Trapnell C. Defining cell types and states with single-cell genomics. Genome Res. 2015;25:1491–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ransohoff RM. A polarizing question: do M1 and M2 microglia exist? Nat Neurosci. 2016;19:987–91.

Article  CAS  PubMed  Google Scholar 

Paolicelli RC, Sierra A, Stevens B, Tremblay M-E, Aguzzi A, Ajami B, et al. Microglia states and nomenclature: a field at its crossroads. Neuron. 2022;110:3458–83.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Guerreiro R, Wojtas A, Bras J, Carrasquillo M, Rogaeva E, Majounie E, et al. TREM2 variants in alzheimer’s disease. N Engl J Med. 2013;368:117–27.

Article  CAS  PubMed  Google Scholar 

Jonsson T, Stefansson H, Steinberg S, Jonsdottir I, Jonsson PV, Snaedal J, et al. Variant of TREM2 associated with the risk of alzheimer’s disease. N Engl J Med. 2013;368:107–16.

Article  CAS  PubMed  Google Scholar 

Ulrich JD, Ulland TK, Mahan TE, Nyström S, Nilsson KP, Song WM, et al. ApoE facilitates the microglial response to amyloid plaque pathology. J Exp Med. 2018;215:1047–58.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Keren-Shaul H, Spinrad A, Weiner A, Matcovitch-Natan O, Dvir-Szternfeld R, Ulland TK, et al. A unique microglia type associated with restricting development of alzheimer’s disease. Cell. 2017;169:1276–.e17.

Article  CAS  PubMed  Google Scholar 

Zhou Y, Song WM, Andhey PS, Swain A, Levy T, Miller KR, et al. Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in alzheimer’s disease. Nat Med. 2020;26:131–42.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mathys H, Davila-Velderrain J, Peng Z, Gao F, Mohammadi S, Young JZ, et al. Single-cell transcriptomic analysis of alzheimer’s disease. Nature. 2019;570:332–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Smith AM, Davey K, Tsartsalis S, Khozoie C, Fancy N, Tang SS, et al. Diverse human astrocyte and microglial transcriptional responses to alzheimer’s pathology. Acta Neuropathol. 2022;143:75–91.

Article  CAS  PubMed  Google Scholar 

Green GS, Fujita M, Yang H-S, Taga M, Cain A, McCabe C, et al. Cellular communities reveal trajectories of brain ageing and alzheimer’s disease. Nature. 2024;633:634–45.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Morabito S, Miyoshi E, Michael N, Shahin S, Martini AC, Head E, et al. Single-nucleus chromatin accessibility and transcriptomic characterization of alzheimer’s disease. Nat Genet. 2021;53:1143–55.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Marinaro F, Haneklaus M, Zhang Z, Strano A, Evans L, Handfield L-F, et al. Molecular and cellular pathology of monogenic alzheimer’s disease at single cell resolution. BioRxiv. 2020.

Gerrits E, Brouwer N, Kooistra SM, Woodbury ME, Vermeiren Y, Lambourne M, et al. Distinct amyloid-β and tau-associated microglia profiles in alzheimer’s disease. Acta Neuropathol. 2021;141:681–96.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sierksma A, Lu A, Mancuso R, Fattorelli N, Thrupp N, Salta E, et al. Novel alzheimer risk genes determine the microglia response to amyloid-β but not to TAU pathology. EMBO Mol Med. 2020;12:e10606.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Luquez T, Algoo J, Chiu R, Mares JA, Yadav A, Lam M, et al. Cell type-specific associations with alzheimer’s disease conserved across racial and ethnic groups. BioRxiv. 2025.

Gabitto MI, Travaglini KJ, Rachleff VM, Kaplan ES, Long B, Ariza J, et al. Integrated multimodal cell atlas of alzheimer’s disease. Nat Neurosci. 2024;27:2366–83.

Article  CAS  PubMed  Google Scholar 

Davila-Velderrain J, Mathys H, Mohammadi S, Ruzicka B, Jiang X, Ng A, et al. Single-cell anatomical analysis of human hippocampus and entorhinal cortex uncovers early-stage molecular pathology in alzheimer’s disease. BioRxiv. 2021: https://doi.org/10.1101/2021.07.01.450715.

Fröhlich AS, Gerstner N, Gagliardi M, Ködel M, Yusupov N, Matosin N, et al. Single-nucleus transcriptomic profiling of human orbitofrontal cortex reveals convergent effects of aging and psychiatric disease. Nat Neurosci. 2024;27:2021–32.

Article  PubMed  PubMed Central  Google Scholar 

Brase L, You S-F, D’Oliveira Albanus R, Del-Aguila JL, Dai Y, Novotny BC, et al. Single-nucleus RNA-sequencing of autosomal dominant alzheimer disease and risk variant carriers. Nat Commun. 2023;14:2314.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sayed FA, Kodama L, Fan L, Carling GK, Udeochu JC, Le D, et al. AD-linked R47H- mutation induces disease-enhancing microglial states via AKT hyperactivation. Sci Transl Med. 2021;13:eabe3947.

Article  CAS  PubMed  PubMed Central  Google Scholar 

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. Proc Natl Acad Sci USA. 2020;117:25800–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Olah M, Menon V, Habib N, Taga MF, Ma Y, Yung CJ, et al. Single cell RNA sequencing of human microglia uncovers a subset associated with alzheimer’s disease. Nat Commun. 2020;11:6129.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fujita M, Gao Z, Zeng L, McCabe C, White CC, Ng B, et al. Cell subtype-specific effects of genetic variation in the alzheimer’s disease brain. Nat Genet. 2024;56:605–14.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zeng B, Yang H, N MP, Venkatesh S, Mathur D, Auluck P, et al. Single-nucleus atlas of cell-type specific genetic regulation in the human brain. Res. Sq. 2024: https://doi.org/10.21203/rs.3.rs-5368620/v1.

Mathys H, Boix CA, Akay LA, Xia Z, Davila-Velderrain J, Ng AP, et al. Single-cell multiregion dissection of alzheimer’s disease. Nature. 2024;632:858–68.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Smajić S, Prada-Medina CA, Landoulsi Z, Ghelfi J, Delcambre S, Dietrich C, et al. Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state. Brain. 2022;145:964–78.

Article  PubMed  PubMed Central  Google Scholar 

Adams L, Song MK, Yuen S, Tanaka Y, Kim Y-S. A single-nuclei paired multiomic analysis of the human midbrain reveals age- and parkinson’s disease-associated glial changes. Nat Aging. 2024;4:364–78.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kamath T, Abdulraouf A, Burris SJ, Langlieb J, Gazestani V, Nadaf NM, et al. Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in parkinson’s disease. Nat Neurosci. 2022;25:588–95.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chatila ZK, Yadav A, Mares J, Flowers X, Yun TD, Rashid M, et al. RNA- and ATAC-sequencing reveals a unique microglial population focally depleted in parkinson’s disease. BioRxiv. 2023: https://doi.org/10.1101/2023.05.17.540842.

Martirosyan A, Ansari R, Pestana F, Hebestreit K, Gasparyan H, Aleksanyan R, et al. Unravelling cell type-specific responses to parkinson’s disease at single cell resolution. Mol Neurodegener. 2024;19:7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee AJ, Kim C, Park S, Joo J, Choi B, Yang D, et al. Characterization of altered molecular mechanisms in Parkinson’s disease through cell type-resolved multiomics analyses. Sci Adv. 2023;9:eabo2467.

Article  CAS