{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,10]],"date-time":"2026-11-10T12:42:25Z","timestamp":1794314545916,"version":"4.9.0"},"reference-count":101,"publisher":"Elsevier BV","issue":"13","license":[{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T00:00:00Z","timestamp":1751328000000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82020108012"],"award-info":[{"award-number":["82020108012"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31900397"],"award-info":[{"award-number":["31900397"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004835","name":"Zhejiang University","doi-asserted-by":"publisher","award":["2024C03098"],"award-info":[{"award-number":["2024C03098"]}],"id":[{"id":"10.13039\/501100004835","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004835","name":"Zhejiang University","doi-asserted-by":"publisher","award":["2021ZD0204400"],"award-info":[{"award-number":["2021ZD0204400"]}],"id":[{"id":"10.13039\/501100004835","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFC3400400"],"award-info":[{"award-number":["2022YFC3400400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100022963","name":"Key Research and Development Program of Zhejiang Province","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100022963","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007225","name":"Ministry of Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007225","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Neuron"],"published-print":{"date-parts":[[2025,7]]},"DOI":"10.1016\/j.neuron.2025.03.002","type":"journal-article","created":{"date-parts":[[2025,4,2]],"date-time":"2025-04-02T09:22:31Z","timestamp":1743585751000},"page":"2123-2140.e9","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":34,"title":["Molecular pathways and diagnosis in spatially resolved Alzheimer\u2019s hippocampal atlas"],"prefix":"10.1016","volume":"113","author":[{"given":"Pan","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lifang","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quyuan","family":"Tao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Youzhe","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhi","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayi","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuyang","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zihan","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bin","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bufan","family":"Jin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanrong","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengnan","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujia","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chen","family":"Tian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiwen","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongqin","family":"Fan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peiran","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yue","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juanli","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengpeng","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bing","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zheng","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junjie","family":"Lei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benyan","family":"Luo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiying","family":"Wen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guoping","family":"Peng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanchun","family":"Tang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenkun","family":"Zhuang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinhui","family":"Su","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Pan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keqing","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiping","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aimin","family":"Bao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianhua","family":"Yao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xun","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Ming","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longqi","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shumin","family":"Duan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7222-8317","authenticated-orcid":false,"given":"Jing","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.neuron.2025.03.002_bib1","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1016\/S0140-6736(20)32205-4","article-title":"Alzheimer's disease","volume":"397","author":"Scheltens","year":"2021","journal-title":"Lancet"},{"key":"10.1016\/j.neuron.2025.03.002_bib2","article-title":"PET Imaging of Neuroinflammation in Alzheimer's Disease","volume":"12","author":"Zhou","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1016\/j.neuron.2025.03.002_bib3","doi-asserted-by":"crossref","first-page":"S51","DOI":"10.3233\/JAD-201059","article-title":"New Frontiers in the Prevention, Diagnosis, and Treatment of Alzheimer's Disease","volume":"82","author":"Guzman-Martinez","year":"2021","journal-title":"J. Alzheimers. Dis."