{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T15:39:06Z","timestamp":1786117146402,"version":"build-2736575974"},"reference-count":145,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T00:00:00Z","timestamp":1782950400000},"content-version":"vor","delay-in-days":1,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35GM155044"],"award-info":[{"award-number":["R35GM155044"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014989","name":"The Chan Zuckerberg Initiative","doi-asserted-by":"publisher","award":["CP2-1-0000000332"],"award-info":[{"award-number":["CP2-1-0000000332"]}],"id":[{"id":"10.13039\/100014989","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014220","name":"Innovative Genomics Institute","doi-asserted-by":"publisher","award":["CA-0204195"],"award-info":[{"award-number":["CA-0204195"]}],"id":[{"id":"10.13039\/100014220","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000900","name":"California Institute for Regenerative Medicine","doi-asserted-by":"publisher","award":["EDUC2-12730"],"award-info":[{"award-number":["EDUC2-12730"]}],"id":[{"id":"10.13039\/100000900","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000957","name":"Alzheimer's Association","doi-asserted-by":"publisher","award":["AARF-22-973222"],"award-info":[{"award-number":["AARF-22-973222"]}],"id":[{"id":"10.13039\/100000957","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000957","name":"Alzheimer's Association","doi-asserted-by":"publisher","award":["ADSF-21-831212-C"],"award-info":[{"award-number":["ADSF-21-831212-C"]}],"id":[{"id":"10.13039\/100000957","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000957","name":"Alzheimer's Association","doi-asserted-by":"publisher","award":["ZEN-22-969903"],"award-info":[{"award-number":["ZEN-22-969903"]}],"id":[{"id":"10.13039\/100000957","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016608","name":"Rainwater Charitable Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016608","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001167","name":"The Larry L Hillblom Foundation Inc","doi-asserted-by":"publisher","award":["2022-A-016-FEL"],"award-info":[{"award-number":["2022-A-016-FEL"]}],"id":[{"id":"10.13039\/100001167","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["1R01AG075802-01"],"award-info":[{"award-number":["1R01AG075802-01"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["P30AG062422"],"award-info":[{"award-number":["P30AG062422"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["U19AG063911"],"award-info":[{"award-number":["U19AG063911"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["U01AG057195"],"award-info":[{"award-number":["U01AG057195"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000049","name":"National Institute on Aging","doi-asserted-by":"publisher","award":["P01AG019724"],"award-info":[{"award-number":["P01AG019724"]}],"id":[{"id":"10.13039\/100000049","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["17528"],"award-info":[{"award-number":["17528"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2034836"],"award-info":[{"award-number":["2034836"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000065","name":"National Institute of Neurological Disorders and Stroke","doi-asserted-by":"publisher","award":["1R01NS144499"],"award-info":[{"award-number":["1R01NS144499"]}],"id":[{"id":"10.13039\/100000065","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":[[2026,7]]},"DOI":"10.1016\/j.neuron.2026.07.001","type":"journal-article","created":{"date-parts":[[2026,7,29]],"date-time":"2026-07-29T14:40:19Z","timestamp":1785336019000},"update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Transcriptional regulation of disease-relevant microglial activation programs"],"prefix":"10.1016","author":[{"given":"Amanda","family":"McQuade","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reet","family":"Mishra","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Venus","family":"Hagan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiwei","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter J.","family":"Colias","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent Cele","family":"Castillo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bianca","family":"Gonzalez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin P.","family":"Lubin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Verena","family":"Haage","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victoria","family":"Marshe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masashi","family":"Fujita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Ta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Layla","family":"Gomes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivia","family":"Teter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xia","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nathaniel","family":"Robichaud","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah E.","family":"Chasins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica E.","family":"Rexach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip L.","family":"De Jager","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James K.","family":"Nu\u00f1ez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3819-7019","authenticated-orcid":false,"given":"Martin","family":"Kampmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.neuron.2026.07.001_bib1","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1038\/nn1472","article-title":"ATP mediates rapid microglial response to local brain injury in vivo","volume":"8","author":"Davalos","year":"2005","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib2","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1126\/science.1110647","article-title":"Resting microglial cells are highly dynamic surveillants of brain parenchyma in vivo","volume":"308","author":"Nimmerjahn","year":"2005","journal-title":"Science"},{"key":"10.1016\/j.neuron.2026.07.001_bib3","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1038\/s41593-025-01931-4","article-title":"Microglia