{"id":"https://openalex.org/W7204015032","doi":null,"title":"Context-dependent remodeling of aging-related and neurodevelopmental pathways in human cerebral organoids across APOE genotypes","display_name":"Context-dependent remodeling of aging-related and neurodevelopmental pathways in human cerebral organoids across APOE genotypes","publication_year":2026,"publication_date":"2026-01-01","ids":{"openalex":"https://openalex.org/W7204015032"},"language":"en","primary_location":{"id":"pmh:oai:imagine.imgge.bg.ac.rs:123456789/3412","doi":null,"is_oa":true,"landing_page_url":"https://belbi.bg.ac.rs","pdf_url":null,"source":{"id":"https://openalex.org/S4377196579","display_name":"IMAGINE - Repository of the Institute of molecular genetics and genetic engineering (University of Belgrade)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4068193","host_organization_name":"University of Belgrade","host_organization_lineage":["https://openalex.org/I4068193"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Book of Abstracts: 6th Belgrade Bioinformatics Conference","raw_type":"conferenceObject"},"volume":null,"type":"conference-paper","indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://belbi.bg.ac.rs","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079149263","display_name":"Minja Beli\u0107","orcid":"https://orcid.org/0000-0002-8910-7650","observed_orcids":["https://orcid.org/0000-0002-8910-7650"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Belic, Minja","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026911791","display_name":"Joanna Bons","orcid":"https://orcid.org/0000-0002-1110-4193","observed_orcids":["https://orcid.org/0000-0002-1110-4193"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bons, Joanna","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074239287","display_name":"Sydney A. Alderfer","orcid":"https://orcid.org/0009-0005-4997-6164","observed_orcids":["https://orcid.org/0009-0005-4997-6164"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alderfer, Sydney","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124678630","display_name":"Mikayla Hady","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hady, Mikayla","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078016862","display_name":"Tyne L.M. McHugh","orcid":"https://orcid.org/0000-0002-6750-5957","observed_orcids":["https://orcid.org/0000-0002-6750-5957"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"McHugh, Tyne L. M.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027162923","display_name":"Kizito\u2010Tshitoko Tshilenge","orcid":"https://orcid.org/0000-0001-9151-2391","observed_orcids":["https://orcid.org/0000-0001-9151-2391"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tshilenge, Kizito-Tshitoko","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5153577355","display_name":"Maria A. Sanchez","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sanchez, Maria A.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5147858917","display_name":"Kevin Schneider","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Schneider, Kevin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5147851260","display_name":"Wu Long","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Long, Wu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5130672573","display_name":"Nikolay Markov","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Markov, Nikola","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003883020","display_name":"Birgit Schilling","orcid":"https://orcid.org/0000-0001-9907-2749","observed_orcids":["https://orcid.org/0000-0001-9907-2749"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Schilling, Birgit","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064943116","display_name":"David Furman","orcid":"https://orcid.org/0000-0002-3654-9519","observed_orcids":["https://orcid.org/0000-0002-3654-9519"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Furman, David","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5043919479","display_name":"Lisa Ellerby","orcid":"https://orcid.org/0000-0002-9050-7977","observed_orcids":["https://orcid.org/0000-0002-9050-7977"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ellerby, Lisa M.