},{"key":"10.1016\/j.neuron.2025.03.002_bib4","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1016\/S1474-4422(20)30440-3","article-title":"New insights into atypical Alzheimer's disease in the era of biomarkers","volume":"20","author":"Graff-Radford","year":"2021","journal-title":"Lancet Neurol."},{"key":"10.1016\/j.neuron.2025.03.002_bib5","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1152\/physrev.00015.2020","article-title":"The complexity of Alzheimer's disease: an evolving puzzle","volume":"101","author":"Ferrari","year":"2021","journal-title":"Physiol. Rev."},{"key":"10.1016\/j.neuron.2025.03.002_bib6","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1038\/s41586-019-1195-2","article-title":"Single-cell transcriptomic analysis of Alzheimer's disease","volume":"570","author":"Mathys","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2025.03.002_bib7","doi-asserted-by":"crossref","first-page":"2087","DOI":"10.1038\/s41593-019-0539-4","article-title":"A single-cell atlas of entorhinal cortex from individuals with Alzheimer's disease reveals cell-type-specific gene expression regulation","volume":"22","author":"Grubman","year":"2019","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2025.03.002_bib8","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/s41591-019-0695-9","article-title":"Human and mouse single-nucleus transcriptomics reveal TREM2-dependent and TREM2-independent cellular responses in Alzheimer's disease","volume":"26","author":"Zhou","year":"2020","journal-title":"Nat. Med."},{"key":"10.1016\/j.neuron.2025.03.002_bib9","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41593-020-00764-7","article-title":"Molecular characterization of selectively vulnerable neurons in Alzheimer's disease","volume":"24","author":"Leng","year":"2021","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2025.03.002_bib10","doi-asserted-by":"crossref","first-page":"25800","DOI":"10.1073\/pnas.2008762117","article-title":"Single-nucleus transcriptome analysis reveals dysregulation of angiogenic endothelial cells and neuroprotective glia in Alzheimer's disease","volume":"117","author":"Lau","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.neuron.2025.03.002_bib11","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/s41593-022-01251-x","article-title":"Integrative in situ mapping of single-cell transcriptional states and tissue histopathology in a mouse model of Alzheimer's disease","volume":"26","author":"Zeng","year":"2023","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2025.03.002_bib12","doi-asserted-by":"crossref","first-page":"2366","DOI":"10.1038\/s41593-024-01774-5","article-title":"Integrated multimodal cell atlas of Alzheimer's disease","volume":"27","author":"Gabitto","year":"2024","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2025.03.002_bib13","doi-asserted-by":"crossref","first-page":"4438","DOI":"10.1016\/j.cell.2023.08.005","article-title":"Early Alzheimer's disease pathology in human cortex involves transient cell states","volume":"186","author":"Gazestani","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2025.03.002_bib14","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1038\/s41588-021-00894-z","article-title":"Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer's disease","volume":"53","author":"Morabito","year":"2021","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neuron.2025.03.002_bib15","doi-asserted-by":"crossref","first-page":"4404","DOI":"10.1016\/j.cell.2023.08.038","article-title":"Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration","volume":"186","author":"Dileep","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2025.03.002_bib16","doi-asserted-by":"crossref","first-page":"4386","DOI":"10.1016\/j.cell.2023.08.037","article-title":"Human microglial state dynamics in Alzheimer's disease progression","volume":"186","author":"Sun","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2025.03.002_bib17","doi-asserted-by":"crossref","DOI":"10.1186\/1750-1326-6-85","article-title":"Adult hippocampal neurogenesis and its role in Alzheimer's disease","volume":"6","author":"Mu","year":"2011","journal-title":"Mol. Neurodegener."