Insights into Alzheimer’s disease from single-cell genomic approaches
Open accessAbstract
Alzheimer's disease (AD) is an age-related disease pathologically defined by the deposition of amyloid plaques and neurofibrillary tangles in the brain parenchyma. Single-cell profiling has shown that Alzheimer's dementia involves the complex interplay of virtually every major brain cell type. Here, we highlight cell-type-specific molecular perturbations in AD. We discuss how genomic information from single cells expands existing paradigms of AD pathogenesis and highlight new opportunities for therapeutic interventions.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Several pathways altered by a short-term E4 to E2 transition are also perturbed across 17 large-scale human AD snRNA-seq studies.
“several pathways altered by a short-term E4 to E2 transition were cellular pathways that are also perturbed across 17 large-scale human AD snRNA-seq studies24.”
From APOE4 to APOE2 allelic switching in mice improves Alzheimer’s disease-related metabolic signatures, neuropathology and cognition (2025) · cites this paper as [24]
The Introduction reports that several human AD snRNA-seq studies find altered cellular pathways, and describes shared disturbances in lipid handling, immune response, and metabolism. It does not establish that these pathways overlap with those altered by a short-term E4-to-E2 transition, or that the finding spans 17 large-scale studies. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
A Unique Microglia Type Associated with Restricting Development of Alzheimer’s Disease
Keren-Shaul, H., Spinrad, A., Weiner, A., Matcovitch-Natan, O., Dvir-Szternfeld, R., Ulland, T. K., David, E., Baruch, K., Lara-Astaiso, D., Toth, B., et al. (2017) · Cell · doi:10.1016/j.cell.2017.05.018 · Cited by 5,493 · see citing works
Complement and microglia mediate early synapse loss in Alzheimer mouse models
Hong, S., Beja-Glasser, V. F., Nfonoyim, B. M., Frouin, A., Li, S., Ramakrishnan, S., Merry, K. M., Shi, Q., Rosenthal, A., Barres, B. A., et al. (2016) · Science · doi:10.1126/science.aad8373 · Cited by 3,343 · see citing works
Molecular Architecture of the Mouse Nervous System
Zeisel, A., Hochgerner, H., Lönnerberg, P., Johnsson, A., Memic, F., van der Zwan, J., Häring, M., Braun, E., Borm, L. E., La Manno, G., et al. (2018) · Cell · doi:10.1016/j.cell.2018.06.021 · Cited by 2,995 · see citing works
Krasemann, S., Madore, C., Cialic, R., Baufeld, C., Calcagno, N., El Fatimy, R., Beckers, L., O’Loughlin, E., Xu, Y., Fanek, Z., et al. (2017) · Immunity · doi:10.1016/j.immuni.2017.08.008 · Cited by 2,979 · see citing works
Reactive astrocyte nomenclature, definitions, and future directions
Escartin, C., Galea, E., Lakatos, A., O’Callaghan, J. P., Petzold, G. C., Serrano-Pozo, A., Steinhäuser, C., Volterra, A., Carmignoto, G., Agarwal, A., et al. (2021) · Nature Neuroscience · doi:10.1038/s41593-020-00783-4 · Cited by 2,533 · see citing works
New insights into the genetic etiology of Alzheimer’s disease and related dementias
Bellenguez, C., Küçükali, F., Jansen, I. E., Kleineidam, L., Moreno-Grau, S., Amin, N., Naj, A. C., Campos-Martin, R., Grenier-Boley, B., Andrade, V., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01024-z · Cited by 2,498 · see citing works
Hammond, T. R., Dufort, C., Dissing-Olesen, L., Giera, S., Young, A., Wysoker, A., Walker, A. J., Segel, M., Nemesh, J., Saunders, A., et al. (2018) · doi:10.1101/406140 · Cited by 2,225 · see citing works
A molecular atlas of cell types and zonation in the brain vasculature
Vanlandewijck, M., He, L., Mäe, M. A., Andrae, J., Ando, K., Del Gaudio, F., Nahar, K., Lebouvier, T., Laviña, B., Gouveia, L., et al. (2018) · Nature · doi:10.1038/nature25739 · Cited by 2,074 · see citing works
Molecular diversity and specializations among the cells of the adult mouse brain
Saunders, A., Macosko, E. Z., Wysoker, A., Goldman, M., Krienen, F. M., de Rivera, H., Bien, E., Baum, M., Bortolin, L., Wang, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.07.028 · Cited by 1,847 · see citing works
Shared and distinct transcriptomic cell types across neocortical areas
Tasic, B., Yao, Z., Graybuck, L. T., Smith, K. A., Nguyen, T. N., Bertagnolli, D., Goldy, J., Garren, E., Economo, M. N., Viswanathan, S., et al. (2018) · Nature · doi:10.1038/s41586-018-0654-5 · Cited by 1,746 · see citing works
Adult mouse cortical cell taxonomy revealed by single cell transcriptomics
Tasic, B., Menon, V., Nguyen, T. N., Kim, T. K., Jarsky, T., Yao, Z., Levi, B., Gray, L. T., Sorensen, S. A., Dolbeare, T., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4216 · Cited by 1,714 · see citing works
Lipid-associated macrophages control metabolic homeostasis in a Trem2-dependent manner