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.63787879,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.43380001187324524,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.43380001187324524,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10086","display_name":"Alzheimer's disease research and treatments","score":0.4120999872684479,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10505","display_name":"Pluripotent Stem Cells Research","score":0.08699999749660492,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/apolipoprotein-e","display_name":"apolipoprotein E","score":0.9309999942779541},{"id":"https://openalex.org/keywords/apoe-epsilon4","display_name":"APOE \u03b54","score":0.8640000224113464},{"id":"https://openalex.org/keywords/apoe2","display_name":"APOE2","score":0.859000027179718},{"id":"https://openalex.org/keywords/apoe3","display_name":"APOE3","score":0.7559999823570251},{"id":"https://openalex.org/keywords/brain-organoids","display_name":"brain organoids","score":0.8180000185966492},{"id":"https://openalex.org/keywords/induced-pluripotent-stem-cells","display_name":"induced pluripotent stem cells","score":0.7789999842643738},{"id":"https://openalex.org/keywords/brain-development","display_name":"brain development","score":0.5889999866485596},{"id":"https://openalex.org/keywords/cellular-senescence","display_name":"cellular senescence","score":0.7799999713897705},{"id":"https://openalex.org/keywords/senescence-associated-secretory-phenotype","display_name":"senescence-associated secretory phenotype","score":0.9629999995231628},{"id":"https://openalex.org/keywords/neuroinflammation","display_name":"neuroinflammation","score":0.7289999723434448},{"id":"https://openalex.org/keywords/secretome","display_name":"secretome","score":0.6179999709129333},{"id":"https://openalex.org/keywords/cell-type-composition","display_name":"cell type composition","score":0.628000020980835},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"transcriptional regulation","score":0.4429999887943268},{"id":"https://openalex.org/keywords/alzheimer-s-disease-risk","display_name":"Alzheimer's disease risk","score":0.7490000128746033},{"id":"https://openalex.org/keywords/aging","display_name":"aging","score":0.37299999594688416}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8195000290870667},{"id":"https://openalex.org/C31695470","wikidata":"https://www.wikidata.org/wiki/Q11293125","display_name":"Organoid","level":2,"score":0.7580000162124634},{"id":"https://openalex.org/C57089818","wikidata":"https://www.wikidata.org/wiki/Q424728","display_name":"Apolipoprotein E","level":3,"score":0.6784999966621399},{"id":"https://openalex.org/C107459253","wikidata":"https://www.wikidata.org/wiki/Q674925","display_name":"Induced pluripotent stem cell","level":4,"score":0.46630001068115234},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.461899995803833},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.4490000009536743},{"id":"https://openalex.org/C522857546","wikidata":"https://www.wikidata.org/wiki/Q2070979","display_name":"Senescence","level":2,"score":0.42820000648498535},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.42660000920295715},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.4034000039100647},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.40049999952316284},{"id":"https://openalex.org/C2777670902","wikidata":"https://www.wikidata.org/wiki/Q492038","display_name":"Human brain","level":2,"score":0.3928000032901764},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.3824999928474426},{"id":"https://openalex.org/C136834591","wikidata":"https://www.wikidata.org/wiki/Q2944097","display_name":"Neural stem cell","level":3,"score":0.35019999742507935},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.34950000047683716},{"id":"https://openalex.org/C2777790613","wikidata":"https://www.wikidata.org/wiki/Q191562","display_name":"Cerebral amyloid angiopathy","level":4,"score":0.29649999737739563},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2921999990940094},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2883000075817108},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.28209999203681946},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.27239999175071716},{"id":"https://openalex.org/C2776925932","wikidata":"https://www.wikidata.org/wiki/Q1755122","display_name":"Neurodegeneration","level":3,"score":0.2605000138282776},{"id":"https://openalex.org/C2781197716","wikidata":"https://www.wikidata.org/wiki/Q864574","display_name":"Biomarker","level":2,"score":0.25920000672340393}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:imagine.imgge.bg.ac.rs:123456789/3412","doi":null,"is_oa":true,"landing_page_url":"https://belbi.bg.ac.rs","pdf_url":null,"source":{"id":"https://openalex.org/S4377196579","display_name":"IMAGINE - Repository of the Institute of molecular genetics and genetic engineering (University of Belgrade)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4068193","host_organization_name":"University of Belgrade","host_organization_lineage":["https://openalex.org/I4068193"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Book of Abstracts: 6th Belgrade Bioinformatics Conference","raw_type":"conferenceObject"}],"best_oa_location":{"id":"pmh:oai:imagine.imgge.bg.ac.rs:123456789/3412","doi":null,"is_oa":true,"landing_page_url":"https://belbi.bg.ac.rs","pdf_url":null,"source":{"id":"https://openalex.org/S4377196579","display_name":"IMAGINE - Repository of the Institute of molecular genetics and genetic engineering (University of Belgrade)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4068193","host_organization_name":"University of Belgrade","host_organization_lineage":["https://openalex.org/I4068193"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Book of Abstracts: 6th Belgrade Bioinformatics Conference","raw_type":"conferenceObject"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.9391000270843506,"display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2981283641","https://openalex.org/W3108195421","https://openalex.org/W3138828571","https://openalex.org/W3095784700","https://openalex.org/W4386033342","https://openalex.org/W3112623395","https://openalex.org/W7161027471","https://openalex.org/W4406050551","https://openalex.org/W7109950692","https://openalex.org/W7213693997"],"abstract_inverted_index":{"Apolipoprotein":[0],"E":[1],"(APOE)":[2],"genotype":[3],"is":[4],"a":[5,14,101,155,259],"major":[6],"determinant":[7],"of":[8,16,22,159],"late-onset":[9],"Alzheimer\u2019s":[10],"disease":[11],"risk":[12,273],"and":[13,63,69,78,95,108,113,134,161,186,198,221,225,246,258,265,281],"modulator":[15],"neural":[17,30],"aging,":[18],"yet":[19],"the":[20,127,183,205],"effects":[21],"APOE":[23,54,147,234],"isoforms":[24,235],"on":[25],"developmental":[26,278],"trajectories":[27,176],"in":[28,44,174,200,262,277],"human":[29,50],"tissue":[31,279],"remain":[32],"incompletely":[33],"understood.":[34],"Here,":[35],"we":[36],"combined":[37],"single-cell":[38,83],"RNA":[39],"sequencing":[40],"with":[41,89,122,140,151,240],"quantitative":[42],"proteomics":[43],"induced":[45],"pluripotent":[46],"stem":[47],"cell-derived":[48],"isogenic":[49],"cerebral":[51],"organoids":[52,153,193],"carrying":[53],"\u03b52/\u03b52,":[55],"\u03b53/\u03b53,":[56],"or":[57],"\u03b54/\u03b54":[58],"alleles":[59],"to":[60,91,99,285],"characterize":[61],"genotype-":[62],"stress-dependent":[64],"remodeling":[65],"across":[66,76,146,218],"cellular,":[67],"transcriptional,":[68],"secretory":[70,250],"axes.":[71],"We":[72],"profiled":[73],"~46,000":[74],"cells":[75],"control":[77],"irradiation-induced":[79],"senescence":[80,226,244,257],"conditions":[81],"using":[82,120],"RNAseq.":[84],"Raw":[85],"counts":[86],"were":[87,118,138],"denoised":[88],"CellBender":[90],"remove":[92],"ambient-RNA":[93],"contamination,":[94],"scVI":[96],"was":[97],"applied":[98],"learn":[100],"latent":[102],"embedding":[103],"while":[104,253],"adjusting":[105,166],"for":[106,167],"stress-related":[107],"technical":[109],"covariates":[110],"before":[111],"clustering":[112],"pseudotime":[114],"trajectory":[115],"analysis.":[116],"Cells":[117],"annotated":[119],"snapseed":[121],"marker":[123],"panels":[124],"adapted":[125],"from":[126],"Human":[128],"Neural":[129],"Organoid":[130],"Cell":[131],"Atlas":[132],"(HNOCA),":[133],"cell-type":[135],"composition":[136,143,280],"differences":[137,173],"tested":[139],"scCODA.":[141],"Cell-type":[142],"differed":[144],"significantly":[145],"genotypes":[148],"at":[149],"baseline,":[150],"APOE4":[152,180,241],"showing":[154],"higher":[156],"relative":[157],"abundance":[158],"glial":[160],"excitatory":[162],"neuronal":[163],"populations.":[164],"After":[165],"these":[168,268],"compositional":[169,207],"differences,":[170],"residual":[171],"genotype-dependent":[172,195],"differentiation":[175],"persisted,":[177],"indicating":[178],"that":[179,271],"affects":[181],"both":[182],"cell":[184],"types":[185],"their":[187],"progression":[188],"through":[189],"development.":[190],"Following":[191],"irradiation,":[192],"exhibited":[194],"transcriptional":[196],"responses":[197],"changes":[199],"inferred":[201],"regulatory":[202],"activity":[203],"beyond":[204],"baseline":[206],"differences.":[208],"In":[209],"parallel,":[210],"data-independent":[211],"acquisition":[212],"mass":[213],"spectrometry":[214],"quantified":[215],">6,500":[216],"proteins":[217],"organoid":[219],"lysates":[220],"secretomes":[222],"under":[223],"basal":[224],"conditions.":[227],"Single-sample":[228],"gene-set":[229],"enrichment":[230],"analysis":[231],"(ssGSEA)":[232],"showed":[233,255],"differentially":[236],"regulated":[237],"aging-associated":[238],"pathways,":[239],"exhibiting":[242],"increased":[243],"signatures":[245],"an":[247],"inflammatory":[248],"senescence-associated":[249],"phenotype":[251],"(SASP),":[252],"APOE2":[254],"reduced":[256],"SASP":[260],"enriched":[261],"antioxidant":[263],"enzymes":[264],"chaperones.":[266],"Together,":[267],"results":[269],"suggest":[270],"APOE4-associated":[272],"biology":[274],"already":[275],"emerges":[276],"stress-response":[282],"programs":[283],"prior":[284],"aging-related":[286],"insults.":[287]},"counts_by_year":[],"updated_date":"2026-10-14T16:39:01.820549","created_date":"2026-08-23T00:00:00"}