},{"key":"10.1016\/j.neuron.2025.03.002_bib18","doi-asserted-by":"crossref","first-page":"S18","DOI":"10.1212\/WNL.51.1_Suppl_1.S18","article-title":"Abnormalities of neural circuitry in Alzheimer's disease: hippocampus and cortical cholinergic innervation","volume":"51","author":"Geula","year":"1998","journal-title":"Neurology"},{"key":"10.1016\/j.neuron.2025.03.002_bib19","doi-asserted-by":"crossref","first-page":"1935","DOI":"10.1093\/brain\/awg191","article-title":"Human anti-beta-amyloid antibodies block beta-amyloid fibril formation and prevent beta-amyloid-induced neurotoxicity","volume":"126","author":"Du","year":"2003","journal-title":"Brain"},{"key":"10.1016\/j.neuron.2025.03.002_bib20","doi-asserted-by":"crossref","first-page":"1434","DOI":"10.1038\/nn.4661","article-title":"Viewpoints: how the hippocampus contributes to memory, navigation and cognition","volume":"20","author":"Lisman","year":"2017","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2025.03.002_bib21","doi-asserted-by":"crossref","DOI":"10.1016\/j.isci.2020.101556","article-title":"Spatial Transcriptomics Reveals Genes Associated with Dysregulated Mitochondrial Functions and Stress Signaling in Alzheimer Disease.","volume":"23","author":"Navarro","year":"2020","journal-title":"iScience"},{"key":"10.1016\/j.neuron.2025.03.002_bib22","article-title":"Mapping the spatial transcriptomic signature of the hippocampus during memory consolidation","author":"Vanrobeys","year":"2023","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2025.03.002_bib23","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1016\/j.cell.2022.04.003","article-title":"Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays","volume":"185","author":"Chen","year":"2022","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2025.03.002_bib24","doi-asserted-by":"crossref","DOI":"10.1126\/science.abp9444","article-title":"Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration","volume":"377","author":"Wei","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.neuron.2025.03.002_bib25","doi-asserted-by":"crossref","first-page":"3726","DOI":"10.1016\/j.cell.2023.06.009","article-title":"Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex","volume":"186","author":"Chen","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2025.03.002_bib26","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/s41576-020-0258-4","article-title":"mRNAs, proteins and the emerging principles of gene expression control","volume":"21","author":"Buccitelli","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.neuron.2025.03.002_bib27","article-title":"Prevalence of mixed neuropathologies in age-related neurodegenerative diseases: A community-based autopsy study in China","volume":"21","author":"Wang","year":"2025","journal-title":"Alzheimers Dement."},{"key":"10.1016\/j.neuron.2025.03.002_bib28","article-title":"An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus","author":"Thompson","year":"2024","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2025.03.002_bib29","doi-asserted-by":"crossref","first-page":"2091","DOI":"10.1016\/j.neuron.2021.05.003","article-title":"Resolving cellular and molecular diversity along the hippocampal anterior-to-posterior axis in humans","volume":"109","author":"Ayhan","year":"2021","journal-title":"Neuron"},{"key":"10.1016\/j.neuron.2025.03.002_bib30","doi-asserted-by":"crossref","first-page":"4365","DOI":"10.1016\/j.cell.2023.08.039","article-title":"Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer's disease pathology","volume":"186","author":"Mathys","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2025.03.002_bib31","doi-asserted-by":"crossref","first-page":"1134","DOI":"10.1126\/science.aay0793","article-title":"Brain cell type-specific enhancer-promoter interactome maps and disease-risk association","volume":"366","author":"Nott","year":"2019","journal-title":"Science"},{"key":"10.1016\/j.neuron.2025.03.002_bib32","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1038\/nrneurol.2012.263","article-title":"Apolipoprotein E and Alzheimer disease: risk, mechanisms and therapy","volume":"9","author":"Liu","year":"2013","journal-title":"Nat. Rev. Neurol."},{"key":"10.1016\/j.neuron.2025.03.002_bib33","doi-asserted-by":"crossref","first-page":"6764","DOI":"10.1523\/JNEUROSCI.5794-10.2011","article-title":"Common Alzheimer's disease risk variant within the CLU gene affects white matter microstructure in young adults","volume":"31","author":"Braskie","year":"2011","journal-title":"J. Neurosci."},{"key":"10.1016\/j.neuron.2025.03.002_bib34","doi-asserted-by":"crossref","DOI":"10.3389\/fnmol.2012.00079","article-title":"Cystatin C in Alzheimer's disease","volume":"5","author":"Kaur","year":"2012","journal-title":"Front. Mol. Neurosci."