Mesoscale Metabolic Channeling Revealed by Multimodal Microscopy

TL;DR

This paper introduces a new microscopy method to track nutrient metabolism at the subcellular level, revealing spatial patterns of glucose and organelle interactions in liver cells.

Contribution

The study pioneers the use of MIMS-EM combined with machine learning to map 13C flux and organelle interactions in hepatocytes at high resolution.

Findings

MIMS-EM quantitatively maps 13C atoms from glucose in hepatocytes at subcellular scale.

Distinct mitochondrial and lipid droplet subpopulations show unique organelle interactions and 13C enrichment.

Glycogenesis initiation is linked to proximity of lipid droplets.

Abstract

Metabolic homeostasis within cells and tissues requires engagement of catabolic and anabolic pathways consuming nutrients needed to generate energy to drive these and other subcellular processes. However, the current understanding of cell homeostasis and metabolism, including how cells utilize nutrients, comes largely from tissue and cell models analyzed after fractionation. These bulk strategies do not reveal the spatial characteristics of cell metabolism at the single cell level, and how these aspects relate to the location of cells and organelles within the complexity of the tissue they reside within. Here we pioneer the use of high-resolution electron and stable isotope microscopy (MIMS-EM) to quantitatively map the fate of nutrient-derived 13C atoms at subcellular scale. When combined with machine-learning image segmentation, our approach allows us to establish the cellular and organellar spatial pattern of glucose 13C flux in hepatocytes in situ. We applied network analysis algorithms to chart the landscape of organelle-organelle contact networks and identified subpopulations of mitochondria and lipid droplets that have distinct organelle interactions and 13C enrichment levels. In addition, we revealed a new relationship between the initiation of glycogenesis and proximity of lipid droplets. Our results establish MIMS-EM as a new tool for tracking and quantifying nutrient metabolism at the subcellular scale, and to identify the spatial channeling of nutrient-derived atoms in the context of organelle-organelle interactions in situ.

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