Jaitin, D. A., Adlung, L., Thaiss, C. A., Weiner, A., Li, B., Descamps, H., Lundgren, P., Bleriot, C., Liu, Z., Deczkowska, A., et al. (2019) · Cell · doi:10.1016/j.cell.2019.05.054 · Cited by 1,377 · see citing works
Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system
Marques, S., Zeisel, A., Codeluppi, S., van Bruggen, D., Mendanha Falcão, A., Xiao, L., Li, H., Häring, M., Hochgerner, H., Romanov, R. A., et al. (2016) · Science · doi:10.1126/science.aaf6463 · Cited by 1,246 · see citing works
Van Hove, H., Martens, L., Scheyltjens, I., De Vlaminck, K., Pombo Antunes, A. R., De Prijck, S., Vandamme, N., De Schepper, S., Van Isterdael, G., Scott, C. L., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0393-4 · Cited by 1,160 · see citing works
Lin, Y.-T., Seo, J., Gao, F., Feldman, H. M., Wen, H.-L., Penney, J., Cam, H. P., Gjoneska, E., Raja, W. K., Cheng, J., et al. (2018) · Neuron · doi:10.1016/j.neuron.2018.05.008 · Cited by 1,125 · see citing works
Self-citationClonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer’s disease
Gate, D., Saligrama, N., Leventhal, O., Yang, A. C., Unger, M. S., Middeldorp, J., Chen, K., Lehallier, B., Channappa, D., De Los Santos, M. B., et al. (2020) · Nature · doi:10.1038/s41586-019-1895-7 · Cited by 992 · see citing works
Zhang, P., Kishimoto, Y., Grammatikakis, I., Gottimukkala, K., Cutler, R. G., Zhang, S., Abdelmohsen, K., Bohr, V. A., Misra Sen, J., Gorospe, M., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0372-9 · Cited by 977 · see citing works
Grubman, A., Chew, G., Ouyang, J. F., Sun, G., Choo, X. Y., McLean, C., Simmons, R. K., Buckberry, S., Vargas-Landin, D. B., Poppe, D., et al. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0539-4 · Cited by 956 · see citing works
Sala Frigerio, C., Wolfs, L., Fattorelli, N., Thrupp, N., Voytyuk, I., Schmidt, I., Mancuso, R., Chen, W.-T., Woodbury, M. E., Srivastava, G., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.099 · Cited by 926 · see citing works
Identification of region-specific astrocyte subtypes at single cell resolution
Batiuk, M. Y., Martirosyan, A., Wahis, J., de Vin, F., Marneffe, C., Kusserow, C., Koeppen, J., Viana, J. F., Oliveira, J. F., Voet, T., et al. (2020) · Nature Communications · doi:10.1038/s41467-019-14198-8 · Cited by 805 · see citing works
Neuron-Astrocyte Metabolic Coupling Protects against Activity-Induced Fatty Acid Toxicity
Ioannou, M. S., Jackson, J., Sheu, S.-H., Chang, C.-L., Weigel, A. V., Liu, H., Pasolli, H. A., Xu, C. S., Pang, S., Matthies, D., et al. (2019) · Cell · doi:10.1016/j.cell.2019.04.001 · Cited by 760 · see citing works
Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease
Olah, M., Menon, V., Habib, N., Taga, M. F., Ma, Y., Yung, C. J., Cimpean, M., Khairallah, A., Coronas-Samano, G., Sankowski, R., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19737-2 · Cited by 722 · see citing works
Amyloid β oligomers constrict human capillaries in Alzheimer's disease via signaling to pericytes
Nortley, R., Korte, N., Izquierdo, P., Hirunpattarasilp, C., Mishra, A., Jaunmuktane, Z., Kyrargyri, V., Pfeiffer, T., Khennouf, L., Madry, C., et al. (2019) · Science · doi:10.1126/science.aav9518 · Cited by 682 · see citing works
Friedman, B. A., Srinivasan, K., Ayalon, G., Meilandt, W. J., Lin, H., Huntley, M. A., Cao, Y., Lee, S.-H., Haddick, P. C. G., Ngu, H., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2017.12.066 · Cited by 662 · see citing works
Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons
Habib, N., Li, Y., Heidenreich, M., Swiech, L., Avraham-Davidi, I., Trombetta, J. J., Hession, C., Zhang, F., & Regev, A. (2016) · Science · doi:10.1126/science.aad7038 · Cited by 601 · see citing works
Neuroinflammatory astrocyte subtypes in the mouse brain
Hasel, P., Rose, I. V. L., Sadick, J. S., Kim, R. D., & Liddelow, S. A. (2021) · Nature Neuroscience · doi:10.1038/s41593-021-00905-6 · Cited by 586 · see citing works
Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis
Falcão, A. M., van Bruggen, D., Marques, S., Meijer, M., Jäkel, S., Agirre, E., Samudyata, Floriddia, E. M., Vanichkina, D. P., ffrench-Constant, C., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0236-y · Cited by 579 · see citing works
Hochgerner, H., Zeisel, A., Lönnerberg, P., & Linnarsson, S. (2018) · Nature Neuroscience · doi:10.1038/s41593-017-0056-2 · Cited by 482 · see citing works
Distinct amyloid-β and tau-associated microglia profiles in Alzheimer’s disease
Gerrits, E., Brouwer, N., Kooistra, S. M., Woodbury, M. E., Vermeiren, Y., Lambourne, M., Mulder, J., Kummer, M., Möller, T., Biber, K., et al. (2021) · Acta Neuropathologica · doi:10.1007/s00401-021-02263-w · Cited by 441 · see citing works
What is a cell type and how to define it?