},{"key":"10.1016\/j.neuron.2025.03.002_bib35","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1038\/s41586-022-04587-3","article-title":"Cell transcriptomic atlas of the non-human primate Macaca fascicularis","volume":"604","author":"Han","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2025.03.002_bib36","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-022-35288-0","article-title":"Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding","volume":"13","author":"Shen","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2025.03.002_bib37","doi-asserted-by":"crossref","first-page":"1594","DOI":"10.1016\/j.stem.2022.09.010","article-title":"A single-cell transcriptome atlas of glial diversity in the human hippocampus across the postnatal lifespan","volume":"29","author":"Su","year":"2022","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.neuron.2025.03.002_bib38","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giae078","article-title":"StereoSiTE: a framework to spatially and quantitatively profile the cellular neighborhood organized iTME","volume":"13","author":"Liu","year":"2024","journal-title":"GigaScience"},{"key":"10.1016\/j.neuron.2025.03.002_bib39","doi-asserted-by":"crossref","DOI":"10.3389\/fmolb.2020.565383","article-title":"The Significance of Secreted Phosphoprotein 1 in Multiple Human Cancers","volume":"7","author":"Wei","year":"2020","journal-title":"Front. Mol. Biosci."},{"key":"10.1016\/j.neuron.2025.03.002_bib40","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/j.immuni.2006.08.020","article-title":"CD44 is the signaling component of the macrophage migration inhibitory factor-CD74 receptor complex","volume":"25","author":"Shi","year":"2006","journal-title":"Immunity"},{"key":"10.1016\/j.neuron.2025.03.002_bib41","doi-asserted-by":"crossref","first-page":"785","DOI":"10.3233\/JAD-230199","article-title":"Microglia-Astrocyte Communication in Alzheimer's Disease","volume":"95","author":"Wu","year":"2023","journal-title":"J. Alzheimers Dis."},{"key":"10.1016\/j.neuron.2025.03.002_bib42","doi-asserted-by":"crossref","first-page":"1395","DOI":"10.1001\/archneur.58.9.1395","article-title":"Neuron number in the entorhinal cortex and CA1 in preclinical Alzheimer disease","volume":"58","author":"Price","year":"2001","journal-title":"Arch. Neurol."},{"key":"10.1016\/j.neuron.2025.03.002_bib43","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1002\/ana.25344","article-title":"Relative neuron loss in hippocampal sclerosis of aging and Alzheimer's disease","volume":"84","author":"Ihara","year":"2018","journal-title":"Ann. Neurol."},{"key":"10.1016\/j.neuron.2025.03.002_bib44","doi-asserted-by":"crossref","first-page":"10843","DOI":"10.1523\/JNEUROSCI.2258-16.2016","article-title":"Selective Degeneration of Entorhinal-CA1 Synapses in Alzheimer's Disease via Activation of DAPK1","volume":"36","author":"Shu","year":"2016","journal-title":"J. Neurosci."},{"key":"10.1016\/j.neuron.2025.03.002_bib45","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1016\/j.neuron.2021.10.036","article-title":"Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells","volume":"110","author":"Franjic","year":"2022","journal-title":"Neuron"},{"key":"10.1016\/j.neuron.2025.03.002_bib46","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1212\/01.WNL.0000106462.72282.90","article-title":"Higher atrophy rate of entorhinal cortex than hippocampus in AD","volume":"62","author":"Du","year":"2004","journal-title":"Neurology"},{"key":"10.1016\/j.neuron.2025.03.002_bib47","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.neurobiolaging.2005.11.012","article-title":"Atrophy rates of the cingulate gyrus and hippocampus in AD and FTLD","volume":"28","author":"Barnes","year":"2007","journal-title":"Neurobiol. Aging"},{"key":"10.1016\/j.neuron.2025.03.002_bib48","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.52291","article-title":"Misfolded proteins bind and activate death receptor 5 to trigger apoptosis during unresolved endoplasmic reticulum stress","volume":"9","author":"Lam","year":"2020","journal-title":"eLife"},{"key":"10.1016\/j.neuron.2025.03.002_bib49","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1007\/978-1-60327-017-5_14","article-title":"Regulation of apoptosis by the unfolded protein response","volume":"559","author":"Fribley","year":"2009","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.neuron.2025.03.002_bib50","doi-asserted-by":"crossref","DOI":"10.1111\/acel.12902","article-title":"Activation of MT2 receptor ameliorates dendritic abnormalities in Alzheimer's disease via C\/EBP\u03b1\/miR-125b pathway","volume":"18","author":"Tang","year":"2019","journal-title":"Aging Cell"},{"key":"10.1016\/j.neuron.2025.03.002_bib51","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.neulet.2014.05.056","article-title":"Regional upregulation of hippocampal melatonin MT2 receptors by valproic acid: therapeutic implications for Alzheimer's disease","volume":"576","author":"Bahna","year":"2014","journal-title":"Neurosci. Lett."