Apoptosis is a process by which unwanted cells are eliminated in a controlled manner. Early in apoptosis, ceramide levels rise and the mitochondrial outer membrane becomes permeable to proteins. The permeability of the outer membrane is attributed to the self-assembly of ceramide in form of channels. In the only direct structural study, to date, ceramide channels were visualized in liposomes using transmission electron microscopy. Those channels were of various sizes, averaging 10 nm in diameter. In concert, using electrophysiological techniques, the estimated diameter of ceramide channels was also around 10 nm. These channels are large enough to release all the pro-apoptotic intermembrane space proteins to initiate apoptosis.

Dihydroceramide desaturase converts the inactive precursor, dihydroceramide to ceramide. Both long and short chain dihydroceramides inhibit ceramide channel formation in mitochondria. The inhibition is strong as one tenth as much dihydroceramide inhibited the outer membrane permeabilization by 95% (C2) and 51% (C16). Other mitochondrial components are not required for such inhibition as comparable amounts prevented the permeabilization of liposomes. Hence, the apoptogenic activity of ceramide may depend on the ceramide to dihydroceramide ratio perhaps resulting in a more abrupt transition from the normal to the apoptotic state.

The location of the desaturase is the endoplasmic reticulum (ER). Only minimal activity was measured in mitochondria. However, newly synthesized ceramide from 14C-C8-dihydroceramide or 3H-sphingosine (in the ER) can transfer rapidly to mitochondria (40 % in 10 min) and permeabilize them to cytochrome c and adenylate kinase. The transfer of sphingolipids is bidirectional and non-specific. The transfer mechanism is consistent with direct membrane contact, since reducing the organellar concentrations by half resulted in a four-fold reduction of the transfer rate. Thus this ceramide exchange obviates the need for a complete ceramide de novo pathway in mitochondria in order for cells to use ceramide to activate mitochondria-mediated apoptosis.

These results demonstrate the ability of ceramide to form large channels capable of releasing proteins from mitochondria. Ceramide can rapidly reach mitochondria and there are mechanisms to control the propensity for ceramide channel formation. Clearly ceramide channels play a central role in the decision to undergo apoptosis.