Zeng, H. (2022) · Cell · doi:10.1016/j.cell.2022.06.031 · Cited by 439 · see citing works
Kirby, L., Jin, J., Cardona, J. G., Smith, M. D., Martin, K. A., Wang, J., Strasburger, H., Herbst, L., Alexis, M., Karnell, J., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-11638-3 · Cited by 436 · see citing works
Marsh, S. E., Walker, A. J., Kamath, T., Dissing-Olesen, L., Hammond, T. R., de Soysa, T. Y., Young, A. M. H., Murphy, S., Abdulraouf, A., Nadaf, N., et al. (2022) · Nature Neuroscience · doi:10.1038/s41593-022-01022-8 · Cited by 432 · see citing works
A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease
The International Genomics of Alzheimer's Project, Huang, K.-L., Initiative, T. A. D. N., Marcora, E., Pimenova, A. A., Di Narzo, A. F., Kapoor, M., Jin, S. C., Harari, O., Bertelsen, S., et al. (2017) · Nature Neuroscience · doi:10.1038/nn.4587 · Cited by 423 · see citing works
Innovations present in the primate interneuron repertoire
Krienen, F. M., Goldman, M., Zhang, Q., C. H. del Rosario, R., Florio, M., Machold, R., Saunders, A., Levandowski, K., Zaniewski, H., Schuman, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2781-z · Cited by 381 · see citing works
Innovations in Primate Interneuron Repertoire
Krienen, F. M., Goldman, M., Zhang, Q., del Rosario, R., Florio, M., Machold, R., Saunders, A., Levandowski, K., Zaniewski, H., Schuman, B., et al. (2019) · doi:10.1101/709501 · Cited by 372 · see citing works
Transcriptional signature in microglia associated with Aβ plaque phagocytosis
Grubman, A., Choo, X. Y., Chew, G., Ouyang, J. F., Sun, G., Croft, N. P., Rossello, F. J., Simmons, R., Buckberry, S., Landin, D. V., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23111-1 · Cited by 357 · see citing works
Enhancing myelin renewal reverses cognitive dysfunction in a murine model of Alzheimer’s disease
Chen, J.-F., Liu, K., Hu, B., Li, R.-R., Xin, W., Chen, H., Wang, F., Chen, L., Li, R.-X., Ren, S.-Y., et al. (2021) · Neuron · doi:10.1016/j.neuron.2021.05.012 · Cited by 346 · see citing works
Microglia phagocytose myelin sheaths to modify developmental myelination
Hughes, A. N., & Appel, B. (2020) · Nature Neuroscience · doi:10.1038/s41593-020-0654-2 · Cited by 344 · see citing works
Microglia in Alzheimer's disease at single-cell level. Are there common patterns in humans and mice?
Chen, Y., & Colonna, M. (2021) · Journal of Experimental Medicine · doi:10.1084/jem.20202717 · Cited by 339 · see citing works
Wang, C., Xiong, M., Gratuze, M., Bao, X., Shi, Y., Andhey, P. S., Manis, M., Schroeder, C., Yin, Z., Madore, C., et al. (2021) · Neuron · doi:10.1016/j.neuron.2021.03.024 · Cited by 334 · see citing works
Single-Nucleus RNA-Seq Is Not Suitable for Detection of Microglial Activation Genes in Humans
Thrupp, N., Sala Frigerio, C., Wolfs, L., Skene, N. G., Fattorelli, N., Poovathingal, S., Fourne, Y., Matthews, P. M., Theys, T., Mancuso, R., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108189 · Cited by 329 · see citing works
Lipid accumulation induced by APOE4 impairs microglial surveillance of neuronal-network activity
Victor, M. B., Leary, N., Luna, X., Meharena, H. S., Scannail, A. N., Bozzelli, P. L., Samaan, G., Murdock, M. H., von Maydell, D., Effenberger, A. H., et al. (2022) · Cell Stem Cell · doi:10.1016/j.stem.2022.07.005 · Cited by 316 · see citing works
Self-citationFranjic, D., Skarica, M., Ma, S., Arellano, J. I., Tebbenkamp, A. T. N., Choi, J., Xu, C., Li, Q., Morozov, Y. M., Andrijevic, D., et al. (2022) · Neuron · doi:10.1016/j.neuron.2021.10.036 · Cited by 308 · see citing works
Molecular signatures underlying neurofibrillary tangle susceptibility in Alzheimer’s disease
Otero-Garcia, M., Mahajani, S. U., Wakhloo, D., Tang, W., Xue, Y.-Q., Morabito, S., Pan, J., Oberhauser, J., Madira, A. E., Shakouri, T., et al. (2022) · Neuron · doi:10.1016/j.neuron.2022.06.021 · Cited by 262 · see citing works
Early emergence of cortical interneuron diversity in the mouse embryo
Mi, D., Li, Z., Lim, L., Li, M., Moissidis, M., Yang, Y., Gao, T., Hu, T. X., Pratt, T., Price, D. J., et al. (2018) · Science · doi:10.1126/science.aar6821 · Cited by 259 · see citing works
