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A framework for performing single-cell spatial metabolomics with cell-type specific protein profiling for tissue systems biology

ABSTRACT: Metabolic reprogramming in cancer and immune cells occurs to support their increasing energy needs in biological tissues. Here we propose Single Cell SPAtially resolved METabolic (scSpaMet) framework for joint protein-metabolite profiling of single immune and cancer cells in male human tissues by incorporating untargeted spatial metabolomics and targeted multiplexed protein imaging in a single pipeline. We utilized the scSpaMet pipeline to profile cell types and spatial metabolomic maps of 19507, 31156, and 8215 single cells in human lung cancer, tonsil and endometrium tissues, respectively. ScSpaMet analysis revealed cell type-dependent metabolite profiles and local metabolite competition of neighboring single cells in human tissues. Deep learning-based joint embedding revealed unique metabolite states within cell types. Trajectory inference showed metabolic patterns along cell differentiation paths. Here we show scSpaMet’s ability to quantify and visualize the cell-type specific and spatially resolved metabolic-protein mapping as an emerging tool for systems-level understanding of tissue biology.

INSTRUMENT(S): Mass spectrometry imaging

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Lung, Liver

DISEASE(S): Lung Adenocarcinoma,Breast Cancer

SUBMITTER: THOMAS HU

LAB HEAD: Thomas Hu

PROVIDER: PXD045840 | Pride | 2023-10-02

REPOSITORIES: Pride

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