Spatially resolved 3D metabolomic profiling in tissues

Spatially resolved RNA and protein molecular analyses have revealed unexpected heterogeneity of cells. Metabolic analysis of individual cells complements these single-cell studies. Here, we present a three-dimensional spatially resolved metabolomic profiling framework (3D-SMF) to map out the spatial organization of metabolic fragments and protein signatures in immune cells of human tonsils. In this method, 3D metabolic profiles were acquired by time-of-flight secondary ion mass spectrometry to profile up to 189 compounds. Ion beams were used to measure sub-5-nanometer layers of tissue across 150 sections of a tonsil. To incorporate cell specificity, tonsil tissues were labeled by an isotope-tagged antibody library. To explore relations of metabolic and cellular features, we carried out data reduction, 3D spatial correlations and classifications, unsupervised K-means clustering, and network analyses. Immune cells exhibited spatially distinct lipidomic fragment distributions in lymphatic tissue. The 3D-SMF pipeline affects studying the immune cells in health and disease.

Automated summary

Researchers presented a three-dimensional spatially resolved metabolomic profiling framework (3D-SMF) to map out the spatial organization of metabolic fragments and protein signatures in immune cells of human tonsils. Various analyses were conducted to explore the relationships between metabolic and cellular features, revealing spatially distinct lipidomic fragment distributions in lymphatic tissue. The 3D-SMF pipeline impacts the study of immune cells in health and disease.