Brain Endothelial Cells Are Exquisite Sensors of Age-Related Circulatory Cues
Chen, M. B., Yang, A. C., Yousef, H., Lee, D., Chen, W., Schaum, N., Lehallier, B., Quake, S. R., & Wyss-Coray, T. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.03.012 · Cited by 233 · see citing works
Novikova, G., Kapoor, M., TCW, J., Abud, E. M., Efthymiou, A. G., Chen, S. X., Cheng, H., Fullard, J. F., Bendl, J., Liu, Y., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21823-y · Cited by 214 · see citing works
Diverse human astrocyte and microglial transcriptional responses to Alzheimer’s pathology
Smith, A. M., Davey, K., Tsartsalis, S., Khozoie, C., Fancy, N., Tang, S. S., Liaptsi, E., Weinert, M., McGarry, A., Muirhead, R. C. J., et al. (2022) · Acta Neuropathologica · doi:10.1007/s00401-021-02372-6 · Cited by 209 · cited 1× · see citing works
“Smith et al.(134) GSE160936 12 Entorhinal and somatosensory cortex NEUN/SOX10 52,706 astrocytes and 27,592 microglia”
BackgroundGonzales, M. M., Garbarino, V. R., Marques Zilli, E., Petersen, R. C., Kirkland, J. L., Tchkonia, T., Musi, N., Seshadri, S., Craft, S., & Orr, M. E. (2022) · The Journal of Prevention of Alzheimer's Disease · doi:10.14283/jpad.2021.62 · Cited by 203 · see citing works
PU.1 regulates Alzheimer’s disease-associated genes in primary human microglia
Rustenhoven, J., Smith, A. M., Smyth, L. C., Jansson, D., Scotter, E. L., Swanson, M. E. V., Aalderink, M., Coppieters, N., Narayan, P., Handley, R., et al. (2018) · Molecular Neurodegeneration · doi:10.1186/s13024-018-0277-1 · Cited by 155 · see citing works
Sayed, F. A., Kodama, L., Fan, L., Carling, G. K., Udeochu, J. C., Le, D., Li, Q., Zhou, L., Wong, M. Y., Horowitz, R., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abe3947 · Cited by 155 · see citing works
Shi, Y., Andhey, P. S., Ising, C., Wang, K., Snipes, L. L., Boyer, K., Lawson, S., Yamada, K., Qin, W., Manis, M., et al. (2021) · Neuron · doi:10.1016/j.neuron.2021.05.034 · Cited by 135 · see citing works
Mechanisms of DNA damage-mediated neurotoxicity in neurodegenerative disease
Welch, G., & Tsai, L. (2022) · The EMBO Reports · doi:10.15252/embr.202154217 · Cited by 129 · see citing works
Self-citationWelch, G. M., Boix, C. A., Schmauch, E., Davila-Velderrain, J., Victor, M. B., Dileep, V., Bozzelli, P. L., Su, Q., Cheng, J. D., Lee, A., et al. (2022) · Science Advances · doi:10.1126/sciadv.abo4662 · Cited by 84 · see citing works
Self-citationYang, H. S., Onos, K. D., Choi, K., Keezer, K. J., Skelly, D. A., Carter, G. W., & Howell, G. R. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108739 · Cited by 69 · see citing works
Association of SPI1 haplotypes with altered SPI1 gene expression and Alzheimer’s disease risk
Cao, H., Initiative, A. D. N., Zhou, X., Chen, Y., Ip, F. C. F., Chen, Y., Lai, N. C. H., Lo, R. M. N., Tong, E. P. S., Mok, V. C. T., et al. (2022) · Journal of Alzheimer s Disease · doi:10.3233/jad-215311 · Cited by 28 · see citing works
Flagged first, then by citations
Research works printed but not linked: 94
- [1]Yao Z A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature 598, 103– 110 (2021). 34616066 PMC8494649
- [5]Lake BB Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. Science 352, 1586– 1590 (2016). 27339989 PMC5038589
- [6]Zhong S A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. Nature 555, 524– 528 (2018). 29539641
- [8]Mathys H Single-cell transcriptomic analysis of Alzheimer’s disease. Nature 570, 332– 337 (2019). 31042697 PMC6865822
- [9]Zhou Y Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer’s disease. Nat Med 26, 131– 142 (2020). 31932797 PMC6980793
- [10]Villa KL Inhibitory synapses are repeatedly assembled and removed at persistent sites in vivo. Neuron 89, 756– 769 (2016). 26853302 PMC4760889
- [11]Kurucu H Inhibitory synapse loss and accumulation of amyloid beta in inhibitory presynaptic terminals in Alzheimer’s disease. European Journal of Neurology n/a,. 34331352
- [13]Davila-Velderrain J Single-cell anatomical analysis of human hippocampus and entorhinal cortex uncovers early-stage molecular pathology in Alzheimer’s disease 2021.07.01.450715 10.1101/2021.07.01.450715v1 (2021) doi:. · DOI