heterogeneity, modeling and cell-state annotation in development and neurodegeneration","volume":"28","author":"Fumagalli","year":"2025","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib4","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\u2019s Disease","volume":"169","author":"Keren-Shaul","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2026.07.001_bib5","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1016\/j.immuni.2017.08.008","article-title":"The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases","volume":"47","author":"Krasemann","year":"2017","journal-title":"Immunity"},{"key":"10.1016\/j.neuron.2026.07.001_bib6","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1093\/brain\/awab446","article-title":"Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state","volume":"145","author":"Smaji\u0107","year":"2022","journal-title":"Brain"},{"key":"10.1016\/j.neuron.2026.07.001_bib7","doi-asserted-by":"crossref","first-page":"116222","DOI":"10.1016\/j.celrep.2025.116222","article-title":"Hypoxic stress dysregulates functions of glioma-associated myeloid cells through epigenomic and transcriptional programs","volume":"44","author":"Dzwigonska","year":"2025","journal-title":"Cell Rep."},{"key":"10.1016\/j.neuron.2026.07.001_bib8","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1038\/s41586-025-09486-x","article-title":"PICALM Alzheimer\u2019s risk allele causes aberrant lipid droplets in microglia","volume":"646","author":"Kozlova","year":"2025","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2026.07.001_bib9","article-title":"MS4A4A modifies the risk of Alzheimer disease by regulating lipid metabolism and immune response in a unique microglia state","author":"You","year":"2023","journal-title":"medRxiv"},{"key":"10.1016\/j.neuron.2026.07.001_bib10","doi-asserted-by":"crossref","first-page":"2994","DOI":"10.3390\/biomedicines11112994","article-title":"Exploring the Disease-Associated Microglia State in Amyotrophic Lateral Sclerosis","volume":"11","author":"Jauregui","year":"2023","journal-title":"Biomedicines"},{"key":"10.1016\/j.neuron.2026.07.001_bib11","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1016\/j.celrep.2017.12.066","article-title":"Diverse Brain Myeloid Expression Profiles Reveal Distinct Microglial Activation States and Aspects of Alzheimer\u2019s Disease Not Evident in Mouse Models","volume":"22","author":"Friedman","year":"2018","journal-title":"Cell Rep."},{"key":"10.1016\/j.neuron.2026.07.001_bib12","doi-asserted-by":"crossref","first-page":"2521","DOI":"10.1038\/s41593-024-01764-7","article-title":"A cross-disease resource of living human microglia identifies disease-enriched subsets and tool compounds recapitulating microglial states","volume":"27","author":"Tuddenham","year":"2024","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib13","doi-asserted-by":"crossref","first-page":"10634","DOI":"10.1038\/s41467-024-54779-w","article-title":"Homeostatic microglia initially seed and activated microglia later reshape amyloid plaques in Alzheimer\u2019s Disease","volume":"15","author":"Balig\u00e1cs","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2026.07.001_bib14","doi-asserted-by":"crossref","first-page":"3015","DOI":"10.1038\/s41467-021-23111-1","article-title":"Transcriptional signature in microglia associated with A\u03b2 plaque phagocytosis","volume":"12","author":"Grubman","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2026.07.001_bib15","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1084\/jem.20151948","article-title":"TREM2-mediated early microglial response limits diffusion and toxicity of amyloid plaques","volume":"213","author":"Wang","year":"2016","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.neuron.2026.07.001_bib16","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/1750-1326-9-20","article-title":"Altered microglial response to A\u03b2 plaques in APPPS1-21 mice heterozygous for TREM2","volume":"9","author":"Ulrich","year":"2014","journal-title":"Mol. Neurodegener."},{"key":"10.1016\/j.neuron.2026.07.001_bib17","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1038\/s41586-024-07871-6","article-title":"Cellular communities reveal trajectories of brain ageing and Alzheimer\u2019s disease","volume":"633","author":"Green","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2026.07.001_bib18","doi-asserted-by":"crossref","first-page":"5370","DOI":"10.1038\/s41467-020-19227-5","article-title":"Gene expression and functional deficits underlie TREM2-knockout microglia responses in human models of Alzheimer\u2019s disease","volume":"11","author":"McQuade","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2026.07.001_bib19","doi-asserted-by":"crossref","first-page":"12620","DOI":"10.1074\/jbc.RA118.001848","article-title":"TREM2-activating antibodies abrogate the negative pleiotropic effects of the Alzheimer\u2019s disease variant Trem2R47H on murine myeloid cell function","volume":"293","author":"Cheng","year":"2018","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.neuron.2026.07.001_bib20","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/s13024-018-0262-8","article-title":"The Trem2 R47H variant confers loss-of-function-like phenotypes in Alzheimer\u2019s disease","volume":"13","author":"Cheng-Hathaway","year":"2018","journal-title":"Mol. Neurodegener."},{"key":"10.1016\/j.neuron.2026.07.001_bib21","first-page":"416","article-title":"A TREM2-activating antibody with a blood-brain barrier transport vehicle enhances microglial metabolism in Alzheimer\u2019s disease models","volume":"26","author":"van Lengerich","year":"2023","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib22","doi-asserted-by":"crossref","first-page":"2099","DOI":"10.1038\/s42255-025-01379-7","article-title":"Cholesterol metabolic reprogramming mediates microglia-induced chronic neuroinflammation and hinders neurorestoration following stroke","volume":"7","author":"Zhao","year":"2025","journal-title":"Nat. Metab."