Subcellular lipid composition and transport significantly influence the physiological and pathological functions of both cells and organelles. However, lipid transport and turnover between organelles remain poorly understood due to a lack of methods for selectively labeling lipids in organelles.
In a study published in Nature Chemistry on Aug. 6, research teams led by Prof. ZHU Zhengjiang and Prof. CHEN Yiyun at Shanghai Institute of Organic Chemistry (SIOC) of the Chinese Academy of Sciences developed a subcellular photocatalytic labeling strategy that enables organelle-selective lipid analysis by mass spectrometry (MS) and the quantitative profiling of lipid transport between organelles.
Based on the structural characteristics of lipids, researchers designed a specifically photocatalytic proximity labeling probe, and optimized it for lipid reactivity. Organic dyes with organelle-specific localization were used as photocatalysts to activate the probe under blue light irradiation, generating reactive intermediates that selectively label lipids within specific organelles and yielding photocatalytically labeled (PL) lipids. Through liquid chromatography-MS-based lipidomic analysis, the detection of PL-lipids was achieved without the need for organelle separation.
Using this strategy, researchers identified 60 to 80 lipid species within mitochondria, nucleus and lysosomes, respectively, covering seven major lipid classes: phosphatidylethanolamine (PE), plasmenylethanolamine, lysophosphatidylethanolamine, lysoplasmenylethanolamine, phosphatidylserine (PS), sphingosine and cholesterol. Immunofluorescence colocalization, conventional organelle fractionation and gene knockout experiments confirmed the high subcellular specificity of proximity labeling lipidomics approach, establishing a powerful tool to investigate the spatial distribution of lipids under physiological conditions.
In eukaryotic cells, most phospholipids are de novo synthesized in the endoplasmic reticulum (ER) and then transported to other organelles. To characterize lipid transport between organelles, researchers developed a dual-labeling strategy by combining subcellular proximity labeling lipidomics with stable isotope tracing, which enables systematic and quantitative characterization of lipid transport from the ER to various organelles.
Researchers revealed key features such as transport kinetics, turnover, and the relative contributions of different lipid biosynthetic and transport pathways to the lipid composition of specific organelles. They uncovered that the lipid transport proteins VPS13A and PDZD8 play crucial and selective roles in mediating ER-mitochondria lipid transfer with fatty acyl chain specificity. Besides, they revealed that mTOR activation selectively increases lysosomal levels of cholesterol, PE, and PS, without altering the global cellular lipidome, providing powerful support to dissect organelle-specific lipid metabolism.
This work provides a powerful tool for analyzing the spatial distribution of subcellular lipids and the spatiotemporal dynamics of inter-organelle lipid transport under physiological conditions, and offers strong support for investigating lipid metabolism at the subcellular level and the underlying mechanisms of related diseases.
