Analysis of Mitochondrial Metabolism in situ: Combining Stable Isotope Labeling with Selective Permeabilization

Mitochondrial metabolism and its role in health and disease have emerged as a field of broad scientific interest in recent years. To date, it is well-established that mitochondrial dysfunction does not only play a vital role in cancer but also in other pathological conditions such as neurodegenerative diseases and inflammation. One important tool for the analysis of cellular metabolism is the application of stable isotope labeled substrates, which allow for the tracing of atoms throughout metabolic networks. While such analyses yield very detailed information about intracellular fluxes, the determination of compartment specific fluxes is far more challenging. Most approaches for the deconvolution of compartmented metabolism use computational models whereas experimental methods are rare. Here, we developed an experimental setup based on selective permeabilization of the cytosolic membrane that allows for the administration of stable isotope labeled substrates directly to mitochondria. In contrast to methods based on differential centrifugation, mitochondria are not removed from the cells but remain inside the permeabilized cell ghosts. We demonstrate how this approach can be used to infer metabolic changes in mitochondria induced by either chemical or genetic perturbations and give an outlook on its potential applications.