Bioinformatic analysis of hippocampal histopathology in Alzheimer's disease and the therapeutic effects of active components of traditional Chinese medicine.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39221152", "kind": "science-record", "revision": 4, "content_hash": "sha256:4536b060414e1d3397f68ad4890611a278b90acbf210f72246cb88bf6556d489", "created_at": "2026-11-01T20:29:21Z", "updated_at": "2026-11-01T22:55:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic analysis of hippocampal histopathology in Alzheimer's disease and the therapeutic effects of active components of traditional Chinese medicine.", "doi": "10.3389/fphar.2024.1424803", "pmid": "39221152", "authors": ["Chen Zhiyan", "Zhan Min", "Du Yida", "He Chunying", "Hu Xiaohua", "Li Yutong", "Wang Huan", "Sun Linjuan"], "journal": "Frontiers in pharmacology", "year": 2024, "abstract": "Background and aim: Pathological changes in the central nervous system (CNS) begin before the clinical symptoms of Alzheimer's Disease (AD) manifest, with the hippocampus being one of the first affected structures. Current treatments fail to alter AD progression. Traditional Chinese medicine (TCM) has shown potential in improving AD pathology through multi-target mechanisms. This study investigates pathological changes in AD hippocampal tissue and explores TCM active components that may alleviate these changes.\nMethods: GSE5281 and GSE173955 datasets were downloaded from GEO and normalized to identify differentially expressed genes (DEGs). Key functional modules and hub genes were analyzed using Cytoscape and R. Active TCM components were identified from literature and the Pharmacopoeia of the People's Republic of China. Enrichment analyses were performed on target genes overlapping with DEGs.\nResult: From the datasets, 76 upregulated and 363 downregulated genes were identified. Hub genes included SLAMF, CD34, ELN (upregulated) and ATP5F1B, VDAC1, VDAC2, HSPA8, ATP5F1C, PDHA1, UBB, SNCA, YWHAZ, PGK1 (downregulated). Literature review identified 33 active components from 23 herbal medicines. Target gene enrichment and analysis were performed for six components: dihydroartemisinin, berberine, naringenin, calycosin, echinacoside, and icariside II.\nConclusion: Mitochondrial to synaptic vesicle dysfunction pathways were enriched in downregulated genes. Despite downregulation, UBB and SNCA proteins accumulate in AD brains. TCM studies suggest curcumin and echinacoside may improve hippocampal pathology and cognitive impairment in AD. Further investigation into their mechanisms is needed.", "claims": [{"id": "claim-method", "statement": "After analyzing GSE5281 using the R software “limma” package and GSE173955 using the “DESeq2” package, the DEGs of the two GSE datasets were obtained.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39221152", "locator": "sections[16] \"4.2 Analysis of DEGs\" paragraph 2", "quote": "After analyzing GSE5281 using the R software “limma” package and GSE173955 using the “DESeq2” package, the DEGs of the two GSE datasets were obtained."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39221152", "locator": "sections[31] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The intersection of DEGs from the two GSE datasets resulted in 76 upregulated genes (adjusted P-value <0.05, logFC >0) and 363 downregulated genes (adjusted P -value <0.05, logFC <0).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Taking the intersection of DEGs from the two GSE datasets resulted in 76 upregulated genes (adjusted P-value <0.05, logFC >0) and 363 downregulated genes (adjusted P -value <0.05, logFC <0)."}, "evidence": [{"asset": "source:pmid:39221152", "locator": "sections[16] \"4.2 Analysis of DEGs\" paragraph 2", "quote": "Taking the intersection of DEGs from the two GSE datasets resulted in 76 upregulated genes (adjusted P-value <0.05, logFC >0) and 363 downregulated genes (adjusted P -value <0.05, logFC <0)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The intersection of DEGs from the two GSE datasets resulted in 76 upregulated genes (adjusted P-value <0.05, logFC >0) and 363 downregulated genes (adjusted P -value <0.05, logFC <0).", "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:39221152"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE173955"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE173955"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39221152", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fphar.2024.1424803", "sha256": 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