NeuroD2 Modulates Hippocampal Neuronal Organization and Axon Guidance During Aging.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40579006", "kind": "science-record", "revision": 4, "content_hash": "sha256:2491ea64879a1fe0a69318280681ba85ff94b56fa8eaec39d995bdd5341920c5", "created_at": "2026-11-01T20:30:40Z", "updated_at": "2026-11-01T22:56:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "NeuroD2 Modulates Hippocampal Neuronal Organization and Axon Guidance During Aging.", "doi": "10.21873/invivo.14000", "pmid": "40579006", "authors": ["Merve Beker", "Busenur Bolat", "Bahar Sarikamis Johnson", "Nilufer Ercin", "Rabia Kalkan Cakmak", "Sare B Kaya", "Nail Besli", "Ulkan Celik", "Mustafa C Beker"], "journal": "In vivo (Athens, Greece)", "year": 2025, "abstract": "BACKGROUND/AIM: Biological aging refers to the progressive deterioration of an organism's functions due to accumulated cellular and molecular damage. NeuroD2, a critical transcription factor, plays a crucial role in neuronal development and synaptic maturation. This study investigates the role of NeuroD2 in hippocampal neuron organization, focusing on hilar mossy cells during aging, and employs bioinformatics to identify NeuroD2 targets linked to cellular aging.\nMATERIALS AND METHODS: We used 21 adult C57Bl/6 mice, categorized into three age groups: young (2 months), old (12 months), and very old (24 months). Mice were administered BrdU intraperitoneally for three consecutive days, 10 days before euthanasia. The brains were harvested and analyzed using immunofluorescence, Western blotting, and quantitative real-time PCR to evaluate NeuroD2 expression and associated signaling pathways in hippocampal tissue. Additionally, bioinformatics analysis was performed using two open-access datasets (ProteomeXchange Consortium, Dataset identifier: PXD043352; Gene Expression Omnibus, GEO: GSE67539) and to explore potential interactions between NeuroD2 targets and biological aging components.\nRESULTS: Our results revealed that NeuroD2 expression changed significantly with age and correlated with AKT signaling. Moreover, we identified a potential link between NeuroD2 activity and the AKT pathway, indicating NeuroD2's role in mitigating aging-related stress. Bioinformatics analysis identified 513 down-regulated and 638 up-regulated proteins, with NeuroD2 targets involved in axonal projection showing increased expression in older mice. Contrary to expectations, pathway enrichment analysis highlighted axon guidance molecules rather than oxidative stress markers.\nCONCLUSION: This study underscores NeuroD2's critical role in preserving hippocampal integrity and reveals molecular mechanisms underlying age-related neuronal changes. Our findings provide insights into the role of NeuroD2 in regulating key pathways during healthy aging, potentially mitigating the impacts of aging.", "claims": [{"id": "claim-method", "statement": "Data were expressed as mean±standard deviation (SD) and were analyzed using a one-way ANOVA test in the statistical package SPSS for group comparisons. Following a significant ANOVA result, the least significant difference (LSD) test was applied as a post hoc analysis to determine specific group differences.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40579006", "locator": "sections[2] \"Materials and Methods\" paragraph 12", "quote": "Data were expressed as mean±standard deviation (SD) and were analyzed using a one-way ANOVA test in the statistical package SPSS for group comparisons. Following a significant ANOVA result, the least significant difference (LSD) test was applied as a post hoc analysis to determine specific group differences."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Supplementary data, obtained and reprocessed from these two sources, is available online at Figshare (19).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40579006", "locator": "sections[2] \"Materials and Methods\" paragraph 11", "quote": "Supplementary data, obtained and reprocessed from these two sources, is available online at Figshare (19)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "NeuroD2 expression changed significantly with age and correlated with AKT signaling.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40579006", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Our results revealed that NeuroD2 expression changed significantly with age and correlated with AKT signaling."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "NeuroD2 expression changed significantly with age and correlated with AKT signaling.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40579006"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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Mice were administered BrdU intraperitoneally for thre", "00). Experimental groups. Adult male C57BL/6 mice were used in this study. Only male mice were chos", "BL/6 mice were used in this study. Only male mice were chosen to prevent hormonal controversies. Mi", "ect newly born cells in the hippocampus, the mice were intraperitoneally injected with 100 mg/kg 5’"], "order_basis": "paper_text_order:656", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["The brains were harvested and analyzed using immunofluorescence, Western blotting, and quantitative real-tim", "ded and kept for protein and RNA extraction. Immunofluorescence. Brain tissues were cut in a cryostat (CM305", "arl Zeiss, Oberkochen, Germany). BrdU double immunofluorescence staining. To analyze newly born cells in the", "ronal sections of 20 μm were used for double immunofluorescence staining of BrdU/NeuN and BrdU/GFAP (16). Br"], "order_basis": "paper_text_order:802", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ested and analyzed using immunofluorescence, Western blotting, and quantitative real-time PCR to evaluate", "focal Zeiss LSM 800 microscope (Carl Zeiss). Western blot. From mice that are 2, 12, and 24 months old"], "order_basis": "paper_text_order:822", "id": "assay:3"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["rescence, Western blotting, and quantitative real-time PCR to evaluate NeuroD2 expression and associate", "ic levels of the proteins (16). Quantitative real-time PCR analysis. Dissected hippocampal tissue was u", "by adding 80 μl of nuclease-free water. For real-time PCR, appropriate NeuroD2 forward (5’-GCTACTCCAAG", "l. Then, 1 μl of cDNA samples was added. The real-time PCR reaction was performed under the determined"], "order_basis": "paper_text_order:857", "id": "assay:4"}, {"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["100, and blocked with 10% normal goat serum (NGS) for 1 h. The sections were treated with ant", "(PBS with 0.3% Triton X-100) containing 10% NGS. Slides were incubated with the NeuN antibod", "AP (3656, Cell Signaling Technologies) in 2% NGS containing PBST. On the next day, after wash", "0, Thermo Fisher Scientific) in PBST with 2% NGS. Afterward, the slides underwent washing and"], "order_basis": "paper_text_order:4105", "id": "assay:5"}, {"role": "data_generation", "definition_id": "cell_imaging", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["cation to identify the nuclei. Subsequently, confocal microscopy was used to study the sections (LSM 800, Car", "identify the nuclei. 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