CRISPR/dCas9-Dnmt3a-mediated targeted DNA methylation of APP rescues brain pathology in a mouse model of Alzheimer’s disease

Translational Neurodegeneration - Tập 11 - Trang 1-12 - 2022
Hanseul Park1,2, Jaein Shin1,2, Yunkyung Kim1,2, Takashi Saito3,4, Takaomi C. Saido3, Jongpil Kim1,2
1Laboratory of Stem Cells and Gene Editing, Department of Chemistry & Biomedical Engineering, Dongguk University, Seoul, Republic of Korea
2Institute for Cellular Rebooting, Dongguk University, Seoul, Korea
3Laboratory for Proteolytic Neuroscience, RIKEN Center for Brain Science, Wako-shi, Saitama, Japan
4Department of Neurocognitive Science, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan

Tóm tắt

Aberrant DNA methylation patterns have been observed in neurodegenerative diseases, including Alzheimer's disease (AD), and dynamic changes in DNA methylation are closely associated with the onset and progression of these diseases. Particularly, hypomethylation of the amyloid precursor protein gene (APP) has been reported in patients with AD. In this study, we used catalytically inactivated Cas9 (dCas9) fused with Dnmt3a for targeted DNA methylation of APP, and showed that the CRISPR/dCas9-Dnmt3a-mediated DNA methylation system could efficiently induce targeted DNA methylation of APP both in vivo and in vitro. We hypothesized that the targeted methylation of the APP promoter might rescue AD-related neuronal cell death by reducing APP mRNA expression. The cultured APP-KI mouse primary neurons exhibited an altered DNA-methylation pattern on the APP promoter after dCas9-Dnmt3a treatment. Likewise, the APP mRNA level was significantly reduced in the dCas9-Dnmt3a-treated wild-type and APP-KI mouse primary neurons. We also observed decreased amyloid-beta (Aβ) peptide level and Aβ42/40 ratio in the dCas9-Dnmt3a-treated APP-KI mouse neurons compared to the control APP-KI mouse neurons. In addition, neuronal cell death was significantly decreased in the dCas9-Dnmt3a-treated APP-KI mouse neurons. Furthermore, the in vivo methylation of APP in the brain via dCas9-Dnmt3a treatment altered Aβ plaques and attenuated cognitive and behavioral impairments in the APP-KI mouse model. These results suggest that the targeted methylation of APP via dCas9-Dnmt3a treatment can be a potential therapeutic strategy for AD.

