Single-nucleus RNA sequencing reveals transcriptional changes of hippocampal neurons in APP23 mouse model of Alzheimer’s disease

References

• Isik AT. Late onset Alzheimer’s disease in older people. Clin Interv Aging. 2010;5:307.
   PubMed Web of Science ®Google Scholar
• Hardy J, Selkoe DJ. The amyloid hypothesis of Alzheimer’s disease: progress and problems on the road to therapeutics. Science. 2002;297(5580):353–356.
   PubMed Web of Science ®Google Scholar
• Forloni G, Artuso V, La Vitola P, et al. Oligomeropathies and pathogenesis of Alzheimer and Parkinson’s diseases. Mov Disord. 2016;31(6):771–781.
   PubMed Web of Science ®Google Scholar
• Shankar GM, Li S, Mehta TH, et al. Amyloid-β protein dimers isolated directly from Alzheimer’s brains impair synaptic plasticity and memory. Nat Med. 2008;14(8):837.
   PubMed Web of Science ®Google Scholar
• Jin M, Shepardson N, Yang T, et al. Soluble amyloid β-protein dimers isolated from Alzheimer cortex directly induce Tau hyperphosphorylation and neuritic degeneration. Proc Nat Acad Sci. 2011;108(14):5819–5824.
   PubMed Web of Science ®Google Scholar
• Sturchler-Pierrat C, Abramowski D, Duke M, et al. Two amyloid precursor protein transgenic mouse models with Alzheimer disease-like pathology. Proc Nat Acad Sci. 1997;94(24):13287–13292.
   PubMed Web of Science ®Google Scholar
• Van Erum J, Van Dam D, Sheorajpanday R, et al. Sleep architecture changes in the APP23 mouse model manifest at onset of cognitive deficits. Behav Brain Res. 2019;373:112089.
   PubMed Web of Science ®Google Scholar
• Janssen L, Dubbelaar ML, Holtman IR, et al. Aging, microglia and cytoskeletal regulation are key factors in the pathological evolution of the APP23 mouse model for Alzheimer’s disease. Biochim Biophys Acta Mol Basis Dis. 2017;1863(2):395–405.
   PubMed Web of Science ®Google Scholar
• Kim KH, Moon M, Yu SB, et al. RNA-Seq analysis of frontal cortex and cerebellum from 5XFAD mice at early stage of disease pathology. J Alzheimers Dis. 2012;29(4):793–808.
   PubMed Web of Science ®Google Scholar
• Landel V, Baranger K, Virard I, et al. Temporal gene profiling of the 5XFAD transgenic mouse model highlights the importance of microglial activation in Alzheimer’s disease. Mol Neurodegener. 2014;9(1):33.
   PubMedGoogle Scholar
• López-González I, Schlüter A, Aso E, et al. Neuroinflammatory signals in Alzheimer disease and APP/PS1 transgenic mice: correlations with plaques, tangles, and oligomeric species. J Neuropathol Exp Neurol. 2015;74(4):319–344.
   PubMed Web of Science ®Google Scholar
• Habib N, Avraham-Davidi I, Basu A, et al. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat Methods. 2017;14(10):955.
   PubMed Web of Science ®Google Scholar
• Zhong S, Zhang S, Fan X, et al. A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. Nature. 2018;555(7697):524.
   PubMed Web of Science ®Google Scholar
• Hu P, Fabyanic E, Kwon DY, et al. Dissecting cell-type composition and activity-dependent transcriptional state in mammalian brains by massively parallel single-nucleus RNA-seq. Mol Cell. 2017;68(5):1006–1015. e7.
   PubMed Web of Science ®Google Scholar
• Habib N, Li Y, Heidenreich M, et al. Div-Seq: single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. Science. 2016;353(6302):925–928.
   PubMed Web of Science ®Google Scholar
• Braak H, Braak E, Bohl J. Staging of Alzheimer-related cortical destruction. Eur Neurol. 1993;33(6):403–408.
   PubMed Web of Science ®Google Scholar
• Squire LR. Memory and the hippocampus: a synthesis from findings with rats, monkeys, and humans. Psychol Rev. 1992;99(2):195.
   PubMed Web of Science ®Google Scholar
• Krishnaswami SR, Grindberg RV, Novotny M, et al. Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat Protoc. 2016;11(3):499.
   PubMed Web of Science ®Google Scholar
• Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105–1111.
   PubMed Web of Science ®Google Scholar
• Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31(2):166–169.
   PubMed Web of Science ®Google Scholar
• Butler A, Hoffman P, Smibert P, et al. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36(5):411.
   PubMed Web of Science ®Google Scholar
• Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun. 2019;10(1):1523.
   PubMed Web of Science ®Google Scholar
• Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30(1):207–210.
   PubMed Web of Science ®Google Scholar
• Schubert V, Dotti CG. Transmitting on actin: synaptic control of dendritic architecture. J Cell Sci. 2007;120(2):205–212.
   PubMed Web of Science ®Google Scholar
• Sekino Y, Kojima N, Shirao T. Role of actin cytoskeleton in dendritic spine morphogenesis. Neurochem Int. 2007;51(2–4):92–104.
   PubMed Web of Science ®Google Scholar
• Mori K, Muto Y, Kokuzawa J, et al. Neuronal protein NP25 interacts with F-actin. Neurosci Res. 2004;48(4):439–446.
   PubMed Web of Science ®Google Scholar
• Mathys H, Davila-Velderrain J, Peng Z, et al. Single-cell transcriptomic analysis of Alzheimer’s disease. Nature. 2019;1. DOI:10.1038/s41586-019-1195-2.
   Google Scholar
• Del-Aguila JL, Li Z, Dube U, et al. A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain. Alzheimers Res Ther. 2019;11(1):71.
   PubMed Web of Science ®Google Scholar
• Vance JE. Dysregulation of cholesterol balance in the brain: contribution to neurodegenerative diseases. Dis Model Mech. 2012;5(6):746–755.
   PubMed Web of Science ®Google Scholar
• Potier MC, Marquer C, Lainé J, et al. Increasing membrane cholesterol of neurons in culture recapitulates Alzheimer’s disease early phenotypes. Neurodegenerative Dis. 2015;15. DOI:10.1186/1750-1326-9-60.
   Google Scholar
• van der Kant R, Langness VF, Herrera CM, et al. Cholesterol metabolism is a druggable axis that independently regulates tau and amyloid-β in iPSC-derived Alzheimer’s disease neurons. Cell Stem Cell. 2019;24(3):363–375. e9.
   PubMed Web of Science ®Google Scholar
• Tambini MD, Pera M, Kanter E, et al. ApoE4 upregulates the activity of mitochondria‐associated ER membranes. EMBO Rep. 2016;17(1):27–36.
   PubMed Web of Science ®Google Scholar
• Liu Q, Zhang J. Lipid metabolism in Alzheimer’s disease. Neurosci Bull. 2014;30(2):331–345.
   PubMed Web of Science ®Google Scholar
• Chang R, Yee KL, Sumbria RK. Tumor necrosis factor α inhibition for Alzheimer’s disease. J Cent Nerv Syst Dis. 2017;9:1179573517709278.
   Web of Science ®Google Scholar
• Decourt B, Lahiri DK, Sabbagh MN. Targeting tumor necrosis factor alpha for Alzheimer’s disease. Curr Alzheimer Res. 2017;14(4):412–425.
   PubMed Web of Science ®Google Scholar