- [14]Lau S-F, Cao H, Fu AKY & Ip NY Single-nucleus transcriptome analysis reveals dysregulation of angiogenic endothelial cells and neuroprotective glia in Alzheimer’s disease. PNAS 117, 25800– 25809 (2020). 32989152 PMC7568283
- [15]Li S & Sheng Z-H Energy matters: presynaptic metabolism and the maintenance of synaptic transmission. Nat Rev Neurosci 1– 19 (2021) doi: 10.1038/s41583-021-00535-8. 34782781 · DOI
- [16]Cheng X-T, Huang N & Sheng Z-H Programming axonal mitochondrial maintenance and bioenergetics in neurodegeneration and regeneration. Neuron 110, 1899– 1923 (2022). 35429433 PMC9233091
- [17]Fu H A tau homeostasis signature is linked with the cellular and regional vulnerability of excitatory neurons to tau pathology. Nat Neurosci 22, 47– 56 (2019). 30559469 PMC6330709
- [18]Leng K Molecular characterization of selectively vulnerable neurons in Alzheimer’s disease. Nat Neurosci 24, 276– 287 (2021). 33432193 PMC7854528
- [19]Barker SJ MEF2 is a key regulator of cognitive potential and confers resilience to neurodegeneration. Science Translational Medicine 13, eabd7695. 34731014 PMC9258338
- [20]Zalocusky KA Neuronal ApoE upregulates MHC-I expression to drive selective neurodegeneration in Alzheimer’s disease. Nat Neurosci 24, 786– 798 (2021). 33958804 PMC9145692
- [21]Tiscione SA IP3R-driven increases in mitochondrial Ca2+ promote neuronal death in NPC disease. PNAS 118, (2021). PMC8501836 34580197
- [23]Lodato MA Aging and neurodegeneration are associated with increased mutations in single human neurons. Science 359, 555– 559 (2018). 29217584 PMC5831169
- [24]Zhu Q, Niu Y, Gundry M & Zong C Single-cell damagenome profiling unveils vulnerable genes and functional pathways in human genome toward DNA damage. Science Advances 7, eabf3329. 34215579 PMC11060043
- [26]Wu W Neuronal enhancers are hotspots for DNA single-strand break repair. Nature 593, 440– 444 (2021). 33767446 PMC9827709
- [27]Madabhushi R Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes. Cell 161, 1592– 1605 (2015). 26052046 PMC4886855
- [30]Durante MA Single-cell analysis of olfactory neurogenesis and differentiation in adult humans. Nat Neurosci 23, 323– 326 (2020). 32066986 PMC7065961
- [31]Rohrback S Submegabase copy number variations arise during cerebral cortical neurogenesis as revealed by single-cell whole-genome sequencing. PNAS 115, 10804– 10809 (2018). 30262650 PMC6196524
- [32]Ayhan F Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans. Neuron 109, 2091– 2105.e6 (2021). 34051145 PMC8273123
- [33]Zhou Y Molecular landscapes of human hippocampal immature neurons across lifespan. Nature 607, 527– 533 (2022). 35794479 PMC9316413
- [35]Arber C Familial Alzheimer’s Disease Mutations in PSEN1 Lead to Premature Human Stem Cell Neurogenesis. Cell Reports 34, (2021). PMC7809623 33440141
- [36]Cosacak MI Single-Cell Transcriptomics Analyses of Neural Stem Cell Heterogeneity and Contextual Plasticity in a Zebrafish Brain Model of Amyloid Toxicity. Cell Reports 27, 1307– 1318. e3 (2019). 31018142
- [40]Yu Y Interneuron origin and molecular diversity in the human fetal brain. Nat Neurosci 24, 1745– 1756 (2021). 34737447
- [41]Bugeon S A transcriptomic axis predicts state modulation of cortical interneurons. Nature 607, 330– 338 (2022). 35794483 PMC9279161
- [42]Martinez-Losa M Nav1.1-Overexpressing Interneuron Transplants Restore Brain Rhythms and Cognition in a Mouse Model of Alzheimer’s Disease. Neuron 98, 75– 89. e5 (2018). 29551491 PMC5886814
- [43]Nuriel T Neuronal hyperactivity due to loss of inhibitory tone in APOE4 mice lacking Alzheimer’s disease-like pathology. Nat Commun 8, 1464 (2017). 29133888 PMC5684208
- [44]Smith SJ Single-cell transcriptomic evidence for dense intracortical neuropeptide networks. eLife 8, e47889 (2019). 31710287 PMC6881117
- [45]Zhong W The neuropeptide landscape of human prefrontal cortex. Proceedings of the National Academy of Sciences 119, e2123146119 (2022). PMC9388106 35947618
- [46]Cauli B Cortical GABA Interneurons in Neurovascular Coupling: Relays for Subcortical Vasoactive Pathways. J. Neurosci 24, 8940– 8949 (2004). 15483113 PMC6730057
- [47]Jansen IE Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat Genet 51, 404– 413 (2019). 30617256 PMC6836675
