Very long-chain ceramides in skeletal muscle associate with systemic insulin resistance independent of obesity

Lipids are bioactive signaling molecules implicated in tissue-specific and whole-body insulin resistance, with ceramides and diacylglycerols (DAGs) as prominent species. Their precise roles remain unclear. Here, we leverage natural genetic variation in 399 male Diversity Outbred Australia (DOz) mice fed chow or a high-fat diet to examine the relationship between muscle lipids and insulin sensitivity. Fat mass was significantly associated with 55% of muscle lipid features and whole-body insulin sensitivity, with DAGs enriched in this association. To disentangle adiposity and muscle lipid contributions, we used: (1) linear models correcting lipid features for fat mass, and (2) insulin sensitivity quartiles within adiposity bins. Both approaches identified very long-chain ceramides, not DAGs, as linked to insulin resistance. RNA sequencing and proteomics from the same muscles associated these ceramides with cellular stress, mitochondrial dysfunction, and protein synthesis regulation. Meanwhile, DAGs correlated with leptin gene expression, suggesting an adipocyte, rather than myocyte, origin. These findings highlight very long-chain ceramides as key muscle lipids associated with insulin resistance, independent of adiposity.