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As the products of complex and often redundant metabolic pathways, lipids are challenging to measure and perturb using genetic tools. Yet by virtue of being the major constituents of cellular membranes, lipids are highly regulated in space and time. Chemists have stepped into this methodological void, developing an array of techniques for the precise quantification and manipulation of lipids at the subcellular, organelle level. Here, we survey the landscape of these methods. For measuring lipids, we summarize the use of metabolic labeling and click chemistry tagging, photoaffinity labeling, isotopic tagging for Raman microscopy, and chemoenzymatic labeling for tracking lipid production and interorganelle transport. For perturbing lipids, we describe synthetic photocaged lipids and membrane editing approaches using optogenetic enzymes for precise manipulation of lipid signaling. Collectively, these chemical and biochemical tools are revealing phenomena and mechanisms underlying lipid functions at the subcellular level.
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http://dx.doi.org/10.1101/cshperspect.a041407 | DOI Listing |
Gen Physiol Biophys
September 2025
Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Nangang District, Harbin, Heilongjiang, China.
Exosomes derived from various cells have been demonstrated to contribute to cardiac repair by regulating macrophage polarization in myocardial infarction. However, how exosomes secreted from cardiomyocytes under hypoxia-ischemia (Hypo-Exo) regulate macrophage polarization in the local tissues is elusive. This study aimed to determine the underlying mechanisms by which Hypo-Exo polarized M2 macrophages.
View Article and Find Full Text PDFJCI Insight
September 2025
Alice and Y. T. Chen Center for Genetics and Genomics, Division of Medical Genetics, Department of Pediatrics.
Methylmalonic acidemia (MMA) is a severe metabolic disorder affecting multiple organs because of a distal block in branched-chain amino acid (BCAA) catabolism. Standard of care is limited to protein restriction and supportive care during metabolic decompensation. Severe cases require liver/kidney transplantation, and there is a clear need for better therapy.
View Article and Find Full Text PDFBioimpacts
August 2025
Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
Introduction: Hepatocellular carcinoma (HCC) remains a major cause of cancer mortality, and effective therapeutic options are limited. MicroRNA‑372‑3p (miR‑372‑3p) has been implicated in HCC, yet its exact role is unclear.
Methods: We established miR‑372‑3p‑overexpressing HCC cell lines (HepG2, SNU‑449, JHH‑4) via lentiviral transduction.
Proc Natl Acad Sci U S A
September 2025
Department of Integrative Biology, University of California, Berkeley, CA 94720-3140.
Microscale symbioses can be critical to ecosystem functions, but the mechanisms of these interactions in nature are often cryptic. Here, we use a combination of stable isotope imaging and tracing to reveal carbon (C) and nitrogen (N) exchanges among three symbiotic primary producers that fuel a salmon-bearing river food web. Bulk isotope analysis, nanoSIMS (secondary ion mass spectrometry) isotope imaging, and density centrifugation for quantitative stable isotope probing enabled quantification of organism-specific C- and N-fixation rates from the subcellular scale to the ecosystem.
View Article and Find Full Text PDFJ Integr Neurosci
August 2025
Department of Anesthesiology, The Fourth Affiliated Hospital of Harbin Medical University, 150001 Harbin, Heilongjiang, China.
Background And Purpose: Ciprofol, a novel intravenous anesthetic, has been shown to exert protective effects against ischemic stroke, a leading cause of death and disability; however, its molecular mechanisms remain unclear. This study aimed to explore the molecular mechanisms underlying the neuroprotective effects of ciprofol using metabolomics.
Methods: This study used a middle cerebral artery occlusion (MCAO) rat model to simulate cerebral ischemia-reperfusion injury (CIRI).