Can BACE2 Protect Against Amyloidosis?

It may seem counterintuitive, but could BACE2 protect against amyloidosis, rather than contribute to it? This is the central question in a manuscript posted to bioRxiv. Non-amyloidogenic processing of APP, and Aβ peptides, by BACE2 may counteract the effect of an extra copy of APP in some people with Down’s syndrome, the authors propose.

  • BACE2 can cut APP at Aβ position 19, in non-amyloidogenic fashion.
  • It can also cleave Aβ peptides at amino acids 20 and 34.
  • Down syndrome CSF/brain organoids contain more of these truncated Aβ peptides.

Led by Dean Nižetić, Queen Mary University, London, Henrik Zetterberg, University of Gothenburg, Sweden, and John Hardy, University College London, scientists found that brain organoids derived from skin cells donated by people with Down’s secrete truncated Aβ peptides. They are cleaved at amino acids 19, 20, and 34—all previously proposed BACE2 cleavage sites. Cerebrospinal fluid from people with Down’s also has more of these truncated peptides than does control CSF, the researchers report. These forms of Aβ are not amyloidogenic.

Given that the BACE2 gene sits on chromosome 21, the findings might explain why some people with an additional copy of this chromosome have an uncharacteristically delayed onset of amyloidosis and dementia. Most people with trisomy 21 get amyloidosis early in life and show symptoms of dementia by age 60 but, curiously, about 30 percent are spared until later (Hithersay et al., 2018). They may be protected by BACE2, whose expression may be sensitive to genetic background, the authors posit. They report several new single-nucleotide polymorphisms near the BACE2 locus that may correlate with age of onset.

Similarly, some trisomy 21 cases have surprisingly little cerebral amyloid angiopathy. The authors suggest this might be because of abundant BACE2 expression in endothelial cells, where it could help clear Aβ peptides from blood vessels. Previous work indicates BACE2 is primarily expressed in the periphery. The findings may have repercussions for BACE inhibitor studies.

“This paper is a technical tour de force. It elegantly demonstrates the relevance of BACE2 as an anti-amyloidogenic protease, at least in trisomy 21 cerebral organoids,” Stefan Lichtenthaler, Technical University of Munich, wrote to Alzforum. “It also opens the exciting possibility that single-nucleotide polymorphisms in BACE2 may control the age of onset of dementia in people with Down’s syndrome.”

Scientists know much less about the endoprotease BACE2 than about its cousin BACE1. Reports have documented BACE2 cleavage sites within APP at position 19 of the Aβ sequence. This BACE2 θ-cleavage of APP—yes, that’s θ, not β—prior to γ-secretase cleavage can thwart Aβ production. Additionally, once Aβ has been released from APP by γ-secretase, BACE2, Aβ-degrading protease (AβDP) activity does just what it suggests, cutting the peptide at amino acids 20 or 34 (Farzan et al., 2000; Yan et al., 2001; Sun et al., 2006). 

Researchers have debated if these activities are physiologically relevant. Nižetić and colleagues wondered if they might explain the paradoxical delayed onset of amyloidosis in some people with Down’s.

To test this, joint first authors Ivan Alić, Pollyanna Goh, Aoife Murray, and Erik Portelius turned to cerebral organoids and CSF analysis. They cultured organoids by reprograming keratinocytes obtained from hair follicles, eking out as many as 10 organoids per donor. All organoids derived from five DS donors—plus from one euploid donor who had an extra copy only of the APP gene, not the whole chromosome—had signs of AD pathology. These included diffuse and compact amyloid deposits, hyperphosphorylated tau, and filamentous tau in plaque-associated neurites.

However, all organoids from two other donors grew free of AD pathology. These were the youngest donors—a woman with trisomy 21 and Down’s who donated follicles at age 31 and remains dementia-free at 37, and a 16-year-old girl with genetic mosaicism, who has both trisomy 21 cells and cells with the normal number of chromosomes.