},{"key":"10.1016\/j.neuron.2026.07.001_bib23","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1186\/s13024-021-00473-0","article-title":"Plaque-associated human microglia accumulate lipid droplets in a chimeric model of Alzheimer\u2019s disease","volume":"16","author":"Claes","year":"2021","journal-title":"Mol. Neurodegener."},{"key":"10.1016\/j.neuron.2026.07.001_bib24","article-title":"Dynamic Brain Lipid Profiles Modulate Microglial Lipid Droplet Accumulation and Inflammation Under Ischemic Conditions in Mice","volume":"11","author":"Wei","year":"2024","journal-title":"Adv. Sci. (Weinh)"},{"key":"10.1016\/j.neuron.2026.07.001_bib25","doi-asserted-by":"crossref","DOI":"10.1084\/jem.20202059","article-title":"Normalization of cholesterol metabolism in spinal microglia alleviates neuropathic pain","volume":"218","author":"Navia-Pelaez","year":"2021","journal-title":"J Exp Med"},{"key":"10.1016\/j.neuron.2026.07.001_bib26","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1038\/s41593-019-0566-1","article-title":"Lipid-droplet-accumulating microglia represent a dysfunctional and proinflammatory state in the aging brain","volume":"23","author":"Marschallinger","year":"2020","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib27","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1007\/s00018-023-05045-7","article-title":"Knockdown of NEAT1 prevents post-stroke lipid droplet agglomeration in microglia by regulating autophagy","volume":"81","author":"Pan","year":"2024","journal-title":"Cell. Mol. Life Sci."},{"key":"10.1016\/j.neuron.2026.07.001_bib28","doi-asserted-by":"crossref","first-page":"111591","DOI":"10.1016\/j.celrep.2022.111591","article-title":"The ApoA-I mimetic peptide 5A enhances remyelination by promoting clearance and degradation of myelin debris","volume":"41","author":"Vanherle","year":"2022","journal-title":"Cell Rep."},{"key":"10.1016\/j.neuron.2026.07.001_bib29","article-title":"HIV-1 infection of human microglia activates inflammatory pathways associated with HIV-associated neurocognitive disorders (HAND)","author":"Hammonds","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2026.07.001_bib30","doi-asserted-by":"crossref","first-page":"1936","DOI":"10.1016\/j.cell.2024.02.020","article-title":"Type-I-interferon-responsive microglia shape cortical development and behavior","volume":"187","author":"Escoubas","year":"2024","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2026.07.001_bib31","doi-asserted-by":"crossref","first-page":"5748","DOI":"10.1038\/ncomms6748","article-title":"Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism","volume":"5","author":"Gupta","year":"2014","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2026.07.001_bib32","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.it.2016.01.006","article-title":"Type I\/II Interferon Balance in the Regulation of Brain Physiology and Pathology","volume":"37","author":"Deczkowska","year":"2016","journal-title":"Trends Immunol."},{"key":"10.1016\/j.neuron.2026.07.001_bib33","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/s13024-024-00736-6","article-title":"Fate-mapping and functional dissection reveal perilous influence of type I interferon signaling in mouse brain aging","volume":"19","author":"Roy","year":"2024","journal-title":"Mol. Neurodegener."},{"key":"10.1016\/j.neuron.2026.07.001_bib34","doi-asserted-by":"crossref","first-page":"1912","DOI":"10.1172\/JCI133737","article-title":"Type I interferon response drives neuroinflammation and synapse loss in Alzheimer disease","volume":"130","author":"Roy","year":"2020","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.neuron.2026.07.001_bib35","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1038\/s41593-023-01315-6","article-title":"Tau activation of microglial cGAS-IFN reduces MEF2C-mediated cognitive resilience","volume":"26","author":"Udeochu","year":"2023","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib36","doi-asserted-by":"crossref","first-page":"3877","DOI":"10.1016\/j.neuron.2024.09.006","article-title":"Alzheimer\u2019s disease-linked risk alleles elevate microglial cGAS-associated senescence and neurodegeneration in a tauopathy model","volume":"112","author":"Carling","year":"2024","journal-title":"Neuron"},{"key":"10.1016\/j.neuron.2026.07.001_bib37","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1038\/s41586-023-05788-0","article-title":"Microglia-mediated T cell Infiltration Drives Neurodegeneration in Tauopathy","volume":"615","author":"Chen","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2026.07.001_bib38","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1126\/science.abf7266","article-title":"CD4+ T cells contribute to neurodegeneration in Lewy body dementia","volume":"374","author":"Gate","year":"2021","journal-title":"Science"},{"key":"10.1016\/j.neuron.2026.07.001_bib39","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/s41586-019-1895-7","article-title":"Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer\u2019s disease","volume":"577","author":"Gate","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2026.07.001_bib40","doi-asserted-by":"crossref","first-page":"6129","DOI":"10.1038\/s41467-020-19737-2","article-title":"Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer\u2019s disease","volume":"11","author":"Olah","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2026.07.001_bib41","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1016\/j.neuron.2019.07.002","article-title":"Development of a Chimeric Model to Study and Manipulate Human Microglia In Vivo","volume":"103","author":"Hasselmann","year":"2019","journal-title":"Neuron"},{"key":"10.1016\/j.neuron.2026.07.001_bib42","article-title":"pTDP-43 levels correlate with cell type specific molecular alterations in the prefrontal cortex of C9orf72 ALS\/FTD patients","volume":"122","author":"Wang","year":"2025","journal-title":"PNAS"},{"key":"10.1016\/j.neuron.2026.07.001_bib43","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1002\/ana.20315","article-title":"Neuroglial activation and neuroinflammation in the brain of patients with autism","volume":"57","author":"Vargas","year":"2005","journal-title":"Ann. Neurol."