{"doi":"10.1101/2020.10.28.359422","title":"<i>APOE</i> <sup>ε3/ε4</sup> and <i>APOE</i> <sup>ε4/ε4</sup> genotypes drive unique gene signatures in the cortex of young mice","abstract":"Abstract Background Restrictions on mouse models have significantly impacted research towards understanding the most common genotype contributing to dementia in the human population – APOE ε3/ε4 . To address this, as part of MODEL-AD, we created new versions of humanized APOE ε4 and APOE ε3 mice on a C57BL/6J background that allow for unrestricted distribution and breeding. Methods To determine similarities and differences between APOE ε3/ε4 and APOE ε4/ε4 risk genotypes, we analyzed peripheral lipid concentrations as well as performed unbiased transcriptional profiling of the cortex at two and four months of age, comparing APOE ε3/ε4 and APOE ε4/ε4 to the reference APOE ε3/ε3 . To further compare APOE genotypes, cohorts of APOE ε3/ε3 , APOE ε3/ε4 , and APOE ε4/ε4 mice were exercised by voluntary running from 1 month to 4 months of age. Results Cholesterol composition was significantly influenced by APOE genotype as early as 2 months, while triglycerides were affected by APOE genotype at 4 months. Importantly, RNA-sequencing of the cortex followed by linear modeling or weighted gene co-expression network analysis (WGCNA) revealed that the APOE ε3/ε4 genotype showed unique transcriptomic signatures to that of APOE ε4/ε4 . Functional enrichment of the APOE ε3/ε4 , but not APOE ε3/ε4 genotype, revealed sulfur and heparin binding as significant terms at 2 months, and extracellular matrix and blood coagulation at 4 months. Further, cell specific contributions of significant genes identified endothelial cells as overrepresented in the APOE ε3/ε4 but not APOE ε4/ε4 genotype. WGCNA analysis confirmed findings from linear modeling but also predicted that running at a young age affects myelination and gliogenesis across APOE genotypes. Conclusions In summary, APOE ε3/ε4 genotype-specific effects were observed in cortical transcriptional profiles, suggesting therapies aimed at modifying APOE biology to treat dementias may need to be targeted to specific APOE genotypes.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2020,"id":124158,"datarank":0.23907150234691338,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.03112734817892977,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.03112734817892977,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8944,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":315764,"name":"Dylan Garceau","orcid":null,"position":1,"is_corresponding":false},{"id":313609,"name":"Kevin P. Kotredes","orcid":"0000-0001-7874-4139","position":2,"is_corresponding":false},{"id":232931,"name":"Gregory W. Carter","orcid":"0000-0002-2834-8186","position":3,"is_corresponding":false},{"id":313610,"name":"Michael Sasner","orcid":"0000-0002-6612-6111","position":4,"is_corresponding":false},{"id":232918,"name":"Gareth R. Howell","orcid":"0000-0003-0565-6474","position":5,"is_corresponding":false},{"id":568473,"name":"Kate E. Foley","orcid":"0000-0001-5110-238X","position":0,"is_corresponding":true}],"reference_count":52,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T23:15:07.789881Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}