- [51]March-Diaz R Hypoxia compromises the mitochondrial metabolism of Alzheimer’s disease microglia via HIF1. Nat Aging 1, 385– 399 (2021). 37117599
- [52]Mathys H Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution. Cell Rep 21, 366– 380 (2017). 29020624 PMC5642107
- [60]Badimon A Negative feedback control of neuronal activity by microglia. Nature 586, 417– 423 (2020). 32999463 PMC7577179
- [61]Merlini M Microglial Gi-dependent dynamics regulate brain network hyperexcitability. Nat Neurosci 24, 19– 23 (2021). 33318667 PMC8118167
- [63]Gunner G Sensory lesioning induces microglial synapse elimination via ADAM10 and fractalkine signaling. Nat Neurosci 22, 1075– 1088 (2019). 31209379 PMC6596419
- [65]Favuzzi E GABA-receptive microglia selectively sculpt developing inhibitory circuits. Cell 184, 4048– 4063. e32 (2021). 34233165 PMC9122259
- [66]Stogsdill JA Pyramidal neuron subtype diversity governs microglia states in the neocortex. Nature 1– 7 (2022) doi: 10.1038/s41586-022-05056-7. PMC10502800 35948630 · DOI
- [67]Bisht K Capillary-associated microglia regulate vascular structure and function through PANX1-P2RY12 coupling in mice. Nat Commun 12, 5289 (2021). 34489419 PMC8421455
- [68]Császár E Microglia modulate blood flow, neurovascular coupling, and hypoperfusion via purinergic actions. Journal of Experimental Medicine 219, e20211071 (2022). 35201268 PMC8932534
- [69]Masuda T Specification of CNS macrophage subsets occurs postnatally in defined niches. Nature 604, 740– 748 (2022). 35444273
- [70]Munro DAD, Movahedi K & Priller J Macrophage compartmentalization in the brain and cerebrospinal fluid system. Science Immunology 7, eabk0391 (2022). 35245085
- [73]Hernández JCC Neutrophil adhesion in brain capillaries reduces cortical blood flow and impairs memory function in Alzheimer’s disease mouse models. Nature Neuroscience 22, 413 (2019). 30742116 PMC6508667
- [74]Sankowski R Mapping microglia states in the human brain through the integration of high-dimensional techniques. Nat Neurosci 22, 2098– 2110 (2019). 31740814
- [75]Safaiyan S White matter aging drives microglial diversity. Neuron 109, 1100– 1117. e10 (2021). 33606969
- [77]Morabito S Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s disease. Nat Genet 53, 1143– 1155 (2021). 34239132 PMC8766217
- [81]Dräger NM A CRISPRi/a platform in human iPSC-derived microglia uncovers regulators of disease states. Nat Neurosci 1– 14 (2022) doi: 10.1038/s41593-022-01131-4. 35953545 PMC9448678 · DOI · Paper page
- [83]Bayraktar OA Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map. Nat Neurosci 23, 500– 509 (2020). 32203496 PMC7116562
- [86]Habib N Disease-associated astrocytes in Alzheimer’s disease and aging. Nat Neurosci 23, 701– 706 (2020). 32341542 PMC9262034
- [89]Ballabio A & Bonifacino JS Lysosomes as dynamic regulators of cell and organismal homeostasis. Nat Rev Mol Cell Biol 21, 101– 118 (2020). 31768005
- [90]Xu Y, Kong J & Hu P Computational Drug Repurposing for Alzheimer’s Disease Using Risk Genes From GWAS and Single-Cell RNA Sequencing Studies. Frontiers in Pharmacology 12, 1614 (2021). PMC8277916 34276354
- [93]Jäkel S Altered human oligodendrocyte heterogeneity in multiple sclerosis. Nature 566, 543– 547 (2019). 30747918 PMC6544546
- [95]Bonetto G, Belin D & Káradóttir RT Myelin: A gatekeeper of activity-dependent circuit plasticity? Science 374, eaba6905. 34618550
- [96]de Faria O Periods of synchronized myelin changes shape brain function and plasticity. Nat Neurosci 24, 1508– 1521 (2021). 34711959
- [97]Yang SM, Michel K, Jokhi V, Nedivi E & Arlotta P Neuron class–specific responses govern adaptive myelin remodeling in the neocortex. Science (2020) doi: 10.1126/science.abd2109. PMC7931669 33335032 · DOI
- [98]Pan S, Mayoral SR, Choi HS, Chan JR & Kheirbek MA Preservation of a remote fear memory requires new myelin formation. Nat Neurosci 23, 487– 499 (2020). 32042175 PMC7213814
- [100]Kenigsbuch M A shared disease-associated oligodendrocyte signature among multiple CNS pathologies. Nat Neurosci 25, 876– 886 (2022). 35760863 PMC9724210
- [101]Arai K & Lo EH An Oligovascular Niche: Cerebral Endothelial Cells Promote the Survival and Proliferation of Oligodendrocyte Precursor Cells. J Neurosci 29, 4351– 4355 (2009). 19357263 PMC3849498
