Metabolic modeling of muscle metabolism identifies key reactions linked to insulin resistance phenotypes.
OBJECTIVE
Dysregulated muscle metabolism is a cardinal feature of human insulin resistance (IR) and associated diseases, including type 2 diabetes (T2D). However, specific reactions contributing to abnormal energetics and metabolic inflexibility in IR are unknown.


METHODS
We utilize flux balance computational modeling to develop the first systems-level analysis of IR metabolism in fasted and fed states, and varying nutrient conditions. We systematically perturb the metabolic network to identify reactions that reproduce key features of IR-linked metabolism.


RESULTS
While reduced glucose uptake is a major hallmark of IR, model-based reductions in either extracellular glucose availability or uptake do not alter metabolic flexibility, and thus are not sufficient to fully recapitulate IR-linked metabolism. Moreover, experimentally-reduced flux through single reactions does not reproduce key features of IR-linked metabolism. However, dual knockdowns of pyruvate dehydrogenase (PDH), in combination with reduced lipid uptake or lipid/amino acid oxidation (ETFDH), does reduce ATP synthesis, TCA cycle flux, and metabolic flexibility. Experimental validation demonstrates robust impact of dual knockdowns in PDH/ETFDH on cellular energetics and TCA cycle flux in cultured myocytes. Parallel analysis of transcriptomic and metabolomics data in humans with IR and T2D demonstrates downregulation of PDH subunits and upregulation of its inhibitory kinase PDK4, both of which would be predicted to decrease PDH flux, concordant with the model.


CONCLUSIONS
Our results indicate that complex interactions between multiple biochemical reactions contribute to metabolic perturbations observed in human IR, and that the PDH complex plays a key role in these metabolic phenotypes.
Graduate Program in Bioinformatics, Boston University, Boston, MA, USA.
Christopher
C
Nogiec
Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, MA, USA.
Alison
A
Burkart
Research Division, Joslin Diabetes Center, and Department of Biomedical Engineering, Boston University, Boston, MA, USA.
Jonathan M
JM
Dreyfuss
Research Division, Joslin Diabetes Center, Boston, MA, USA.
Carles
C
Lerin
Biomedical Engineering, Boston University, Boston, MA, USA ; Research Division, Joslin Diabetes Center and Children's Hospital Informatics Program, Harvard-MIT Division of Health Sciences and Technology, Boston, MA, USA.
Simon
S
Kasif
Research Division, Joslin Diabetes Center and Harvard Medical School, Boston, MA, USA.
Mary-Elizabeth
ME
Patti
Computational modeling; Flux balance analysis; Muscle insulin resistance; Muscle metabolism