Imaging Cellular Metabolic Rewiring with SuMMIT-SRS

Li, Y.; Li, Z.; Rhine, K.; Ranamukhaarachchi, S.; Qin, S.; Jang, H.; Villazon, J.; Bai, Z.; Fraley, S. I.; Yeo, G. W.; Fan, R.; Shi, L.

doi:10.1101/2025.10.10.681769

bioRxiv · 10.1101/2025.10.10.681769

Imaging Cellular Metabolic Rewiring with SuMMIT-SRS

Li, Y.·Li, Z.·Rhine, K.·Ranamukhaarachchi, S.·Qin, S.·Jang, H.·Villazon, J.·Bai, Z.·Fraley, S. I.·Yeo, G. W.·Fan, R.·Shi, L.

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Abstract

Cells dynamically rewire their metabolic pathways in response to physiological and pathological cues. Such plasticity is particularly critical in neurons, stem cells, cancer cells, and immune cells, where biosynthetic demands can shift rapidly. However, current metabolic imaging techniques using isotope labeling typically track only one metabolite at a time, limiting their ability to capture the rapid dynamics of complex metabolic networks including coordinated precursor utilization, crosstalk, and turnover. Here, we present Subcellular Multiplexed Metabolic Isotope Tracing Stimulated Raman Scattering microscopy (SuMMIT-SRS), a platform that enables simultaneous visualization of multiple metabolic dynamics at subcellular resolution. By exploiting the distinct vibrational signatures of carbon-deuterium bonds derived from multiple deuterated amino acids, lipids, and monosaccharide tracers, SuMMIT-SRS maps co-regulated DNA, RNA, protein, and lipid synthesis at the same time and resolves various individual amino acid-mediated metabolic pathways within intact cells and tissues. We demonstrate SuMMITs broad utility across Drosophila fat body tissue and developing brain, tumor organoids, aged human neurons, and mouse liver, capturing cell type-specific metabolic rewiring under genetic and pathological perturbations. This approach extends SRS to multiplexed isotope tracing, offering a powerful tool to uncover dynamic and complex biosynthesis programs in development, health, and disease.

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Li, Y., Li, Z., Rhine, K., Ranamukhaarachchi, S., Qin, S., Jang, H., Villazon, J., Bai, Z., Fraley, S. I., Yeo, G. W., Fan, R., Shi, L.. 2025-10-13. Imaging Cellular Metabolic Rewiring with SuMMIT-SRS. https://doi.org/10.1101/2025.10.10.681769

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