Could BACE2 explain why organoids from these two donors escaped AD-like pathology? To address this question, Alić and colleagues used mass spectrometry to analyze peptides in the conditioned medium (CM) of organoids that were 100 to 137 days old. In CM of trisomy 21 organoids, the amount of θ-secretase and AβDP products, i.e., Aβ1-19, Aβ1-20 and Aβ1-34, were double those in CM from isogenic normal karyotype organoids. Levels of these non-amyloidogenic Aβ peptides were normal in CM from organoids grown from the donor with the extra copy of the APP gene, indicating that overexpression of the precursor protein does not explain the pattern. Likewise, all CMs had similar levels of α-secretase products, suggesting the difference lay elsewhere.

To directly test if BACE2 was responsible, the authors used CRISPR to delete one copy of it from trisomy 21 organoids grown from the 16-year-old donor. This reduced BACE2 expression by 30 percent without affecting APP expression. The ratio of non-amyloidogenic to amyloidogenic Aβ peptides fell by 20 percent. Tellingly, these organoids began to accumulate Aβ aggregates, such that, by day 96, cells were beginning to die. Incubating these organoids with β- and γ-secretase inhibitors prevented amyloid accumulation and protected the cells. The authors also found BACE2, but not BACE1, co-localized with Aβ1-34 in organoids lysosomes.

Do Aβ peptide profiles differ between people with trisomy 21 and euploid controls? The authors reanalyzed CSF data Portelius and colleagues had obtained from 17 DS donors and 12 age-matched controls (Portelius et al., 2014). Levels of θ-secretase and AβDP were higher in DS CSF than control fluid.

Then why are not all people with DS protected from amyloidosis? This is where genetic background may be important. Working with Hardy, Nižetić and colleagues found two new single-nucleotide polymorphisms, rs746064 and rs9983496, in the BACE2 locus that correlated with age of onset in the LonDownS Consortium cohort. These are near rs7510366, a previously identified locus that also correlates with age at onset in DS (Mok et al., 2014). All three lie in a region that causes early onset AD when deleted (Rovelet-Lecrux et al., 2015). All told, the data point to BACE2 as a potential anti-amyloidogenic protease.

Might this have ramifications for inhibitors that block BACE2 as well as BACE1? BACE inhibitors clearly reduce amyloid, so preventing non-amyloidogenic processing by BACE2 would not seem to explain the worsening cognition that has scuppered this class of drug (Dec 2019 news). Still, there are other BACE2 functions that might be more germane. “We still know relatively little about physiological BACE2 functions beyond APP cleavage,” noted Lichtenthaler. “Such additional functions may also be affected by BACE inhibitors and therefore potentially contribute to side effects seen in the clinical trials,” he wrote (see comment below).—Tom Fagan

Comments

  1. This paper is a technical tour de force and elegantly demonstrates the relevance of BACE2 as an anti-amyloidogenic protease, at least in trisomy 21 cerebral organoids. It also opens the exciting possibility that SNPs in BACE2 may control the age of onset of dementia in people with Down’s syndrome. An important merit of this work is to put BACE2 back on the research agenda. For example, we still do not know when and where exactly BACE2 is expressed in the brain, which is one of the reasons why it has been difficult to understand whether BACE1 inhibitor side effects are (partly) due to BACE2 inhibition. Likewise, we still know relatively little about physiological BACE2 functions beyond APP cleavage. Such additional functions may also be affected by BACE inhibitors and therefore potentially contribute to side effects seen in the clinical trials with BACE inhibitors.

    View all comments by Stefan Lichtenthaler

  2. Human BACE2 is an aspartyl protease, encoded by the BACE2 gene on chromosome 21 (Acquati et al., 2000; Bennett et al., 2000; Lin et al., 2000). BACE2 is homologous to BACE1 (the β-secretase). These two proteins are 45 percent identical in amino acid sequence (Sun et al., 2015). BACE2 was found to cleave the Flemish mutant APP for Aβ production (Farzan et al., 2000) and it was initially considered to be another β-secretase that contributed to Alzheimer’s development in Down’s syndrome (DS) by cleaving APP for Aβ production in the amyloidogenic pathway (Saunders et al., 1999; Solans et al., 2000). However, later studies have clearly demonstrated that BACE2 is not a β-secretase. It is the θ-secretase that cleaves APP at phenylalanine 20 within the Aβ domain to produce APP CTFθ (C80) and it prevents Aβ generation (Sun et al., 2015; Sun et al., 2006). 

