualizing suborganellar lipid distribution using correlative light and electron microscopy

AU - Lennartz, H. Mathilda

AU - Khan, Suman

AU - Leng, Weihua

AU - Böhlig, Kristin

AU - Fabig, Gunar

AU - Kieswald, Yannick

AU - Elsner, Falk

AU - Scher, Nadav

AU - Wilsch-Bräuninger, Michaela

AU - Avinoam, Ori

AU - Nadler, André

PY - 2026/3/20

Y1 - 2026/3/20

N2 - Lipids and proteins compartmentalize biological membranes into nanoscale domains, which are crucial for signalling, intracellular trafficking and many other cellular processes. Studying nanodomain function requires the ability to measure protein and lipid localization at the nanoscale. Current methods for visualizing lipid localization do not meet this requirement. Here we introduce a correlative light and electron microscopy workflow to image lipids (Lipid-CLEM), combining near-native lipid probes and on-section labelling by click chemistry. This approach enables the quantification of relative lipid densities in membrane nanodomains. We find differential partitioning of sphingomyelin into intraluminal vesicles, recycling tubules and the boundary membrane of the early endosome, representing a degree of nanoscale organization previously observed only for proteins. We anticipate that our Lipid-CLEM workflow will greatly facilitate the mechanistic analysis of lipid functions in cell biology, allowing for the simultaneous investigation of proteins and lipids during membrane nanodomain assembly and function.

AB - Lipids and proteins compartmentalize biological membranes into nanoscale domains, which are crucial for signalling, intracellular trafficking and many other cellular processes. Studying nanodomain function requires the ability to measure protein and lipid localization at the nanoscale. Current methods for visualizing lipid localization do not meet this requirement. Here we introduce a correlative light and electron microscopy workflow to image lipids (Lipid-CLEM), combining near-native lipid probes and on-section labelling by click chemistry. This approach enables the quantification of relative lipid densities in membrane nanodomains. We find differential partitioning of sphingomyelin into intraluminal vesicles, recycling tubules and the boundary membrane of the early endosome, representing a degree of nanoscale organization previously observed only for proteins. We anticipate that our Lipid-CLEM workflow will greatly facilitate the mechanistic analysis of lipid functions in cell biology, allowing for the simultaneous investigation of proteins and lipids during membrane nanodomain assembly and function.

UR - https://www.scopus.com/pages/publications/105034199631

U2 - 10.1038/s41556-026-01915-x

DO - 10.1038/s41556-026-01915-x

M3 - Article

C2 - 41862633

AN - SCOPUS:105034199631

SN - 1465-7392

JO - Nature Cell Biology

JF - Nature Cell Biology

ER -

Visualizing suborganellar lipid distribution using correlative light and electron microscopy

Abstract

Funding

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this