Spatially resolved 3D metabolomic profiles in tissues


Spatially resolved molecular RNA and protein analyzes have shown unexpected heterogeneity of cells. The metabolic analysis of single cells complements these single cell studies. Here we present a three-dimensional spatially resolved Metabolomic Profiling Framework (3D-SMF) to map the spatial organization of metabolic fragments and protein signatures in immune cells of human tonsils. In this method, 3D metabolic profiles were captured by time-of-flight secondary ion mass spectrometry to profile up to 189 compounds. Ion beams have been used to measure layers of tissue in the sub-5 nanometer range over 150 sections of a tonsil. To include cell specificity, tonsil tissues were labeled using an isotope-labeled antibody library. To investigate the relationships between metabolic and cellular traits, we performed data reduction, 3D spatial correlations and classifications, unsupervised K-means clustering, and network analysis. Immune cells showed spatially different distributions of lipidoma fragments in the lymph tissue. The 3D SMF pipeline is influencing the study of immune cells for health and disease.

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