},{"key":"10.1016\/j.neuron.2026.07.001_bib44","article-title":"CXCL1 contributes to \u03b2-amyloid-induced transendothelial migration of monocytes in Alzheimer\u2019s disease","volume":"8","author":"Zhang","year":"2013","journal-title":"PLOS One"},{"key":"10.1016\/j.neuron.2026.07.001_bib45","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1186\/s12974-019-1646-6","article-title":"CXCL12 is involved in \u03b1-synuclein-triggered neuroinflammation of Parkinson\u2019s disease","volume":"16","author":"Li","year":"2019","journal-title":"J. Neuroinflamm."},{"key":"10.1016\/j.neuron.2026.07.001_bib46","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.73021","article-title":"TREM2 regulates purinergic receptor-mediated calcium signaling and motility in human iPSC-derived microglia","volume":"11","author":"Jairaman","year":"2022","journal-title":"eLife"},{"key":"10.1016\/j.neuron.2026.07.001_bib47","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1111\/j.1600-065X.2012.01127.x","article-title":"Inflammatory cell trafficking across the blood-brain barrier: chemokine regulation and in vitro models","volume":"248","author":"Takeshita","year":"2012","journal-title":"Immunol. Rev."},{"key":"10.1016\/j.neuron.2026.07.001_bib48","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/nmeth.4463","article-title":"SCENIC: Single-cell regulatory network inference and clustering","volume":"14","author":"Aibar","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.neuron.2026.07.001_bib49","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1186\/s12967-023-04516-6","article-title":"Integrating single-nucleus sequence profiling to reveal the transcriptional dynamics of Alzheimer\u2019s disease, Parkinson\u2019s disease, and multiple sclerosis","volume":"21","author":"Fan","year":"2023","journal-title":"J. Transl. Med."},{"key":"10.1016\/j.neuron.2026.07.001_bib50","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.3390\/brainsci12091196","article-title":"Biomarker Genes Discovery of Alzheimer\u2019s Disease by Multi-Omics-Based Gene Regulatory Network Construction of Microglia","volume":"12","author":"Gao","year":"2022","journal-title":"Brain Sci."},{"key":"10.1016\/j.neuron.2026.07.001_bib51","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1186\/s12964-024-01590-1","article-title":"Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson\u2019s disease","volume":"22","author":"Quan","year":"2024","journal-title":"Cell Commun. Signal."},{"key":"10.1016\/j.neuron.2026.07.001_bib52","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1177\/13872877251378007","article-title":"HIF-1\u03b1-induced microglia-mediated neuroinflammation is involved in Alzheimer\u2019s disease: Evidence from single-cell transcriptomic analysis","volume":"108","author":"Dong","year":"2025","journal-title":"J. Alzheimers Dis."},{"key":"10.1016\/j.neuron.2026.07.001_bib53","doi-asserted-by":"crossref","first-page":"1382","DOI":"10.1038\/s41590-023-01558-2","article-title":"Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro","volume":"24","author":"Dolan","year":"2023","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.neuron.2026.07.001_bib54","doi-asserted-by":"crossref","first-page":"4386","DOI":"10.1016\/j.cell.2023.08.037","article-title":"Human microglial state dynamics in Alzheimer\u2019s disease progression","volume":"186","author":"Sun","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2026.07.001_bib55","doi-asserted-by":"crossref","first-page":"2058","DOI":"10.1038\/s41467-024-46315-7","article-title":"BHLHE40\/41 regulate microglia and peripheral macrophage responses associated with Alzheimer\u2019s disease and other disorders of lipid-rich tissues","volume":"15","author":"Podle\u015bny-Drabiniok","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2026.07.001_bib56","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.gde.2017.02.007","article-title":"Transcription factor\u2013DNA binding: beyond binding site motifs","volume":"43","author":"Inukai","year":"2017","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.neuron.2026.07.001_bib57","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.1038\/s41593-022-01131-4","article-title":"A CRISPRi\/a platform in human iPSC-derived microglia uncovers regulators of disease states","volume":"25","author":"Dr\u00e4ger","year":"2022","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib58","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1038\/s41467-017-00769-0","article-title":"Mef2C restrains microglial inflammatory response and is lost in brain ageing in an IFN-I-dependent manner","volume":"8","author":"Deczkowska","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2026.07.001_bib59","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1007\/s00401-021-02263-w","article-title":"Distinct amyloid-\u03b2 and tau-associated microglia profiles in Alzheimer\u2019s disease","volume":"141","author":"Gerrits","year":"2021","journal-title":"Acta Neuropathol."},{"key":"10.1016\/j.neuron.2026.07.001_bib60","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1038\/s41593-024-01600-y","article-title":"Xenografted human microglia display diverse transcriptomic states in response to Alzheimer\u2019s disease-related amyloid-\u03b2 pathology","volume":"27","author":"Mancuso","year":"2024","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib61","doi-asserted-by":"crossref","first-page":"2152","DOI":"10.1016\/j.immuni.2023.07.016","article-title":"Human microglia maturation is underpinned by specific gene regulatory networks","volume":"56","author":"Han","year":"2023","journal-title":"Immunity"},{"key":"10.1016\/j.neuron.2026.07.001_bib62","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1038\/nn.3599","article-title":"Identification of a unique TGF-\u03b2-dependent molecular and functional signature in microglia","volume":"17","author":"Butovsky","year":"2014","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib63","doi-asserted-by":"crossref","first-page":"12019","DOI":"10.1093\/nar\/gkac230","article-title":"YY1 