Deletions in the ATAD3 gene cluster cause cerebellar developmental defects with mitochondrial DNA abnormalities owing to local cholesterol insufficiency. Homo sapiens

The DNA in mitochondria is associated with the inner of two membranes and it co-fractionates with the limited amount of cholesterol in the organelles. However, the effects of mitochondrial cholesterol deficiency are largely unknown, and mitochondrial disorders relating to this area of cell metabolism have not been reported hitherto. Using detailed SNP array analysis we have identified patients with impaired cerebellar development and neurological dysfunction who have large deletions in the locus encoding the ATAD3A, ATAD3B and ATAD3C genes. Patient cells with inherited ATAD3 defects display aberrant mitochondrial DNA organization and synthesis associated with disrupted cholesterol metabolism. Moreover drug-induced perturbations of cholesterol metabolism cause mitochondrial DNA disorganization in control cells. The interdependence of mitochondria and cholesterol homeostasis is further corroborated by the presence of mitochondrial DNA aggregation in the genetic cholesterol trafficking disorder Niemann Pick type C disease. Thus, we conclude, mitochondria are fully integrated in the circuitry of cellular cholesterol homeostasis, in which ATAD3 plays a critical role, and the dual problem of perturbed cholesterol homeostasis and mitochndrila dysfunction may be widespread in neurological and neurodegenerative diseases. Overall design: We designed the experiment to compare the expression profiles of cells carrying deletions in the ATAD3 gene cluster (ATAD3CAS & ATAD3F) with that of a normal control cell line. Because we suspected that cholesterol metabolism would be altered by ATAD3 deficiency we also prepared RNA from the same three cell lines treated with a drug, pravastatin, that inhibits the rate limiting step of cholesterol synthesis, to determine if the drug produced similar effects on gene expression to ATAD3 deficiency. In practice, pravastatin had almost no signficant effects (FDR 0.05) on any of the cells and none related to cholesterol homeostasis, indicating the drug does not act at the level of gene expression. This proved convenient as two RNA samples from ATAD3CAS failed QC, but the ATAD3CAS + pravastatin versus control (with or without pravastatin) provided additional replicates and displayed almost identical differences to ATAD3CAS (no drug) vs Control.