Successive High-Resolution (H₂O)_n-GCIB and C₆₀-SIMS Imaging Integrates Multi-Omics in Different Cell Types in Breast Cancer Tissue

Abstract

The temporo-spatial organization of different cells in the tumor microenvironment (TME) is the key to understanding their complex communication networks and the immune landscape that exists within compromised tissues. Multi-omics profiling of single-interacting cells in the native TME is critical for providing further information regarding the reprograming mechanisms leading to immunosuppression and tumor progression. This requires new technologies for biomolecular profiling of phenotypically heterogeneous cells on the same tissue sample. Here, we developed a new methodology for comprehensive lipidomic and metabolomic profiling of individual cells on frozen-hydrated tissue sections using water gas cluster ion beam secondary ion mass spectrometry ((H2O) n -GCIB-SIMS) (at 1.6 μm beam spot size), followed by profiling cell-type specific lanthanide antibodies on the same tissue section using C60-SIMS (at 1.1 μm beam spot size). We revealed distinct variations of distribution and intensities of >150 key ions (e.g., lipids and important metabolites) in different types of the TME individual cells, such as actively proliferating tumor cells as well as infiltrating immune cells. The demonstrated feasibility of SIMS imaging to integrate the multi-omics profiling in the same tissue section at the single-cell level will lead to new insights into the role of lipid reprogramming and metabolic response in normal regulation or pathogenic discoordination of cell–cell interactions in a variety of tissue microenvironments.

Evaluation of 6 MALDI-Matrices for 10 μm Lipid Imaging and On-Tissue MSn with AP-MALDI-Orbitrap

“…For this reason, an increasing number of MSI devices offer high-resolution mass analyzers and tandem-MS capability for structural identification to enhance specificity . With these capabilities, MSI has significantly contributed to the field of lipidomics by revealing lipid alterations in various diseases. − …”

Emerging metabolomic tools to study cancer metastasis

“…Single-cell analysis is an extremely promising technology that provides insight into cellular heterogeneity and dynamics in individual cells and has been employed to measure transcriptome, proteome, and metabolome abundance [22][23][24]. In primary and metastatic tumors, single-cell metabolomics (SCM) can be used to reveal metabolic heterogeneity within a cancer cell population.…”

“…These limitations can be overcome by improvements in matrix composition and sample preparation regarding the method of choice for matrix application. Additionally, matrix-free in situ metabolomics technologies are also available including desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) and secondary ion mass spectrometry (SIMS) [23,41]. While SIMS and MALDI-MSI have a single-cell/subcellular spatial resolution, DESI-MSI does not and has a spatial resolution of ~200 μm.…”

Single-Cell Metabolomics in Hematopoiesis and Hematological Malignancies

“…Different strategies, such as frozen hydration and capillary extraction, can be used to prepare samples for single-cell metabolomics analysis. Frozen hydration preserved the integrity and compartmentalization of the pristine molecular constituents of cells, reflecting a near-natural state of the metabolome ( 109 ). Capillary extraction efficiently separates the sample molecules with less damage to biological specimens than traditional dissection methods ( 111 ).…”

“…Multi-omics profiling of single-interacting cells in the native TME is essential for deeper understanding of the complex communication networks and the immune landscape that exist within compromised tissues. Tian et al developed a new methodology called high-energy gas cluster ion beam-secondary ion mass spectrometry (GCIB-SIMS), which combined the chemical specificity of mass spectrometry with imaging resolution approaching 1 micron, small enough to image a single cell (109). GCIB-SIMS can comprehensively identify lipidomic and metabolomic profiling in different cell types, leading to new insights into the role of lipid reprogramming and metabolic response in normal regulation or pathogenic discoordination of cell-cell interactions in a variety of tissue microenvironments.…”