safeguard multidimensional epigenetic landscape associated with extended pluripotency","volume":"50","author":"Dong","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.neuron.2026.07.001_bib64","doi-asserted-by":"crossref","first-page":"587","DOI":"10.18632\/oncotarget.1782","article-title":"Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers","volume":"5","author":"Li","year":"2014","journal-title":"Oncotarget"},{"key":"10.1016\/j.neuron.2026.07.001_bib65","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1002\/ijc.1452","article-title":"Rexpression of HLA class I antigens and restoration of antigen-specific CTL response in melanoma cells following 5-aza-2\u2032-deoxycytidine treatment","volume":"94","author":"Serrano","year":"2001","journal-title":"Int. J. Cancer"},{"key":"10.1016\/j.neuron.2026.07.001_bib66","doi-asserted-by":"crossref","first-page":"1376","DOI":"10.1093\/cvr\/cvx134","article-title":"CCAAT\/enhancer-binding protein delta promotes intracellular lipid accumulation in M1 macrophages of vascular lesions","volume":"113","author":"Lai","year":"2017","journal-title":"Cardiovasc. Res."},{"key":"10.1016\/j.neuron.2026.07.001_bib67","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.cyto.2018.02.026","article-title":"How post-translational modifications influence the biological activity of chemokines","volume":"109","author":"Vanheule","year":"2018","journal-title":"Cytokine"},{"key":"10.1016\/j.neuron.2026.07.001_bib68","doi-asserted-by":"crossref","first-page":"3794","DOI":"10.1111\/febs.15362","article-title":"Post-transcriptional regulation of C-C motif chemokine ligand 2 expression by ribosomal protein L22 during LPS-mediated inflammation","volume":"287","author":"Das","year":"2020","journal-title":"FEBS Journal"},{"key":"10.1016\/j.neuron.2026.07.001_bib69","doi-asserted-by":"crossref","DOI":"10.1002\/mgg3.2051","article-title":"Neurodevelopmental disorder with dystonia due to SOX6 mutations","volume":"10","author":"Schneider","year":"2022","journal-title":"Mol. Genet. Genomic Med."},{"key":"10.1016\/j.neuron.2026.07.001_bib70","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s13229-019-0286-0","article-title":"Disruption of PHF21A causes syndromic intellectual disability with craniofacial anomalies, epilepsy, hypotonia, and neurobehavioral problems including autism","volume":"10","author":"Kim","year":"2019","journal-title":"Mol. Autism"},{"key":"10.1016\/j.neuron.2026.07.001_bib71","doi-asserted-by":"crossref","first-page":"3921","DOI":"10.1111\/ejn.16155","article-title":"Dissection of cellular disruptions in autism spectrum disorder comorbidities","volume":"58","author":"Griffin","year":"2023","journal-title":"Eur. J. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib72","article-title":"Regulators of Interferon-Responsive Microglia Uncovered by Genome-wide CRISPRi Screening","author":"McQuade","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2026.07.001_bib73","doi-asserted-by":"crossref","first-page":"4176","DOI":"10.1038\/s41380-025-02997-z","article-title":"CRISPRi-based screen of autism spectrum disorder risk genes in microglia uncovers roles of ADNP in microglia endocytosis and synaptic pruning","volume":"30","author":"Teter","year":"2025","journal-title":"Mol. Psychiatry"},{"key":"10.1016\/j.neuron.2026.07.001_bib74","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1038\/nature01850","article-title":"Integration of interferon-\u03b1\/\u03b2 signalling to p53 responses in tumour suppression and antiviral defence","volume":"424","author":"Takaoka","year":"2003","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2026.07.001_bib75","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1084\/jem.20080383","article-title":"Transcriptional role of p53 in interferon-mediated antiviral immunity","volume":"205","author":"Mu\u00f1oz-Fontela","year":"2008","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.neuron.2026.07.001_bib76","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1016\/j.stem.2022.06.007","article-title":"Type-I-interferon signaling drives microglial dysfunction and senescence in human iPSC models of Down syndrome and Alzheimer\u2019s disease","volume":"29","author":"Jin","year":"2022","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.neuron.2026.07.001_bib77","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1038\/nmeth.4177","article-title":"Pooled CRISPR screening with single-cell transcriptome readout","volume":"14","author":"Datlinger","year":"2017","journal-title":"Nat. Methods"},{"key":"10.1016\/j.neuron.2026.07.001_bib78","doi-asserted-by":"crossref","first-page":"3220","DOI":"10.1016\/j.celrep.2017.11.058","article-title":"Diverging mRNA and Protein Networks in Activated Microglia Reveal SRSF3 Suppresses Translation of Highly Upregulated Innate Immune Transcripts","volume":"21","author":"Boutej","year":"2017","journal-title":"Cell Rep."},{"key":"10.1016\/j.neuron.2026.07.001_bib79","article-title":"A factor-based analysis of individual human microglia uncovers regulators of an Alzheimer-related transcriptional signature","author":"Marshe","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2026.07.001_bib80","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/s13024-018-0297-x","article-title":"Development and validation of a simplified method to generate human microglia from pluripotent stem cells","volume":"13","author":"McQuade","year":"2018","journal-title":"Mol. Neurodegener."