    Although DS patients with trisomy-21 develop typical Alzheimer’s neuropathology, including neuritic plaques and neurofibrillary tangles, approximately 30 percent will not develop dementia during their lifetimes. In this recent publication, Alić et al. reported that trisomy 21 organoids secrete more BACE2-cleaved non-amyloidogenic APP products (Aβ1-19, 1-20, and 1-34). The profile of these truncated Aβ species in CSF of the DS patients is similar to the profile from the trisomy 21 organoids. Elimination of the extra copy of the BACE2 gene resulted in AD-like pathology in pathology-negative trisomy 21 organoids, and inhibition of either β- or γ-secretase activity resulted in less plaque deposits and hyperphosphorylated tau in the trisomy-21 organoids. More interestingly, the authors showed that BACE2’s anti-amyloidogenic activity is gene-dose-dependent in DS patients, and the SNP allelic differences in BACE2 correlate with age of dementia onset in the patients.

    This is an exciting study with convincing data generated from the trisomy-21 organoids and the large cohort of patients from The London Down Syndrome Consortium (LonDownS). These results indicate that BACE2 could play a physiological role as a dose-sensitive AD suppressor in DS patients, explaining why some DS patients have delayed or no dementia. In addition to BACE2’s anti-amyloidogenic effect, recently we also discovered that BACE2 protects neuronal cells by cleavage of Kv2.1 to prevent the outward potassium currents (Liu et al., 2018), suggesting that BACE2 could be a promising therapeutic target for AD. These studies suggest that more selective and specific BACE1 inhibitors that do not affect BACE2’s protective functions are warranted for AD drug development. Regarding the effect of different BACE2 SNP alleles on Alzheimer-related pathologies and clinical manifestations, as well as the potential for using BACE2-cleaved APP products as biomarkers, a much larger sample size is needed for future study.

    References:

    Acquati F, Accarino M, Nucci C, Fumagalli P, Jovine L, Ottolenghi S, Taramelli R. The gene encoding DRAP (BACE2), a glycosylated transmembrane protein of the aspartic protease family, maps to the down critical region. FEBS Lett. 2000 Feb 18;468(1):59-64. PubMed.

    Bennett BD, Babu-Khan S, Loeloff R, Louis JC, Curran E, Citron M, Vassar R. Expression analysis of BACE2 in brain and peripheral tissues. J Biol Chem. 2000 Jul 7;275(27):20647-51. PubMed.

    Lin X, Koelsch G, Wu S, Downs D, Dashti A, Tang J. Human aspartic protease memapsin 2 cleaves the beta-secretase site of beta-amyloid precursor protein. Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1456-60. PubMed.

    Sun X, Wang Y, Qing H, Christensen MA, Liu Y, Zhou W, Tong Y, Xiao C, Huang Y, Zhang S, Liu X, Song W. Distinct transcriptional regulation and function of the human BACE2 and BACE1 genes. FASEB J. 2005 May;19(7):739-49. PubMed.

    Farzan M, Schnitzler CE, Vasilieva N, Leung D, Choe H. BACE2, a beta -secretase homolog, cleaves at the beta site and within the amyloid-beta region of the amyloid-beta precursor protein. Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9712-7. PubMed.

    Saunders AJ, Kim TW, Tanzi RE. BACE maps to chromosome 11 and a BACE homolog, BACE2, reside in the obligate Down’s syndrome region of chromosome 21. Science 1999 Nov 12;(286):1255a.

    Solans A, Estivill X, de La Luna S. A new aspartyl protease on 21q22.3, BACE2, is highly similar to Alzheimer's amyloid precursor protein beta-secretase. Cytogenet Cell Genet. 2000;89(3-4):177-84. PubMed.

    Sun X, He G, Song W. BACE2, as a novel APP theta-secretase, is not responsible for the pathogenesis of Alzheimer's disease in Down syndrome. FASEB J. 2006 Jul;20(9):1369-76. PubMed.

