Analysis of mitochondrial metabolism in situ: Combining stable isotope labeling with selective permeabilization

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. An 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. 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. •Selective permeabilization for direct determination of mitochondrial metabolic fluxes.•Mitochondria remain active within permebilized cells and without cytosol.•Mitochondrial PC is activated under gln-limiting conditions in in situ mitochondria.•DCA increases PDH flux within minutes in in situ mitochondria.•In situ mitochondria perform reductive carboxylation of AKG upon Complex I inhibition.