},{"key":"10.1016\/j.neuron.2026.07.001_bib81","article-title":"A proteogenomic tool uncovers protein markers for human microglial states","author":"Haage","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2026.07.001_bib82","doi-asserted-by":"crossref","first-page":"1830","DOI":"10.1038\/s41593-025-02020-2","article-title":"Alzheimer\u2019s disease transcriptional landscape in ex vivo human microglia","volume":"28","author":"Kosoy","year":"2025","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib83","doi-asserted-by":"crossref","first-page":"2375","DOI":"10.1038\/s41592-025-02861-6","article-title":"nELISA: a high-throughput, high-plex platform enables quantitative profiling of the inflammatory secretome","volume":"22","author":"Dagher","year":"2025","journal-title":"Nat. Methods"},{"key":"10.1016\/j.neuron.2026.07.001_bib84","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1038\/s41586-025-09662-z","article-title":"Lymphoid gene expression supports neuroprotective microglia function","volume":"648","author":"Ayata","year":"2025","journal-title":"Nature"},{"key":"10.1016\/j.neuron.2026.07.001_bib85","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/s41556-025-01622-z","article-title":"Systematic reconstruction of molecular pathway signatures using scalable single-cell perturbation screens","volume":"27","author":"Jiang","year":"2025","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.neuron.2026.07.001_bib86","doi-asserted-by":"crossref","first-page":"29862","DOI":"10.1073\/pnas.2010723117","article-title":"Type I interferon remodels lysosome function and modifies intestinal epithelial defense","volume":"117","author":"Zhang","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.neuron.2026.07.001_bib87","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1038\/ng.3258","article-title":"Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells","volume":"47","author":"Liao","year":"2015","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neuron.2026.07.001_bib88","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1016\/0092-8674(92)90611-F","article-title":"Targeted mutation of the DNA methyltransferase gene results in embryonic lethality","volume":"69","author":"Li","year":"1992","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2026.07.001_bib89","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1177\/1947601910373794","article-title":"Dnmt1\/Transcription Factor Interactions: an Alternative Mechanism of DNA Methylation Inheritance","volume":"1","author":"Hervouet","year":"2010","journal-title":"Genes Cancer"},{"key":"10.1016\/j.neuron.2026.07.001_bib90","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.1016\/j.bbagrm.2016.09.007","article-title":"Distinct and overlapping DNMT1 interactions with multiple transcription factors in erythroid cells: Evidence for co-repressor functions","volume":"1859","author":"Papageorgiou","year":"2016","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.neuron.2026.07.001_bib91","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1007\/s13237-021-00367-y","article-title":"DNA methylation and regulation of gene expression: Guardian of our health","volume":"64","author":"Dhar","year":"2021","journal-title":"Nucleus (Calcutta)"},{"key":"10.1016\/j.neuron.2026.07.001_bib92","doi-asserted-by":"crossref","first-page":"1528","DOI":"10.1038\/s41593-022-01180-9","article-title":"CRISPRi screens in human iPSC-derived astrocytes elucidate regulators of distinct inflammatory reactive states","volume":"25","author":"Leng","year":"2022","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib93","doi-asserted-by":"crossref","first-page":"107843","DOI":"10.1016\/j.celrep.2020.107843","article-title":"Alzheimer\u2019s Patient Microglia Exhibit Enhanced Aging and Unique Transcriptional Activation","volume":"31","author":"Srinivasan","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.neuron.2026.07.001_bib94","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1002\/path.1752","article-title":"PRDM1\/Blimp-1 is expressed in human B-lymphocytes committed to the plasma cell lineage","volume":"206","author":"Cattoretti","year":"2005","journal-title":"J. Pathol."},{"key":"10.1016\/j.neuron.2026.07.001_bib95","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/S1074-7613(02)00335-7","article-title":"Blimp-1 orchestrates plasma cell differentiation by extinguishing the mature B cell gene expression program","volume":"17","author":"Shaffer","year":"2002","journal-title":"Immunity"},{"key":"10.1016\/j.neuron.2026.07.001_bib96","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s12974-023-02809-7","article-title":"Analysis of the microglia transcriptome across the human lifespan using single cell RNA sequencing","volume":"20","author":"Yaqubi","year":"2023","journal-title":"J. Neuroinflamm."},{"key":"10.1016\/j.neuron.2026.07.001_bib97","article-title":"Integrative analysis reveals generalizable human neurodegenerative disease-associated glial states","author":"Horan-Portelance","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2026.07.001_bib98","article-title":"HDAC Inhibitors recapitulate Human Disease-Associated Microglia Signatures in vitro","author":"Haage","year":"2024","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2026.07.001_bib99","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1016\/j.stem.2022.07.005","article-title":"Lipid accumulation induced by APOE4 impairs microglial surveillance of neuronal-network activity","volume":"29","author":"Victor","year":"2022","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.neuron.2026.07.001_bib100","doi-asserted-by":"crossref","first-page":"108398","DOI":"10.1016\/j.celrep.2020.108398","article-title":"Tau Pathology Drives Dementia Risk-Associated Gene Networks toward Chronic Inflammatory States and Immunosuppression","volume":"33","author":"Rexach","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.neuron.2026.07.001_bib101","doi-asserted-by":"crossref","first-page":"1048","DOI":"10.1016\/S1474-4422(23)00247-8","article-title":"Stimulation of TREM2 with agonistic antibodies-an emerging therapeutic option for Alzheimer\u2019s disease","volume":"22","author":"Schlepckow","year":"2023","journal-title":"Lancet Neurol."},{"key":"10.1016\/j.neuron.2026.07.001_bib102","doi-asserted-by":"crossref","first-page":"6670","DOI":"10.1038\/s41467-023-42505-x","article-title":"Soluble TREM2 ameliorates tau phosphorylation and cognitive deficits through activating transgelin-2 in Alzheimer\u2019s disease","volume":"14","author":"Zhang","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2026.07.001_bib103","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/s13024-017-0216-6","article-title":"TREM2 deficiency exacerbates tau pathology through dysregulated kinase signaling in a mouse model of tauopathy","volume":"12","author":"Bemiller","year":"2017","journal-title":"Mol. Neurodegener."