Chen J, Zhang Z, Liu Y, Huang L, Liu Y, Yang D, Bao X, Liu P, Ge Y, Li Q (2024) Progressive reduction of nuclear receptor Nr4a1 mediates age‐dependent cognitive decline. Alzheimer's Dement. https://doi.org/10.1002/alz.13819
Scheltens P, De Strooper B, Kivipelto M, Holstege H, Chételat G, Teunissen CE, Cummings J, van der Flier WM (2021) Alzheimer’s disease. Lancet 397(10284):1577–1590
Article CAS PubMed PubMed Central Google Scholar
Spires TL, Hyman Β (2004) Neuronal structure is altered by amyloid plaques. Rev Neurosci 15(4):267–278
Sharma P, Sharma A, Fayaz F, Wakode S, Pottoo FH (2020) Biological signatures of Alzheimer’s disease. Curr Top Med Chem 20(9):770–781
Article CAS PubMed Google Scholar
Sharma K, Pradhan S, Duffy LK, Yeasmin S, Bhattarai N, Schulte MK (2021) Role of receptors in relation to plaques and tangles in Alzheimer’s disease pathology. Int J Mol Sci 22(23):12987
Article CAS PubMed PubMed Central Google Scholar
Jobson DD, Hase Y, Clarkson AN, Kalaria RN (2021) The role of the medial prefrontal cortex in cognition, ageing and dementia. Brain Commun, 3(3):fcab125.
Article PubMed PubMed Central Google Scholar
Yan Z, Rein B (2022) Mechanisms of synaptic transmission dysregulation in the prefrontal cortex: pathophysiological implications. Mol Psychiatry 27(1):445–465
Torres-Flores M, Peña-Ortega F (2022) Amyloid beta alters prefrontal-dependent functions along with its excitability and synaptic plasticity in male rats. Neuroscience 498:260–279
Article CAS PubMed Google Scholar
Sadick JS, O’Dea MR, Hasel P, Dykstra T, Faustin A, Liddelow SA (2022) Astrocytes and oligodendrocytes undergo subtype-specific transcriptional changes in Alzheimer’s disease. Neuron 110(11):1788-1805. e1710
Article CAS PubMed PubMed Central Google Scholar
Chen JF, Wang F, Huang NX, Xiao L, Mei F (2022) Oligodendrocytes and myelin: active players in neurodegenerative brains? Dev Neurobiol 82(2):160–174
Han S, Gim Y, Jang E-H, Hur E-M (2022) Functions and dysfunctions of oligodendrocytes in neurodegenerative diseases. Front Cell Neurosci 16:1083159
Article CAS PubMed PubMed Central Google Scholar
Xie Y, Chen L, Wang L, Liu T, Zheng Y, Si L, Ge H, Xu H, Xiao L, Wang G (2024) Single-nucleus transcriptomic analysis reveals the relationship between gene expression in oligodendrocyte lineage and major depressive disorder. J Transl Med 22(1):109
Article CAS PubMed PubMed Central Google Scholar
Ali M, Huarte OU, Heurtaux T, Garcia P, Rodriguez BP, Grzyb K, Halder R, Skupin A, Buttini M, Glaab E (2024) Single-cell transcriptional profiling and gene regulatory network modeling in Tg2576 mice reveal gender-dependent molecular features preceding Alzheimer-like pathologies. Mol Neurobiol 61(2):541–566
Article CAS PubMed Google Scholar
Yu M, Risacher SL, Nho KT, Wen Q, Oblak AL, Unverzagt FW, Apostolova LG, Farlow MR, Brosch JR, Clark DG (2024) Spatial transcriptomic patterns underlying amyloid-β and tau pathology are associated with cognitive dysfunction in Alzheimer’s disease. Cell Rep, 43(2). https://doi.org/10.1016/j.celrep.2024.113691
Zhang L, Xiong Z, Xiao M (2024) A review of the application of spatial transcriptomics in neuroscience. Interdisciplinary Sci: Comput Life Sci, 1–18. https://doi.org/10.1007/s12539-024-00603-4
Goralski TM, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse DJ (2024) Spatial transcriptomics reveals molecular dysfunction associated with cortical Lewy pathology. Nat Commun 15(1):2642
Article CAS PubMed PubMed Central Google Scholar
Wang C, McNutt M, Ma A, Fu H, Ma Q (2023) ssREAD: a single-cell and spatial RNA-seq database for Alzheimer’s disease. bioRxiv. https://doi.org/10.1101/2023.09.08.556944
Maynard KR, Collado-Torres L, Weber LM, Uytingco C, Barry BK, Williams SR, Catallini JL, Tran MN, Besich Z, Tippani M (2021) Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nat Neurosci 24(3):425–436