},{"key":"10.1016\/j.neuron.2025.03.002_bib52","doi-asserted-by":"crossref","first-page":"976","DOI":"10.1016\/j.cell.2020.06.038","article-title":"Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer's Disease","volume":"182","author":"Chen","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2025.03.002_bib53","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1002\/alz.12723","article-title":"Blood extracellular vesicles carrying synaptic function- and brain-related proteins as potential biomarkers for Alzheimer's disease","volume":"19","author":"Tian","year":"2023","journal-title":"Alzheimers Dement."},{"key":"10.1016\/j.neuron.2025.03.002_bib54","doi-asserted-by":"crossref","DOI":"10.1186\/s40478-024-01727-w","article-title":"Blood-based CNS regionally and neuronally enriched extracellular vesicles carrying pTau217 for Alzheimer's disease diagnosis and differential diagnosis","volume":"12","author":"Guo","year":"2024","journal-title":"Acta Neuropathol. Commun."},{"key":"10.1016\/j.neuron.2025.03.002_bib55","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1038\/s41591-021-01382-x","article-title":"Biomarkers for neurodegenerative diseases","volume":"27","author":"Hansson","year":"2021","journal-title":"Nat. Med."},{"key":"10.1016\/j.neuron.2025.03.002_bib56","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.tem.2024.07.009","article-title":"Exploring the heterogeneous targets of metabolic aging at single-cell resolution","volume":"36","author":"Sun","year":"2025","journal-title":"Trends Endocrinol. Metab."},{"key":"10.1016\/j.neuron.2025.03.002_bib57","article-title":"Inflammation and aging: signaling pathways and intervention therapies","volume":"8","author":"Li","year":"2023","journal-title":"Signal Transduct. Target. Ther."},{"key":"10.1016\/j.neuron.2025.03.002_bib58","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1016\/j.tins.2021.06.007","article-title":"Cellular senescence at the crossroads of inflammation and Alzheimer's disease","volume":"44","author":"Guerrero","year":"2021","journal-title":"Trends Neurosci."},{"key":"10.1016\/j.neuron.2025.03.002_bib59","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.1016\/j.neuron.2022.03.015","article-title":"Programming axonal mitochondrial maintenance and bioenergetics in neurodegeneration and regeneration","volume":"110","author":"Cheng","year":"2022","journal-title":"Neuron"},{"key":"10.1016\/j.neuron.2025.03.002_bib60","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1016\/j.trci.2018.06.014","article-title":"Inflammation as a central mechanism in Alzheimer's disease","volume":"4","author":"Kinney","year":"2018","journal-title":"Alzheimers Dement. (NY)"},{"key":"10.1016\/j.neuron.2025.03.002_bib61","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/s41582-022-00749-z","article-title":"Synaptic degeneration in Alzheimer disease","volume":"19","author":"Tzioras","year":"2023","journal-title":"Nat. Rev. Neurol."},{"key":"10.1016\/j.neuron.2025.03.002_bib62","doi-asserted-by":"crossref","first-page":"1899","DOI":"10.4103\/1673-5374.390974","article-title":"How do neurons age? A focused review on the aging of the microtubular cytoskeleton","volume":"19","author":"Richardson","year":"2024","journal-title":"Neural Regen. Res."},{"key":"10.1016\/j.neuron.2025.03.002_bib63","doi-asserted-by":"crossref","first-page":"1794","DOI":"10.1016\/j.immuni.2023.06.016","article-title":"TREM2 receptor protects against complement-mediated synaptic loss by binding to complement C1q during neurodegeneration","volume":"56","author":"Zhong","year":"2023","journal-title":"Immunity"},{"key":"10.1016\/j.neuron.2025.03.002_bib64","series-title":"Methods in Neurosciences","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/S1043-9471(96)80099-1","article-title":"[7] - Basal Forebrain Cholinergic Lesions and Complete Transection of Septal\u2013Hippocampal Pathway","author":"Williams","year":"1996"},{"key":"10.1016\/j.neuron.2025.03.002_bib65","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1016\/j.cell.2017.05.018","article-title":"A Unique Microglia Type Associated with Restricting Development of Alzheimer's Disease","volume":"169","author":"Keren-Shaul","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2025.03.002_bib66","doi-asserted-by":"crossref","first-page":"1293","DOI":"10.1016\/j.celrep.2019.03.099","article-title":"The Major Risk Factors for Alzheimer's Disease: Age, Sex, and Genes Modulate the Microglia Response to A\u03b2 Plaques","volume":"27","author":"Sala Frigerio","year":"2019","journal-title":"Cell Rep."