Lipidomic profiling of PEX11β knockout T-REx 293 cells reveals lipid shifts suggesting potential metabolic perturbations

Peroxisomes function in reactive oxygen species (ROS) and lipid metabolism. Genetic defects in peroxisome biogenesis cause severe neurological disorders collectively termed peroxisome biogenesis disorders (PBDs). Dysregulated peroxisomes are also increasingly implicated in cancer and therapy resistance. Our comparative analysis of peroxin knockouts (PEX KO) in a human embryonic kidney-derived cell line by untargeted lipidomics reveals distinct lipid fingerprints across PEX KO conditions. PEX3 and PEX14 KO cell lines are highly enriched in very-long-chain fatty acids (VLCFAs) and depleted in ether- and plasmalogen-linked phospholipids. While they differ in the same lipids, PEX3 KO cells demonstrate stronger shifts from the wild-type profile than PEX14 KO cells. In contrast, PEX11β KO cells nearly match the wild-type lipid profile except for several highly enriched lipid analytes, most notably ceramides. These distinct metabolic adaptations are paralleled by the cell lines’ divergent responses to glucose-6-phosphate dehydrogenase (G6PD) inhibition, suggesting PEX KO phenotype-specific differences in redox stress and NADPH source reliance.