- [102]Pham L-DD Crosstalk between oligodendrocytes and cerebral endothelium contributes to vascular remodeling after white matter injury. Glia 60, 875– 881 (2012). 22392631 PMC3325331
- [103]Marques S Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development. Developmental Cell 46, 504– 517. e7 (2018). 30078729 PMC6104814
- [104]Beiter RM Evidence for oligodendrocyte progenitor cell heterogeneity in the adult mouse brain. Sci Rep 12, 12921 (2022). 35902669 PMC9334628
- [105]Huang W Origins and Proliferative States of Human Oligodendrocyte Precursor Cells. Cell 182, 594– 608. e11 (2020). 32679030 PMC7415734
- [106]Fu Y Heterogeneity of glial progenitor cells during the neurogenesis-to-gliogenesis switch in the developing human cerebral cortex. Cell Reports 34, 108788 (2021). 33657375
- [107]Káradóttir R, Hamilton NB, Bakiri Y & Attwell D Spiking and nonspiking classes of oligodendrocyte precursor glia in CNS white matter. Nat Neurosci 11, 450– 456 (2008). 18311136 PMC2615224
- [109]Zhang H Cerebral blood flow in mild cognitive impairment and Alzheimer’s disease: A systematic review and meta-analysis. Ageing Research Reviews 71, 101450 (2021). 34419673
- [111]Kalucka J Single-Cell Transcriptome Atlas of Murine Endothelial Cells. Cell 180, 764– 779. e20 (2020). 32059779
- [112]Yousef H Aged blood impairs hippocampal neural precursor activity and activates microglia via brain endothelial cell VCAM1. Nat Med 25, 988– 1000 (2019). 31086348 PMC6642642
- [113]Zhao L Pharmacologically reversible zonation-dependent endothelial cell transcriptomic changes with neurodegenerative disease associations in the aged brain. Nat Commun 11, 4413 (2020). 32887883 PMC7474063
- [114]Wälchli T Molecular atlas of the human brain vasculature at the single-cell level 2021.10.18.464715 10.1101/2021.10.18.464715v1 (2021) doi:. · DOI
- [115]Sun N Single-cell multi-region dissection of brain vasculature in Alzheimer′s Disease 2022.02.09.479797 Preprint at 10.1101/2022.02.09.479797 (2022). · DOI
- [116]Yang AC A human brain vascular atlas reveals diverse mediators of Alzheimer’s risk. Nature 1– 8 (2022) doi: 10.1038/s41586-021-04369-3. PMC9635042 35165441 · DOI · Paper page
- [117]Winkler EA A single-cell atlas of the normal and malformed human brain vasculature. Science 375, eabi7377 (2022). 35084939 PMC8995178
- [118]Profaci CP, Munji RN, Pulido RS & Daneman R The blood–brain barrier in health and disease: Important unanswered questions. J Exp Med 217, e20190062 (2020). 32211826 PMC7144528
- [119]Zou C Reduction of mNAT1/hNAT2 Contributes to Cerebral Endothelial Necroptosis and Aβ Accumulation in Alzheimer’s Disease. Cell Reports 33, 108447 (2020). 33296651
- [120]Gonzales AL Contractile pericytes determine the direction of blood flow at capillary junctions. PNAS 117, 27022– 27033 (2020). 33051294 PMC7604512
- [121]Hartmann DA Brain capillary pericytes exert a substantial but slow influence on blood flow. Nat Neurosci 24, 633– 645 (2021). 33603231 PMC8102366
- [123]Blanchard JW Reconstruction of the human blood–brain barrier in vitro reveals a pathogenic mechanism of APOE4 in pericytes. Nat Med 26, 952– 963 (2020). 32514169 PMC7704032
- [124]Yamazaki Y Vascular ApoE4 Impairs Behavior by Modulating Gliovascular Function. Neuron 109, 438– 447. e6 (2021). 33321072 PMC7864888
- [125]Barnes LL Alzheimer disease in African American individuals: increased incidence or not enough data? Nat Rev Neurol 18, 56– 62 (2022). 34873310 PMC8647782
- [126]Vila-Castelar C, Fox-Fuller JT, Guzmán-Vélez E, Schoemaker D & Quiroz YT A cultural approach to dementia — insights from US Latino and other minoritized groups. Nat Rev Neurol 18, 307– 314 (2022). 35260817 PMC9113534
- [127]Alsema AM Profiling Microglia From Alzheimer’s Disease Donors and Non-demented Elderly in Acute Human Postmortem Cortical Tissue. Frontiers in Molecular Neuroscience 13, 134 (2020). 33192286 PMC7655794
- [128]Marinaro F Molecular and cellular pathology of monogenic Alzheimer’s disease at single cell resolution 2020.07.14.202317 10.1101/2020.07.14.202317v1 (2020) doi:. · DOI