},{"key":"10.1016\/j.neuron.2025.03.002_bib67","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/nature21029","article-title":"Neurotoxic reactive astrocytes are induced by activated microglia","volume":"541","author":"Liddelow","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2025.03.002_bib68","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1212\/WNL.0b013e3181f736a1","article-title":"Hippocampal CA1 apical neuropil atrophy in mild Alzheimer disease visualized with 7-T MRI","volume":"75","author":"Kerchner","year":"2010","journal-title":"Neurology"},{"key":"10.1016\/j.neuron.2025.03.002_bib69","doi-asserted-by":"crossref","first-page":"5315","DOI":"10.1523\/JNEUROSCI.0208-21.2021","article-title":"Modality-Specific Impairment of Hippocampal CA1 Neurons of Alzheimer's Disease Model Mice","volume":"41","author":"Takamura","year":"2021","journal-title":"J. Neurosci."},{"key":"10.1016\/j.neuron.2025.03.002_bib70","doi-asserted-by":"crossref","first-page":"1389","DOI":"10.1172\/JCI0216886","article-title":"Orchestrating the unfolded protein response in health and disease","volume":"110","author":"Kaufman","year":"2002","journal-title":"J. Clin. Invest."},{"key":"10.1016\/j.neuron.2025.03.002_bib71","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/nrm2199","article-title":"Signal integration in the endoplasmic reticulum unfolded protein response","volume":"8","author":"Ron","year":"2007","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.neuron.2025.03.002_bib72","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1016\/S0140-6736(10)61349-9","article-title":"Alzheimer's disease","volume":"377","author":"Ballard","year":"2011","journal-title":"Lancet"},{"key":"10.1016\/j.neuron.2025.03.002_bib73","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1038\/s41573-022-00391-w","article-title":"The amyloid hypothesis in Alzheimer disease: new insights from new therapeutics","volume":"21","author":"Karran","year":"2022","journal-title":"Nat. Rev. Drug Discov."},{"key":"10.1016\/j.neuron.2025.03.002_bib74","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1001\/jamaneurol.2013.5847","article-title":"Amyloid-\u03b2 and tau: the trigger and bullet in Alzheimer disease pathogenesis","volume":"71","author":"Bloom","year":"2014","journal-title":"JAMA Neurol."},{"key":"10.1016\/j.neuron.2025.03.002_bib75","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2024.114216","article-title":"Microglia-astrocyte crosstalk in the amyloid plaque niche of an Alzheimer's disease mouse model, as revealed by spatial transcriptomics","volume":"43","author":"Mallach","year":"2024","journal-title":"Cell Rep."},{"key":"10.1016\/j.neuron.2025.03.002_bib76","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive Integration of Single-Cell Data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2025.03.002_bib77","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1038\/s41587-021-00935-2","article-title":"Spatial transcriptomics at subspot resolution with BayesSpace","volume":"39","author":"Zhao","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.neuron.2025.03.002_bib78","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.neuron.2025.03.002_bib79","article-title":"StereoCell enables highly accurate single-cell segmentation for spatial transcriptomics","author":"Mei","year":"2023","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2025.03.002_bib96","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"},{"key":"10.1016\/j.neuron.2025.03.002_bib97","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/s41592-021-01358-2","article-title":"Squidpy: a scalable framework for spatial omics analysis","volume":"19","author":"Palla","year":"2022","journal-title":"Nat. Methods"},{"key":"10.1016\/j.neuron.2025.03.002_bib98","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors","volume":"8","author":"McGinnis","year":"2019","journal-title":"Cell Syst."},{"key":"10.1016\/j.neuron.2025.03.002_bib99","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giaa151","article-title":"SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data","volume":"9","author":"Young","year":"2020","journal-title":"Gigascience"},{"key":"10.1016\/j.neuron.2025.03.002_bib100","first-page":"1","article-title":"Generalizing the Convex Hull of a Sample: The R Package alphahull","volume":"35","author":"Pateiro-L\u00f3pez","year":"2010","journal-title":"J. Stat. Softw."},{"key":"10.1016\/j.neuron.2025.03.002_bib101","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the Tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"J. Open Source Softw."},{"key":"10.1016\/j.neuron.2025.03.002_bib102","article-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"10.1016\/j.neuron.2025.03.002_bib80","doi-asserted-by":"crossref","first-page":"763","DOI":"10.1097\/RLU.0000000000004251","article-title":"PET Imaging of Dementia: Update 2022","volume":"47","author":"Burkett","year":"2022","journal-title":"Clin. Nucl. Med."},{"key":"10.1016\/j.neuron.2025.03.002_bib81","doi-asserted-by":"crossref","first-page":"2381","DOI":"10.1038\/s41591-022-02049-x","article-title":"Amyloid and tau PET-positive cognitively unimpaired individuals are at high risk for future cognitive decline","volume":"28","author":"Ossenkoppele","year":"2022","journal-title":"Nat. Med."