},{"key":"10.1016\/j.neuron.2026.07.001_bib104","doi-asserted-by":"crossref","first-page":"11524","DOI":"10.1073\/pnas.1710311114","article-title":"TREM2 deficiency attenuates neuroinflammation and protects against neurodegeneration in a mouse model of tauopathy","volume":"114","author":"Leyns","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.neuron.2026.07.001_bib105","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1016\/j.neuron.2021.02.010","article-title":"Trem2 restrains the enhancement of tau accumulation and neurodegeneration by \u03b2-amyloid pathology","volume":"109","author":"Lee","year":"2021","journal-title":"Neuron"},{"key":"10.1016\/j.neuron.2026.07.001_bib106","doi-asserted-by":"crossref","first-page":"1452","DOI":"10.1038\/ng.2802","article-title":"Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer\u2019s disease","volume":"45","author":"Lambert","year":"2013","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neuron.2026.07.001_bib107","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/j.stem.2009.08.016","article-title":"DNA Methyltransferase 1 is essential for and uniquely regulates hematopoietic stem and progenitor cells","volume":"5","author":"Trowbridge","year":"2009","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.neuron.2026.07.001_bib108","doi-asserted-by":"crossref","first-page":"1194","DOI":"10.1016\/j.cell.2013.05.039","article-title":"The Hallmarks of Aging","volume":"153","author":"L\u00f3pez-Ot\u00edn","year":"2013","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2026.07.001_bib109","doi-asserted-by":"crossref","first-page":"1156","DOI":"10.1038\/nn.3786","article-title":"Alzheimer\u2019s disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci","volume":"17","author":"De Jager","year":"2014","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib110","doi-asserted-by":"crossref","first-page":"682247","DOI":"10.3389\/fnins.2021.682247","article-title":"Decreased MEF2A Expression Regulated by Its Enhancer Methylation Inhibits Autophagy and May Play an Important Role in the Progression of Alzheimer\u2019s Disease","volume":"15","author":"Li","year":"2021","journal-title":"Front. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib111","doi-asserted-by":"crossref","first-page":"5620","DOI":"10.1038\/s41467-022-33394-7","article-title":"DNA methylation signatures of Alzheimer\u2019s disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types","volume":"13","author":"Shireby","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.neuron.2026.07.001_bib112","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1038\/ng.830","article-title":"Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss","volume":"43","author":"Klein","year":"2011","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neuron.2026.07.001_bib113","doi-asserted-by":"crossref","first-page":"2205","DOI":"10.1093\/hmg\/dds035","article-title":"Mutations in DNMT1 cause autosomal dominant cerebellar ataxia, deafness and narcolepsy","volume":"21","author":"Winkelmann","year":"2012","journal-title":"Hum. Mol. Genet."},{"key":"10.1016\/j.neuron.2026.07.001_bib125","doi-asserted-by":"crossref","first-page":"6439","DOI":"10.1038\/s41467-026-73007-1","article-title":"Single-nucleus epigenomic dysregulation unmasks genetic risk-associated neurodegenerative glia states","volume":"17","author":"Han","year":"2026","journal-title":"Nat.Commun."},{"key":"10.1016\/j.neuron.2026.07.001_bib115","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1016\/j.neuron.2019.07.014","article-title":"CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons","volume":"104","author":"Tian","year":"2019","journal-title":"Neuron"},{"key":"10.1016\/j.neuron.2026.07.001_bib120","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1186\/s12859-021-04344-9","article-title":"CellProfiler 4: improvements in speed, utility and usability","volume":"22","author":"Stirling","year":"2021","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.neuron.2026.07.001_bib126","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1038\/s41588-021-00790-6","article-title":"ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis","volume":"53","author":"Granja","year":"2021","journal-title":"Nat. Genet."},{"key":"10.1016\/j.neuron.2026.07.001_bib128","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.neuron.2026.07.001_bib129","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","article-title":"edgeR: a Bioconductor package for differential expression analysis of digital gene expression data","volume":"26","author":"Robinson","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2026.07.001_bib121","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet J."},{"key":"10.1016\/j.neuron.2026.07.001_bib122","doi-asserted-by":"crossref","first-page":"1571","DOI":"10.1093\/bioinformatics\/btr167","article-title":"Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications","volume":"27","author":"Krueger","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2026.07.001_bib123","doi-asserted-by":"crossref","first-page":"R83","DOI":"10.1186\/gb-2012-13-10-r83","article-title":"BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions","volume":"13","author":"Hansen","year":"2012","journal-title":"Genome Biol."},{"key":"10.1016\/j.neuron.2026.07.001_bib124","doi-asserted-by":"crossref","first-page":"e69","DOI":"10.1093\/nar\/gku154","article-title":"A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data","volume":"42","author":"Feng","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.neuron.2026.07.001_bib130","doi-asserted-by":"crossref","first-page":"2129","DOI":"10.1038\/s41593-025-02043-9","article-title":"CRISPR screening by AAV episome-sequencing (CrAAVe-seq): a scalable cell-type-specific in vivo platform uncovers neuronal essential genes","volume":"28","author":"Ramani","year":"2025","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.neuron.2026.07.001_bib131","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/s41596-024-01057-0","article-title":"kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq","volume":"20","author":"Sullivan","year":"2025","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.neuron.2026.07.001_bib132","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s13059-021-02577-8","article-title":"MUON: multimodal omics analysis framework","volume":"23","author":"Bredikhin","year":"2022","journal-title":"Genome Biol."