Article CAS PubMed PubMed Central Google Scholar
Narayanan M, Huynh JL, Wang K, Yang X, Yoo S, McElwee J, Zhang B, Zhang C, Lamb JR, Xie T (2014) Common dysregulation network in the human prefrontal cortex underlies two neurodegenerative diseases. Mol Syst Biol 10(7):743
Article PubMed PubMed Central Google Scholar
McKay EC, Beck JS, Khoo SK, Dykema KJ, Cottingham SL, Winn ME, Paulson HL, Lieberman AP, Counts SE (2019) Peri-infarct upregulation of the oxytocin receptor in vascular dementia. J Neuropathol Exp Neurol 78(5):436–452
Article CAS PubMed PubMed Central Google Scholar
Berchtold NC, Cribbs DH, Coleman PD, Rogers J, Head E, Kim R, Beach T, Miller C, Troncoso J, Trojanowski JQ (2008) Gene expression changes in the course of normal brain aging are sexually dimorphic. Proc Natl Acad Sci 105(40):15605–15610
Article CAS PubMed PubMed Central Google Scholar
Sood S, Gallagher IJ, Lunnon K, Rullman E, Keohane A, Crossland H, Phillips BE, Cederholm T, Jensen T, van Loon LJ (2015) A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status. Genome Biol 16:1–17
Nachun D, Ramos E, Karydas A, Dokuru D, Gao F, Yang Z, Van Berlo V, Sears R, Kramer J, Boxer A (2019) Systems-level analysis of peripheral blood gene expression in dementia patients reveals an innate immune response shared across multiple disorders. bioRxiv.2019.2012. 2013.875112. https://doi.org/10.1101/2019.12.13.875112
Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, Hao Y, Stoeckius M, Smibert P, Satija R (2019) Comprehensive integration of single-cell data. Cell 177(7):1888-1902e1821
Article CAS PubMed PubMed Central Google Scholar
Korsunsky I, Millard N, Fan J, Slowikowski K, Zhang F, Wei K, Baglaenko Y, Brenner M, Loh PR, Raychaudhuri S (2019) Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods 16(12):1289–1296
Article CAS PubMed PubMed Central Google Scholar
Yang YT, Gan Z, Zhang J, Zhao X, Yang Y, Han S, Wu W, Zhao X-M (2024) STAB2: an updated spatio-temporal cell atlas of the human and mouse brain. Nucleic Acids Res 52(D1):D1033–D1041
Phipson B, Sim CB, Porrello ER, Hewitt AW, Powell J, Oshlack A (2022) Propeller: testing for differences in cell type proportions in single cell data. Bioinformatics 38(20):4720–4726
Article CAS PubMed PubMed Central Google Scholar
Li H, Sharma A, Ming W, Sun X, Liu H (2020) A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples. BMC Genomics 21(1):1–15
Ma Y, Zhou X (2022) Spatially informed cell-type deconvolution for spatial transcriptomics. Nat biotechnol, 1–11. https://doi.org/10.1038/s41587-022-01273-7
Street K, Risso D, Fletcher RB, Das D, Ngai J, Yosef N, Purdom E, Dudoit S (2018) Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19:1–16
McInnes L, Healy J, Melville J (2018) Umap: uniform manifold approximation and projection for dimension reduction. arXiv preprint arXiv:180203426. https://doi.org/10.48550/arXiv.1802.03426
Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine J-C, Geurts P, Aerts J (2017) SCENIC: single-cell regulatory network inference and clustering. Nat Methods 14(11):1083–1086
Article CAS PubMed PubMed Central Google Scholar
Hao Y, Hao S, Andersen-Nissen E, Mauck WM III, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M (2021) Integrated analysis of multimodal single-cell data. Cell 184(13):3573-3587. e3529
Article CAS PubMed PubMed Central Google Scholar
Yu G, Wang L-G, Han Y, He Q-Y (2012) ClusterProfiler: an R package for comparing biological themes among gene clusters. Omics: J Integr Biol, 16(5):284–287.
Wang C, Acosta D, McNutt M, Bian J, Ma A, Fu H, Ma Q (2024) A single-cell and spatial RNA-seq database for Alzheimer’s disease (ssREAD). Nat Commun 15(1):4710
Comments (0)