It has long been postulated that apolipoprotein E (apoE) may play a role in lipid metabolism in the brain. However, direct evidence that apoE plays such a role is lacking. We investigated whether apoE isoforms influence lipid content in the brain. We compared the brains of wild-type mice to apoE knockout (؊/؊) and human apoE3 and apoE4 transgenic mice and compared cerebrospinal fluid (CSF) of humans with different apoE isoforms. We found that there was no effect of apoE on the content of multiple phospholipids, sphingolipids, and cholesterol. There was, however, a marked effect of apoE on the sulfatide (ST) content in both the brain and CSF. The sulfatide mass in hippocampus and cortex of apoE knockout mice was found to be 61 and 114 mol% higher than wild-type mice counterparts at 12 months of age. In contrast, the sulfatide content in brain tissues from human apoE4-expressing mice was ϳ60% less than those found in wild-type mice of the same age. The ST mass in human CSF was significantly dependent on the APOE genotypes of the subjects. Examination of potential sulfatide carrier(s) in human CSF demonstrated that sulfatides are specifically associated with apoEcontaining high density lipoproteins, suggesting that sulfatide levels in the central nervous system (CNS) are likely to be directly modulated by the same metabolic pathways that regulate levels of apoE-containing CNS lipoproteins. This novel role for apoE in the CNS may provide new insights into the connection of apoE with Alzheimer's disease and poor recovery after brain injury.Human apolipoprotein E (apoE, protein; APOE, gene), 1 a 34-kDa protein coded for by a gene on chromosome 19, plays a prominent role in the transport and metabolism of plasma cholesterol and triacylglycerides through its ability to interact with the low density lipoprotein (LDL) receptor and the LDL receptor-related protein (1, 2). It has been postulated that apoE may also play an important role in the redistribution of cholesterol and phospholipids within the central nervous system (CNS) (3) where apoE is expressed mainly in astrocytes (4, 5).In vitro and in vivo data suggest that apoE can play a role in neurite outgrowth and sprouting (4, 6 -9), however, whether this is due to effects on cholesterol and lipid metabolism is unclear. In addition to its role as a plasma lipid transport protein, apoE participates in pathobiological processes, including Alzheimer's disease (AD) (10). The effect of apoE in AD is likely to occur at least in part via interactions with the amyloid- (A) peptide (see Ref. 11 for review). To date, the mechanisms of how apoE is involved in all of these biological processes have not been completely clarified.There are three common isoforms of human apoE that differ in amino acids at positions 112 and 158 (1). The most common isoform, apoE3, has cysteine at position 112 and arginine at 158, whereas apoE2 has cysteine at both positions, and apoE4 contains arginine at both positions. The isoforms are encoded by three alleles at the same gene locus. ApoE4 has bee...