},{"key":"10.1016\/j.neuron.2026.07.001_bib133","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol."},{"key":"10.1016\/j.neuron.2026.07.001_bib139","doi-asserted-by":"crossref","first-page":"3796","DOI":"10.1016\/j.csbj.2021.06.043","article-title":"UCell: Robust and scalable single-cell gene signature scoring","volume":"19","author":"Andreatta","year":"2021","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"10.1016\/j.neuron.2026.07.001_bib145","article-title":"Presto scales Wilcoxon and auROC analyses to millions of observations","author":"Korsunsky","year":"2019","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2026.07.001_bib136","series-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2009"},{"key":"10.1016\/j.neuron.2026.07.001_bib137","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","article-title":"Complex heatmaps reveal patterns and correlations in multidimensional genomic data","volume":"32","author":"Gu","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2026.07.001_bib138","unstructured":"Blighe, K., Rana, S., and Lewis, M. EnhancedVolcano: Publication-Ready Volcano Plots with Enhanced Colouring and Labeling. R Package.https:\/\/doi.org\/10.18129\/B9.bioc.EnhancedVolcano."},{"key":"10.1016\/j.neuron.2026.07.001_bib143","article-title":"Autism genes converge on microtubule biology and RNA-binding proteins during excitatory neurogenesis","author":"Sun","year":"2024","journal-title":"bioRxiv"},{"key":"10.1016\/j.neuron.2026.07.001_bib142","doi-asserted-by":"crossref","first-page":"2159","DOI":"10.1093\/bioinformatics\/bty916","article-title":"GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks","volume":"35","author":"Moerman","year":"2019","journal-title":"Bioinformatics"},{"key":"10.1016\/j.neuron.2026.07.001_bib141","doi-asserted-by":"crossref","first-page":"C1","DOI":"10.1007\/978-1-0716-1534-8_20","article-title":"Correction to: Inference of Gene Regulatory Network from Single-Cell Transcriptomic Data Using pySCENIC","volume":"2328","author":"Kumar","year":"2021","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.neuron.2026.07.001_bib114","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1007\/7651_2021_429","article-title":"Human Induced Pluripotent Stem Cell-Derived Microglia (hiPSC-Microglia)","volume":"2454","author":"McQuade","year":"2022","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.neuron.2026.07.001_bib116","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.19760","article-title":"Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation","volume":"5","author":"Horlbeck","year":"2016","journal-title":"eLife"},{"key":"10.1016\/j.neuron.2026.07.001_bib117","doi-asserted-by":"crossref","first-page":"1517","DOI":"10.1016\/j.cell.2025.12.038","article-title":"CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis","volume":"189","author":"Samelson","year":"2026","journal-title":"Cell"},{"key":"10.1016\/j.neuron.2026.07.001_bib118","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1038\/s41565-018-0205-0","article-title":"Ensemble multicolour FRET model enables barcoding at extreme FRET levels","volume":"13","author":"Dagher","year":"2018","journal-title":"Nat. Nanotechnol."},{"key":"10.1016\/j.neuron.2026.07.001_bib119","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0005251","article-title":"The post-synaptic density of human postmortem brain tissues: an experimental study paradigm for neuropsychiatric illnesses","volume":"4","author":"Hahn","year":"2009","journal-title":"PLOS One"},{"key":"10.1016\/j.neuron.2026.07.001_bib127","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"10.1016\/j.neuron.2026.07.001_bib134","doi-asserted-by":"crossref","first-page":"5233","DOI":"10.1038\/s41598-019-41695-z","article-title":"From Louvain to Leiden: guaranteeing well-connected communities","volume":"9","author":"Traag","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.neuron.2026.07.001_bib135","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.2026.07.001_bib140","doi-asserted-by":"crossref","first-page":"e8557","DOI":"10.15252\/msb.20188557","article-title":"De novo gene signature identification from single-cell RNA-seq with hierarchical Poisson factorization","volume":"15","author":"Levitin","year":"2019","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.neuron.2026.07.001_bib144","doi-asserted-by":"crossref","first-page":"e90","DOI":"10.1002\/cpz1.90","article-title":"Gene Set Knowledge Discovery with Enrichr","volume":"1","author":"Xie","year":"2021","journal-title":"Curr. Protoc."}],"container-title":["Neuron"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0896627326005301?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0896627326005301?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T13:12:47Z","timestamp":1786021967000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0896627326005301"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7]]},"references-count":145,"alternative-id":["S0896627326005301"],"URL":"https:\/\/doi.org\/10.1016\/j.neuron.2026.07.001","relation":{},"ISSN":["0896-6273"],"issn-type":[{"value":"0896-6273","type":"print"}],"subject":[],"published":{"date-parts":[[2026,7]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Transcriptional regulation of disease-relevant microglial activation programs","name":"articletitle","label":"Article Title"},{"value":"Neuron","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.neuron.2026.07.001","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}