LONDON – New human brain organoids that precisely model the three hallmarks of Alzheimer’s disease – amyloid plaque-like lesions, progressive neuronal death and abnormal accumulations of tau – are now ready to be developed for use in high-throughput drug screening.

At the same time, the organoids have led to the discovery that the BACE2 (beta amyloid precursor protein cleaving enzyme) gene can act as a natural suppressor of Alzheimer’s pathology. The finding points to a possible reason why BACE1 inhibitors have failed to show protective effects in clinical trials, since those drugs also block the effects of BACE2.

The Alzheimer’s-like pathology is seen in cerebral organoids derived from hair donated by people with Down syndrome, or trisomy 21, who, because they carry an extra copy of the beta-amyloid precursor protein (APP) gene, have a very high risk of developing Alzheimer’s disease.

In the study, published in the July 10, 2020, online issue of Molecular Psychiatry, group leader Dean Nizetic, professor of cellular and molecular biology at Queen Mary University of London, and national and international collaborators, reprogrammed hair cells to induced pluripotent stem cells (iPSCs) and then prompted them to become brain organoids.

Those organoids, containing markers of all six layers of the human cortex, rapidly developed Alzheimer’s-like pathology.

While there are other cell model systems of Alzheimer’s brain pathology, they are based on promoting overexpression of introduced genes. “This work represents a remarkable achievement, as this is the first cell-based system that has the full trio of Alzheimer’s pathologies, without any artificial gene overexpression,” Nizetic said. “This system opens up the prospect for screening for new drugs aimed at delaying or even preventing Alzheimer’s before neuronal death starts.”

It was “very surprising” to find all three hallmarks of Alzheimer’s disease in the organoids, Nizetic said. “It has been shown that brain organoids are relevant to the study of neurodevelopmental disorders, but it was thought they were not suitable for neurodegeneration studies,” he told BioWorld.

Getting to the BACE of things

Despite having three copies of the APP gene, around 30% of people with Down syndrome do not develop Alzheimer’s disease by the age of 60, suggesting that some of the other 400 or so genes on chromosome 21 have a protective effect.

One of the genes on chromosome 21 is BACE2, the homologue of BACE1. As the main beta secretase gene cleaving APP in the brain, BACE1 is a major drug target in Alzheimer’s disease. BACE2 is found in the brain, but its function is less clear, with evidence of both pro- and anti-amyloidogenic activity.

Profiling non-amyloidogenic peptides that had the signature of BACE2 cleavage in Down syndrome organoids, compared to organoids derived from normal, disomy 21 donors, showed average levels of those peptides were doubled in trisomy 21.

That result was reproduced in three separate experiments, starting from undifferentiated induced pluripotent stem cells (iPSCs) from different individuals.

However, looking at an organoid from a sporadic case of Alzheimer’s disease caused by an extra copy of the APP gene, in an individual who was otherwise disomic, the researchers found the non-amyloidogenic peptide profile was similar to normal controls.

The researchers concluded that a third copy of a gene other than APP was behind those peptide profiles, and they said, BACE2 is the gene in question.

To assess if that might have any relevance in vivo, they compared the peptide profile from the trisomy organoids with those found in cerebrospinal fluid of people with Down syndrome, and to controls. They found similar increases in BACE2 cleaved peptides in the fluid samples, validating the observations made in the organoids.

The researchers next designed an assay to see if BACE1 inhibitors that have been tested in clinical trials in Alzheimer’s block the beta-amyloid degrading activity of BACE2. They found two BACE1 inhibitors had that effect.

“It’s not the only reason, but BACE2 inhibition could have been confounding clinical trials [of BACE1] inhibitors,” Nizetic said. That should be taken into consideration when designing new BACE1 inhibitors, he said.

As Nizetic acknowledged, the findings rest on “a very small number” of Down syndrome organoids from seven donors. Interestingly, two of those did not show any changes in BACE2 cleaved peptides. One was from a 37-year-old man with Down syndrome, who unlike the rest of the cohort did not have a clinical diagnosis of Alzheimer’s disease. The other was from an anonymous donor whose medical history is not known.

Using CRISPR/Cas9, the researchers edited out a single copy of the BACE2 gene in iPSCs from the unaffected donor, maintaining the trisomy of the rest of chromosome 21. The resulting organoids showed a 27% to 34 % reduction in BACE2 activity compared to an unedited trisomy 21 control, and no significant differences in activity compared to a normal control.

Notably, eliminating the third copy of the BACE2 gene caused the brain organoids derived from the unaffected Down syndrome donor to develop extremely early Alzheimer’s plaque-like deposits. Those progressed at pace, becoming much denser by day 96, with associated massive cell death.

“This pinpoints triplication of BACE2 as a likely cause of specific anti-amyloidogenic trisomy 21 effects,” the researchers said. It appears that reducing BACE2 by a third tips the balance against anti-amyloidogenic activity and provokes Alzheimer’s-like pathology.

“The drug screening application opens up immediately, once we scale-up, speed-up and do some refinements,” Nizetic said. Discussions with potential commercialization partners are underway.

In addition, the brain organoids could form the basis of biomarkers for detecting people at risk of developing Alzheimer’s disease, well before there are any symptoms.

The organoids also provide the means to discover other natural suppressor genes of neurodegenerative diseases.

Taken overall, the researchers said the data prove the physiological role of BACE2 as a dose-sensitive Alzheimer’s disease suppressor gene. That potentially explains the delay in developing Alzheimer’s disease in 30% of people with Down syndrome.

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