- [130]Del-Aguila JL A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain. Alzheimer’s Research & Therapy 11, 71 (2019). PMC6689177 31399126
- [132]Xu H & Jia J Single-Cell RNA Sequencing of Peripheral Blood Reveals Immune Cell Signatures in Alzheimer’s Disease. Frontiers in Immunology 12, 2727 (2021). PMC8382575 34447367
- [135]Krishnaswami SR Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. Nat Protoc 11, 499– 524 (2016). 26890679 PMC4941947
- [140]Sanchez PE Levetiracetam suppresses neuronal network dysfunction and reverses synaptic and cognitive deficits in an Alzheimer’s disease model. Proceedings of the National Academy of Sciences 109, E2895– E2903 (2012). PMC3479491 22869752
- [141]Vossel K Effect of Levetiracetam on Cognition in Patients With Alzheimer Disease With and Without Epileptiform Activity: A Randomized Clinical Trial. JAMA Neurology 78, 1345– 1354 (2021). 34570177 PMC8477304
- [143]Wightman DP A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease. Nat Genet 53, 1276– 1282 (2021). 34493870 PMC10243600
- [146]Grone BP Early and lifelong effects of APOE4 on neuronal gene expression networks relevant to Alzheimer’s disease 2022.06.16.496371 Preprint at 10.1101/2022.06.16.496371 (2022). · DOI
- [147]Da Mesquita S Aging-associated deficit in CCR7 is linked to worsened glymphatic function, cognition, neuroinflammation, and β-amyloid pathology. Science Advances 7, eabe4601. 34020948 PMC8139596
- [148]Taubes A Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer’s disease. Nat Aging 1, 932– 947 (2021). 36172600 PMC9514594
Cited by
Sorted by citations
Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases
Loh, J. S., Mak, W. Q., Tan, L. K. S., Ng, C. X., Chan, H. H., Yeow, S. H., Foo, J. B., Ong, Y. S., How, C. W., & Khaw, K. Y. (2024) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-024-01743-1 · Cited by 1,193 · see citing works
Emerging diagnostics and therapeutics for Alzheimer disease
Self, W. K., & Holtzman, D. M. (2023) · Nature Medicine · doi:10.1038/s41591-023-02505-2 · Cited by 381 · see citing works
Golden, L. R., Siano, D. S., Stephens, I. O., MacLean, S. M., Saito, K., Nolt, G. L., Funnell, J. L., Pallerla, A. V., Lee, S., Smith, C., et al. (2025) · Nature Neuroscience · doi:10.1038/s41593-025-02094-y · Cited by 18 · see citing works
Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression
Nassiri, I., Kwok, A. J., Bhandari, A., Bull, K. R., Garner, L. C., Klenerman, P., Webber, C., Parkkinen, L., Lee, A. W., Wu, Y., et al. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbae085 · Cited by 8 · see citing works
Zhong, J., Li, M., Dai, Z., & Wan, J. (2025) · Neurochemistry International · doi:10.1016/j.neuint.2025.106049 · Cited by 3 · see citing works
Park, J. H., Kim, B., Al‐Amin, M. M., Tate, M. D., Sharify, A. D., John, S. K., Karahan, H., Lu, H., Dabin, L. C., & Kim, J. (2026) · Alzheimer's & Dementia · doi:10.1002/alz.71742
- Authors
- Murdock, M. H., & Tsai, L.-H.
- Affiliations
- Massachusetts Institute of Technology (US)
- Corresponding author
- Tsai, Li-Huei
- Venue
- Nature Neuroscience
- Published
- 2023-01-02
- Volume
- 26
- Issue
- 2
- Pages
- 181-195
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- PMC
- PMC10155598
- OpenAlex
- W4313454730
- Cited by
- 148
- References
- 56
- Citations by year
- 2026: 25 · 2025: 45 · 2024: 51 · 2023: 27
- FWCI
- 4.96
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Neuroscience (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- Funders
- Glenn Foundation for Medical Research
- Cure Alzheimer's Fund
- Fondation pour la Recherche Médicale
- National Institutes of Health (NS051874)
- National Institute of Neurological Disorders and Stroke (R37NS051874, R01NS051874)
- National Center for Complementary and Integrative Health (R01AT011460)
- Topics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
- Keywords
- Alzheimer's disease, single-cell genomics, amyloid plaques, neurofibrillary tangles, lipid metabolism, immune signaling, metabolic reprogramming, brain cell types, therapeutic interventions, pathogenesis
- MeSH terms
- Alzheimer Disease, Brain, Humans, Amyloid beta-Peptides, Neurofibrillary Tangles, Genomics, Plaque, Amyloid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review