Genetic defects in peroxisome morphogenesis (Pex11β, DLP1, and NME3) affect DHA-phospholipid metabolism.

Abe Y, Wanders RJA, Waterham HR, Mandel H, Falik-Zaccai TC, Ishihara N, and Fujiki Y. (2022) Genetic defects in peroxisome morphogenesis (Pex11β, DLP1, and NME3) affect DHA-phospholipid metabolism. Journal of Inherited Metabolic Disease

Peroxisomes are membrane-bound organelles in the cytoplasm of eukaryote cells that are responsible for the oxidation of specific biomolecules and is the location of the first steps of plasmalogen biosynthesis. For peroxisome numbers to increase they must grow and divide. The division stage has three steps, elongation, constriction, and fission, and is facilitated by three proteins: peroxisomal membrane protein 11β (PEX11β), dynamin-like protein 1 (DLP1), and nucleoside diphosphate kinase 3 (NME3). When people have mutations in any of these three it causes central nervous system dysfunction including hypotonia in people with ΔNME3 or DLP1mut15, and intellectual disability in people with ΔPEX11β, however the mechanisms behind these effects are not known. To learn more about how these mutations are affecting peroxisome proliferation and causing the pathology seen in patients, Abe et al applied metabolomic approaches using fibroblasts from DLP1mut, ΔPEX11β, and ΔNME3 patients

To perform this study, human skin fibroblasts from DLP1mut, ΔPEX11β, and ΔNME3 patients were used as well as skin fibroblasts from healthy controls. When peroxisome morphology was evaluated in the patients, they found that ΔNME3 fibroblasts had elongated peroxisomes while mitochondria looked normal, DLP1mut fibroblasts had elongated peroxisomes and mitochondria, and ΔPEX11β fibroblasts contained tubular peroxisomes and normal mitochondria. These results indicate that peroxisomal fission is disrupted in all three cases, but mitochondrial fission is only affected in the DLP1mut fibroblasts.

The lipidome of the patient fibroblasts were also analyzed. ΔNME3 fibroblasts showed a reduction in docosahexaenoic acid (DHA)-containing plasmalogens (pPE 16:0/22:6), phosphatidylethanolamine (PE 18:1/22:6), and phosphatidylcholines (PC 18:1/22:6) while arachidonic acid (AA) containing phosphatidylcholines (PC 16:0/20:4 and PC 18:0/20:4) were increased. DLP1mut fibroblasts also demonstrated reductions in DHA-containing plasmalogens (pPE 16:0/22:6 and pPE 18:1/22:6) and phosphatidylethanolamines (PE 16:1/22:6, PE 16:0/22:6, 18:0/22:6, and 18:1/22:6). Similarly, AA-containing (pPE 18:1/20:4) and oleic acid (OA)-containing (pPE 16:0/18:1) plasmalogens were elevated. Finally, in ΔPEX11β fibroblasts there was a reduction in DHA-containing and AA-containing phosphatidylethanolamines (PE 16:0/22:6, PE 18:0/22:6, PE 20:2/20:4, and PE 20:1, 20:4) and an increase in OA-containing plasmalogens (pPE 16:0/18:1). In total, the amount of plasmalogens in ΔNME3 fibroblasts was decreased, however the total amount in DLP1mut or ΔPEX11β fibroblasts were unaffected.

Abe et al were interested in determining how mutations in genes that encode the proteins that influence peroxisomal division affect the lipidome. To accomplish this, they harvested fibroblasts from DLP1mut, ΔPEX11β, or ΔNME3 patients and analyzed their morphology and evaluated if the mutations altered the lipidome when compared to fibroblasts from healthy controls. They found that the peroxisome morphology was affected in the three patient lines and the DLP1mut fibroblasts also demonstrated altered mitochondria. All three had a reduction in DHA-containing plasmalogens while other alterations in AA-containing plasmalogens and other phospholipids were also present. These findings indicate that proteins involved with peroxisome division alter the organelle’s shape and its function by changing the lipidome, however only the ΔNME3 fibroblasts had a global plasmalogen reduction. This could indicate that the other two lines had ways of compensating for the genetic affects while ΔNME3 could not be compensated for. Many diseases are associated to changes to the lipidome, for example Zellweger syndrome is characterized by accumulations in very long-chain fatty acids and a reduction in plasmalogens and Rhizomelia chondrodysplasia punctata is caused by plasmalogen deficiency. Further studies are needed to know exactly how the entire lipidome is affected including plasmalogens, phospholipids, and fatty acid remodeling and to demonstrate how vast the effects are from a single peroxisome mutation.