MIT neuroscientists have performed a comprehensive study of the APOE4 gene, which increases risk for Alzheimer’s disease, and the more common form of the gene, APOE3. Courtesy of the researchers

Researchers have begun to learn more about a gene that has long been linked to Alzheimer’s disease.

A team from the Massachusetts Institute of Technology has performed a comprehensive study of APOE4—a gene variant that is three times more common among Alzheimer’s patients than non-Alzheimer’s individuals—and found that it promotes the accumulation of the beta amyloid proteins that cause the characteristic plaques seen in the brains of Alzhmeimer’s patients.

“APOE4 influences every cell type that we studied, to facilitate the development of Alzheimer’s pathology, especially amyloid accumulation,” Li-Huei Tsai, director of MIT’s Picower Institute for Learning and Memory and the senior author of the study, said in a statement.

The gene APOE, which comes in three variants—APOE2, APOE3, and APOE4—binds cholesterol and lipids in cells’ environments to enable the cells to absorb the lipids.

The researchers stimulated human induced pluripotent stem cells—stem cells derived from skin and other cell types—to differentiate them into neurons, astrocytes and microglia. They then used the gene-editing tool CRISPR/Cas9 to genetically convert APOE3 in the stem cells derived from a healthy subject to APOE4.

In the neurons, the cells expressing APOE3 and APOE4 differed in the expression of hundreds of genes, where about 250 genes went down and 190 went up in cells with APOE4.

For the astrocytes, the numbers were higher and in microglia, 1,100 genes showed reduced activity and 300 increased activity.

The researchers also observed that neurons with APOE4 formed more synapses and secreted higher levels of amyloid protein. Cholesterol metabolism was highly deregulated in APOE4 astrocytes and the cells produced twice as much cholesterol as APOE3 astrocytes. Also, their ability to remove amyloid proteins from their surroundings was dramatically impaired.

Microglia cells also became much slower at removing amyloid proteins and pathogens such as bacteria, when they had the APOE4 gene.

However, the researchers discovered the ability to reverse most of the negative effects using CRISPR/Cas9 to convert the APOE4 gene to APOE3 in brain cells derived from induced stem cells from a patient with late-onset Alzheimer’s.    

 The researchers also developed 3D organoids from cells with genes that are known to cause early-onset Alzheimer’s. The organoids had high levels of amyloid aggregates. However, when they were exposed to APOE3 microglia, most of the aggregates were cleared away.

“From this gene expression profiling, we can narrow down to certain signaling pathways that are dysregulated by APOE4,” Tsai said. “I think that this definitely can reveal potential targets for therapeutic intervention.”

Among the general population, about 8 percent of people have APOE2, 78 percent have APOE3, and 14 percent have APOE4. However, only 4 percent of those suffering from late onset, nonfamilial Alzheimer’s, which is overwhelmingly the most common form of the disease, have APOE2. The percentage of patients with APOE3 drops to 60 percent, while 37 percent of the patients carry the APOE4 gene variant.

“APOE4 is by far the most significant risk gene for late-onset, sporadic Alzheimer’s disease,” Tsai said. “However, despite that, there really has not been a whole lot of research done on it. We still don’t have a very good idea of why APOE4 increases the disease risk.”