Tài liệu tham khảo

Castellani RJ, Rolston RK, Smith MA. Alzheimer disease. Dis Mon. 2010;56(9):484–546. O’Brien RJ, Wong PC. Amyloid precursor protein processing and Alzheimer’s disease. Annu Rev Neurosci. 2011;34:185–204. Silva MVF, Loures CMG, Alves LCV, de Souza LC, Borges KBG, Carvalho MDG. Alzheimer’s disease: risk factors and potentially protective measures. J Biomed Sci. 2019;26(1):33. Mastroeni D, Grover A, Delvaux E, Whiteside C, Coleman PD, Rogers J. Epigenetic mechanisms in Alzheimer’s disease. Neurobiol Aging. 2011;32(7):1161–80. Bennett DA, Yu L, Yang J, Srivastava GP, Aubin C, De Jager PL. Epigenomics of Alzheimer’s disease. Transl Res. 2015;165(1):200–20. Lardenoije R, Iatrou A, Kenis G, Kompotis K, Steinbusch HW, Mastroeni D, et al. The epigenetics of aging and neurodegeneration. Prog Neurobiol. 2015;131:21–64. Liu X, Jiao B, Shen L. The epigenetics of Alzheimer’s disease: factors and therapeutic implications. Front Genet. 2018;9:579. Moore LD, Le T, Fan G. DNA methylation and its basic function. Neuropsychopharmacology. 2013;38(1):23–38. Razin A, Cedar H. DNA methylation and gene expression. Microbiol Rev. 1991;55(3):451–8. Oka M, Rodic N, Graddy J, Chang LJ, Terada N. CpG sites preferentially methylated by Dnmt3a in vivo. J Biol Chem. 2006;281(15):9901–8. Pervjakova N, Kasela S, Morris AP, Kals M, Metspalu A, Lindgren CM, et al. Imprinted genes and imprinting control regions show predominant intermediate methylation in adult somatic tissues. Epigenomics. 2016;8(6):789–99. Vilain A, Bernardino J, Gerbault-Seureau M, Vogt N, Niveleau A, Lefrancois D, et al. DNA methylation and chromosome instability in lymphoblastoid cell lines. Cytogenet Cell Genet. 2000;90(1–2):93–101. Bourc’his D, Xu GL, Lin CS, Bollman B, Bestor TH. Dnmt3L and the establishment of maternal genomic imprints. Science. 2001;294(5551):2536–9. Tadic V, Josipovic G, Zoldos V, Vojta A. CRISPR/Cas9-based epigenome editing: an overview of dCas9-based tools with special emphasis on off-target activity. Methods. 2019;164–165:109–19. Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S, et al. Editing DNA methylation in the mammalian genome. Cell. 2016;167(1):233-247e217. Stepper P, Kungulovski G, Jurkowska RZ, Chandra T, Krueger F, Reinhardt R, et al. Efficient targeted DNA methylation with chimeric dCas9-Dnmt3a-Dnmt3L methyltransferase. Nucleic Acids Res. 2017;45(4):1703–13. Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK. CRISPR RNA-guided activation of endogenous human genes. Nat Methods. 2013;10(10):977–9. Hilton IB, D’Ippolito AM, Vockley CM, Thakore PI, Crawford GE, Reddy TE, et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat Biotechnol. 2015;33(5):510–7. Lu Z, Liu Z, Mao W, Wang X, Zheng X, Chen S, et al. Locus-specific DNA methylation of Mecp2 promoter leads to autism-like phenotypes in mice. Cell Death Dis. 2020;11(2):85. Liu XS, Wu H, Krzisch M, Wu X, Graef J, Muffat J, et al. Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene. Cell. 2018;172(5):979-992 e976. McDonald JI, Celik H, Rois LE, Fishberger G, Fowler T, Rees R, et al. Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation. Biol Open. 2016;5(6):866–74. Vojta A, Dobrinic P, Tadic V, Bockor L, Korac P, Julg B, et al. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Res. 2016;44(12):5615–28. Saito T, Matsuba Y, Mihira N, Takano J, Nilsson P, Itohara S, et al. Single App knock-in mouse models of Alzheimer’s disease. Nat Neurosci. 2014;17(5):661–3. Bae S, Park J, Kim JS. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics. 2014;30(10):1473–5. Mijalkov M, Volpe G, Fernaud-Espinosa I, DeFelipe J, Pereira JB, Merino-Serrais P. Dendritic spines are lost in clusters in Alzheimer’s disease. Sci Rep. 2021;11(1):12350. Appel SH. A unifying hypothesis for the cause of amyotrophic lateral sclerosis, parkinsonism, and Alzheimer disease. Ann Neurol. 1981;10(6):499–505. Harman D. Alzheimer’s disease pathogenesis: role of aging. Ann N Y Acad Sci. 2006;1067:454–60. Serrano-Pozo A, Frosch MP, Masliah E, Hyman BT. Neuropathological alterations in Alzheimer disease. Cold Spring Harb Perspect Med. 2011;1(1): a006189. Birks J. Cholinesterase inhibitors for Alzheimer's disease. Cochrane Database Syst Rev. 2006(1):CD005593. Mueller C, Perera G, Hayes RD, Shetty H, Stewart R. Associations of acetylcholinesterase inhibitor treatment with reduced mortality in Alzheimer’s disease: a retrospective survival analysis. Age Ageing. 2018;47(1):88–94. Iwata A, Nagata K, Hatsuta H, Takuma H, Bundo M, Iwamoto K, et al. Altered CpG methylation in sporadic Alzheimer’s disease is associated with APP and MAPT dysregulation. Hum Mol Genet. 2014;23(3):648–56. Herms J, Anliker B, Heber S, Ring S, Fuhrmann M, Kretzschmar H, et al. Cortical dysplasia resembling human type 2 lissencephaly in mice lacking all three APP family members. EMBO J. 2004;23(20):4106–15. Brohede J, Rinde M, Winblad B, Graff C. A DNA methylation study of the amyloid precursor protein gene in several brain regions from patients with familial Alzheimer disease. J Neurogenet. 2010;24(4):179–81. Cali CP, Park DS, Lee EB. Targeted DNA methylation of neurodegenerative disease genes via homology directed repair. Nucleic Acids Res. 2019;47(22):11609–22. Dashtipour K, Tafreshi A, Adler C, Beach T, Chen X, Serrano G, et al. Hypermethylation of synphilin-1, alpha-synuclein-interacting protein (SNCAIP) gene in the cerebral cortex of patients with sporadic Parkinson’s disease. Brain Sci. 2017;7(7):74. Pickar-Oliver A, Gersbach CA. The next generation of CRISPR-Cas technologies and applications. Nat Rev Mol Cell Biol. 2019;20(8):490–507. Duan Y, Ye T, Qu Z, Chen Y, Miranda A, Zhou X, et al. Brain-wide Cas9-mediated cleavage of a gene causing familial Alzheimer’s disease alleviates amyloid-related pathologies in mice. Nat Biomed Eng. 2022;6(2):168–80. Tremblay G, Rousseau J, Mbakam CH, Tremblay JP. Insertion of the Icelandic mutation (A673T) by prime editing: a potential preventive treatment for familial and sporadic Alzheimer’s disease. CRISPR J. 2022;5(1):109–22. Guyon A, Rousseau J, Begin FG, Bertin T, Lamothe G, Tremblay JP. Base editing strategy for insertion of the A673T mutation in the APP gene to prevent the development of AD in vitro. Mol Ther Nucleic Acids. 2021;24:253–63. Konstantinidis E, Molisak A, Perrin F, Streubel-Gallasch L, Fayad S, Kim DY, et al. CRISPR-Cas9 treatment partially restores amyloid-beta 42/40 in human fibroblasts with the Alzheimer’s disease PSEN 1 M146L mutation. Mol Ther Nucleic Acids. 2022;28:450–61. Gyorgy B, Loov C, Zaborowski MP, Takeda S, Kleinstiver BP, Commins C, et al. CRISPR/Cas9 mediated disruption of the Swedish APP allele as a therapeutic approach for early-onset Alzheimer’s disease. Mol Ther Nucleic Acids. 2018;11:429–40.