    Liu F, Zhang Y, Liang Z, Sun Q, Liu H, Zhao J, Xu J, Zheng J, Yun Y, Yu X, Song W, Sun X. Cleavage of potassium channel Kv2.1 by BACE2 reduces neuronal apoptosis. Mol Psychiatry. 2018 Jul;23(7):1542-1554. Epub 2018 Apr 27 PubMed.

    View all comments by Yun Zhang View all comments by Weihong Song

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References

News Citations

  1. Picking Through the Rubble, Field Tries to Salvage BACE Inhibitors

Paper Citations

  1. Hithersay R, Startin CM, Hamburg S, Mok KY, Hardy J, Fisher EM, Tybulewicz VL, Nizetic D, Strydom A. Association of Dementia With Mortality Among Adults With Down Syndrome Older Than 35 Years. JAMA Neurol. 2018 Nov 19; PubMed.
  2. Farzan M, Schnitzler CE, Vasilieva N, Leung D, Choe H. BACE2, a beta -secretase homolog, cleaves at the beta site and within the amyloid-beta region of the amyloid-beta precursor protein. Proc Natl Acad Sci U S A. 2000 Aug 15;97(17):9712-7. PubMed.
  3. Yan R, Munzner JB, Shuck ME, Bienkowski MJ. BACE2 functions as an alternative alpha-secretase in cells. J Biol Chem. 2001 Sep 7;276(36):34019-27. PubMed.
  4. Sun X, He G, Song W. BACE2, as a novel APP theta-secretase, is not responsible for the pathogenesis of Alzheimer's disease in Down syndrome. FASEB J. 2006 Jul;20(9):1369-76. PubMed.
  5. Portelius E, Hölttä M, Soininen H, Bjerke M, Zetterberg H, Westerlund A, Herukka SK, Blennow K, Mattsson N. Altered cerebrospinal fluid levels of amyloid β and amyloid precursor-like protein 1 peptides in Down's syndrome. Neuromolecular Med. 2014 Jun;16(2):510-6. Epub 2014 Apr 18 PubMed.
  6. Mok KY, Jones EL, Hanney M, Harold D, Sims R, Williams J, Ballard C, Hardy J. Polymorphisms in BACE2 may affect the age of onset Alzheimer's dementia in Down syndrome. Neurobiol Aging. 2014 Jun;35(6):1513.e1-5. Epub 2013 Dec 27 PubMed.
  7. Rovelet-Lecrux A, Charbonnier C, Wallon D, Nicolas G, Seaman MN, Pottier C, Breusegem SY, Mathur PP, Jenardhanan P, Le Guennec K, Mukadam AS, Quenez O, Coutant S, Rousseau S, Richard AC, Boland A, Deleuze JF, Frebourg T, Hannequin D, Campion D, CNR-MAJ collaborators. De novo deleterious genetic variations target a biological network centered on Aβ peptide in early-onset Alzheimer disease. Mol Psychiatry. 2015 Sep;20(9):1046-56. Epub 2015 Jul 21 PubMed.

External Citations

  1. bioRxiv

Further Reading

No Available Further Reading

Primary Papers

  1. Alić I, Goh PA, Murray A, Portelius E, Gkanatsiou E, Gough G, Mok KY, Koschut D, Brunmeir R, Yeap YJ, O'Brien NL, Groet J, Shao X, Havlicek S, Dunn NR, Kvartsberg H, Brinkmalm G, Hithersay R, Startin C, Hamburg S, Phillips M, Pervushin K, Turmaine M, Wallon D, Rovelet-Lecrux A, Soininen H, Volpi E, Martin JE, Foo JN, Becker DL, Rostagno A, Ghiso J, Krsnik Ž, Šimić G, Kostović I, Mitrečić D, LonDownS Consortium, Francis PT, Blennow K, Strydom A, Hardy J, Zetterberg H, Nižetić D. Patient-specific Alzheimer-like pathology in trisomy 21 cerebral organoids reveals BACE2 as a gene dose-sensitive AD suppressor in human brain. Mol Psychiatry. 2021 Oct;26(10):5766-5788. Epub 2020 Jul 10 PubMed. bioRxiv

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