Single-cell lipidomics enabled by dual-polarity ionization and ion mobility-mass spectrometry imaging

Abstract

Single-cell (SC) analysis provides unique insight into individual cell dynamics and cell-to-cell heterogeneity. Here, we utilize trapped ion mobility separation coupled with dual-polarity ionization mass spectrometry imaging (MSI) to enable high-throughput in situ profiling of the SC lipidome. Multimodal SC imaging, in which dual-polarity-mode MSI is used to perform serial data acquisition runs on individual cells, significantly enhanced SC lipidome coverage. High-spatial resolution SC-MSI identifies both inter- and intracellular lipid heterogeneity; this heterogeneity is further explicated by Uniform Manifold Approximation and Projection and machine learning-driven classifications. We characterize SC lipidome alteration in response to stearoyl-CoA desaturase 1 inhibition and, additionally, identify cell-layer specific lipid distribution patterns in mouse cerebellar cortex. This integrated multimodal SC-MSI technology enables high-resolution spatial mapping of intercellular and cell-to-cell lipidome heterogeneity, SC lipidome remodeling induced by pharmacological intervention, and region-specific lipid diversity within tissue.

Seeing is Believing: Developing Multimodal Metabolic Insights at the Molecular Level

“…Zhang et. al employed a multimodal strategy for analyzing single cells across various cell lines, integrating trapped ion mobility (TIMS) with dual-polarity ionization MSI to conduct sequential data acquisitions on individual cells . This method enhances the coverage of the single-cell lipidome, enabling high-resolution spatial mapping of intracellular components and capturing lipidome heterogeneity between individual cells.…”

Single-Cell Untargeted Lipidomics Using Liquid Chromatography and Data-Dependent Acquisition after Live Cell Selection

“…Lipids are an essential part of a cell’s biomolecular pool and play important roles in a myriad of complex biological processes with biophysical, energy storage, and signaling functions (reviewed in − ). Recent studies demonstrate that analyzing lipids at the single-cell level not only reveals significant variation in lipid profiles between different cells − but is also capable of observing putative response to stimuli, such as treatment with drugs or exogenous fatty acids. − Cancer cells are highly heterogeneous and very diverse in their phenotype which makes them hard to extinguish, but the analysis of single cells and the characterization of the heterogeneity could provide new treatment strategies . Pancreatic ductal adenocarcinoma is the most common pancreatic cancer with the poorest prognosis for pancreatic diseases .…”

Microfluidic Sampling of Undissolved Components from Subcellular Regions of Living Single Cells for Mass Spectrometry Analysis

“…28,29 Insoluble lipids are also important indicators for distinguishing cell types and subtypes, and reveal cell-to-cell heterogeneity. 30,31 Besides, undissolved membrane proteins (e.g., lipoproteins, glycoproteins) are also widely involved in the biological process including ion transport, adhesion, and cell−cell communications. 32,33 Some soluble biomolecules confined by microstructure are also considered to be "undissolved", e.g., some TCA cycle components are encapsulated in the mitochondria matrix, 34 and the mitochondria is anchored by cytoskeleton, 35 so the components are not freely dissolved in cytosol that can be aspired by micropipette.…”

“…Typical “undissolved cellular components” include the compounds in the cytomembrane, cytoskeleton, mitochondria, and nucleus, which are closely related to pathological and physiological processes. For example, the cytomembrane lipid composition affects membrane physical properties and protein functions, which are linked to various genetic diseases. , Insoluble lipids are also important indicators for distinguishing cell types and subtypes, and reveal cell-to-cell heterogeneity. , Besides, undissolved membrane proteins (e.g., lipoproteins, glycoproteins) are also widely involved in the biological process including ion transport, adhesion, and cell–cell communications. , Some soluble biomolecules confined by microstructure are also considered to be “undissolved”, e.g., some TCA cycle components are encapsulated in the mitochondria matrix, and the mitochondria is anchored by cytoskeleton, so the components are not freely dissolved in cytosol that can be aspired by micropipette. To sample these important components, proper solvents must be introduced to dissolve the components and send them to the analyzer.…”