},{"key":"10.1016\/j.neuron.2025.03.002_bib82","doi-asserted-by":"crossref","DOI":"10.1038\/nrdp.2015.56","article-title":"Alzheimer's disease","volume":"1","author":"Masters","year":"2015","journal-title":"Nat. Rev. Dis. Primers"},{"key":"10.1016\/j.neuron.2025.03.002_bib83","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1016\/j.jalz.2016.04.003","article-title":"CNS tau efflux via exosomes is likely increased in Parkinson's disease but not in Alzheimer's disease","volume":"12","author":"Shi","year":"2016","journal-title":"Alzheimers. Dement."},{"key":"10.1016\/j.neuron.2025.03.002_bib84","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1007\/s00401-014-1314-y","article-title":"Plasma exosomal \u03b1-synuclein is likely CNS-derived and increased in Parkinson's disease","volume":"128","author":"Shi","year":"2014","journal-title":"Acta Neuropathol."},{"key":"10.1016\/j.neuron.2025.03.002_bib85","doi-asserted-by":"crossref","first-page":"e2332","DOI":"10.1212\/WNL.0000000000011853","article-title":"Development of a Sensitive Diagnostic Assay for Parkinson Disease Quantifying \u03b1-Synuclein-Containing Extracellular Vesicles","volume":"96","author":"Hong","year":"2021","journal-title":"Neurology"},{"key":"10.1016\/j.neuron.2025.03.002_bib86","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1002\/ana.22311","article-title":"Cerebrospinal fluid biomarkers for Parkinson disease diagnosis and progression","volume":"69","author":"Shi","year":"2011","journal-title":"Ann. Neurol."},{"key":"10.1016\/j.neuron.2025.03.002_bib87","doi-asserted-by":"crossref","first-page":"1350","DOI":"10.1001\/archneurol.2010.279","article-title":"SNCA variant associated with Parkinson disease and plasma alpha-synuclein level","volume":"67","author":"Mata","year":"2010","journal-title":"Arch. Neurol."},{"key":"10.1016\/j.neuron.2025.03.002_bib88","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.neulet.2010.06.009","article-title":"Significance and confounders of peripheral DJ-1 and alpha-synuclein in Parkinson's disease","volume":"480","author":"Shi","year":"2010","journal-title":"Neurosci. Lett."},{"key":"10.1016\/j.neuron.2025.03.002_bib89","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/s41422-023-00831-1","article-title":"An invasive zone in human liver cancer identified by Stereo-seq promotes hepatocyte-tumor cell crosstalk, local immunosuppression and tumor progression","volume":"33","author":"Wu","year":"2023","journal-title":"Cell Res."},{"key":"10.1016\/j.neuron.2025.03.002_bib90","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0209648","article-title":"Single-nucleus and single-cell transcriptomes compared in matched cortical cell types","volume":"13","author":"Bakken","year":"2018","journal-title":"PloS One"},{"key":"10.1016\/j.neuron.2025.03.002_bib91","article-title":"Reliable multiplex sequencing with rare index mis-assignment on DNB-based NGS platform","volume":"20","author":"Li","year":"2019","journal-title":"BMC Genomics"},{"key":"10.1016\/j.neuron.2025.03.002_bib92","doi-asserted-by":"crossref","DOI":"10.15252\/msb.202010108","article-title":"Joint cell segmentation and cell type annotation for spatial transcriptomics","volume":"17","author":"Littman","year":"2021","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.neuron.2025.03.002_bib94","article-title":"EPSANet: An Efficient Pyramid Squeeze Attention Block on Convolutional Neural Network","author":"Zhang","year":"2021","journal-title":"arXiv"},{"key":"10.1016\/j.neuron.2025.03.002_bib93","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/s41592-021-01358-2","article-title":"Squidpy: a scalable framework for spatial omics analysis","volume":"19","author":"Palla","year":"2022","journal-title":"Nat. Methods"}],"container-title":["Neuron"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0896627325001746?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0896627325001746?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T04:22:13Z","timestamp":1762316533000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0896627325001746"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7]]},"references-count":101,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2025,7]]}},"alternative-id":["S0896627325001746"],"URL":"https:\/\/doi.org\/10.1016\/j.neuron.2025.03.002","relation":{},"ISSN":["0896-6273"],"issn-type":[{"value":"0896-6273","type":"print"}],"subject":[],"published":{"date-parts":[[2025,7]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Molecular pathways and diagnosis in spatially resolved Alzheimer\u2019s hippocampal atlas","name":"articletitle","label":"Article Title"},{"value":"Neuron","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.neuron.2025.03.002","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2025 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}]}}