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Protective, Risk-Linked APOE Alleles Affect Glial Cell Transcriptome

NEW YORK — Two APOE alleles known for influencing Alzheimer's disease risk also affect the glial cell transcriptome, a new study has found.

The apolipoprotein E ε4 allele is a strong genetic risk factor for developing Alzheimer's disease, increasing one's risk of developing the disease between three- and 12-fold. At the same time, the APOEε2 allele reduces one's disease risk by between 60 percent and 85 percent, as compared to APOEε3 homozygotes.

Researchers led by Massachusetts General Hospital's Sudeshna Das theorized that the APOEε4 and the APOEε2 alleles are linked to opposing phenotypes affecting microglial and astrocytic cells, an idea they tested in Nature Aging using brain RNA-sequencing data from individuals with and without Alzheimer's disease.

Through this, they uncovered a set of genes that are upregulated among APOEε4 and downregulated among APOEε2 carriers. This cluster, which is enriched for phagocytosis and proinflammatory genes, is present both in individuals with normal aging brains and those with neuritic plaques. These and further findings in mice suggested that the APOEε4 allele might prime microglia to a phagocytosis and proinflammatory state.

"[T]he upregulation of phagocytosis and inflammation gene sets may well place APOEε4 microglia in a predisposition state to react to Aβ plaques and [neurofibrillary tangles], as well as to inflammatory and other noxious stimuli," Das and her colleagues wrote in their paper.

To uncover this gene set, the researchers applied spectral clustering — which can help find genes with similar expression profiles — to bulk dorsolateral prefrontal cortex RNA-seq data from the Religious Orders Study and Memory and Aging Project, or ROSMAP.

Within ROSMAP samples from individuals with no neuritic plaques, they identified a cluster of 172 genes that are typically expressed in microglial cells that are both downregulated in APOEε2 carriers and upregulated in APOEε4 carriers, as compared to APOEε3 carriers. These genes included ones involved in phagocytosis and the proinflammatory response. This microglia-APOE gene cluster exhibited a similar trend in a second cohort from the Mount Sinai Brain Bank, or MSBB.

This suggested to the researchers that APOE alleles affect the transcriptional profiles of microglia among normal, aging brains, and that APOEε4 encourages a shift toward a phagocytic and proinflammatory phenotype.

Further, within ROSMAP samples from individuals with neuritic plaques, the researchers uncovered a cluster of 181 genes that are downregulated in APOEε2 carriers and upregulated in APOEε4 carriers, as compared to APOEε3 carriers. This set included 87 genes from the cluster found among non-Alzheimer's disease samples. The MSBB dataset additionally supported gene expression differences between APOEε2 and APOEε4 carriers with neuritic plaques — again indicating that APOEε4 encourages a shift toward a phagocytic and proinflammatory phenotype.

But when the researchers examined the expression of these genes across samples from different disease stages, they noted that the microglial gene expression changes were most noticeable when no neuritic plaques were present and again later when they were frequent. Sparse and moderate neuritic plaques were associated with less obvious differences.

In a series of knock-in studies in mice, the researchers further found that APOE regulated microglial gene expression through the TREM2-TYROBP axis. Additionally, mice exposed to acute and chronic insults could partially recapitulate the APOE-associated gene expression patterns seen in humans.

In all, these findings suggested to the researchers that the APOEε4 allele might prime microglia toward a phagocytic and proinflammatory state, both in normal aging and in Alzheimer's disease.

They noted that further large-scale, single-nucleus studies of human brains from across disease stages and APOE genotypes will be needed to further confirm these findings and better understand how they relate to Alzheimer's disease progression.

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