SOX9 Expression Is Increased in Alzheimer's Disease (AD) and Is Associated With Disease Progression and APOE4 Genotype: A Computational Approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37065298", "kind": "science-record", "revision": 4, "content_hash": "sha256:d0d553a885f0c3c5f0648d01bf61a64228ce7156b47b2373cb57a5507fb3ea2b", "created_at": "2026-11-01T19:01:43Z", "updated_at": "2026-11-01T22:51:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "SOX9 Expression Is Increased in Alzheimer's Disease (AD) and Is Associated With Disease Progression and APOE4 Genotype: A Computational Approach.", "doi": "10.7759/cureus.36129", "pmid": "37065298", "authors": ["Aliaa A Alamoudi"], "journal": "Cureus", "year": 2023, "abstract": "INTRODUCTION: Alzheimer's disease (AD) is a neurodegenerative disease characterized by depositions of amyloid-β protein leading to neuronal loss. Despite our understanding of the disease several gaps remain, including the role of astrocytes and astrocytic genes in the disease development and progression. Recently, some reports have suggested that SOX9 transcription factor (TF), an important mediator of astrocyte differentiation and maturation, might be linked to AD. Using human AD publicly available dataset, we aimed to analyze SOX9 expression and its relation to disease.\nMETHODOLOGY: The AD gene expression data set was obtained from National Center for Bioinformatics-Gene Expression Omnibus (NCBI-GEO). The GSE48350 consisted of mRNA microarray data from 55 normal controls (173 samples) and 26 AD cases (81 samples) obtained, from four brain regions. The SOX9 expression profile and correlations were analyzed using the R2 Genomics Analysis and Visualization platform.\nRESULTS: The SOX9 was significantly upregulated (p<0.001) in AD tissue compared to control cases. The increased expression appeared to be more in the entorhinal cortex (EC) and hippocampus (HC) regions. The SOX9 expression positively correlated with BRAAK stages (p<0.05). Interestingly in AD patients the SOX9 expression was significantly less in APOE3/3 genotypes compared with genotypes containing APOE4 allele. The SOX9 expression negatively correlated with oxidative phosphorylation genes which could suggest a metabolic role for the TF.\nCONCLUSION: From these data we hypothesize that SOX9 acts as a metabolic regulator responding to lipid metabolism disruption associated with APOE4 genotypes. In turn, SOX9 expression could be associated with astrocyte maturation and survival in the disease contributing thus to disease burden and disease progression.", "claims": [{"id": "claim-method", "statement": "R2 platform was used to conduct statistical analysis using t-test or ANOVA when comparing two groups or more than two groups respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37065298", "locator": "sections[2] \"Materials and methods\" paragraph 5", "quote": "R2 platform was used to conduct statistical analysis using t-test or ANOVA when comparing two groups or more than two groups respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The AD gene expression dataset was obtained from National Center for Bioinformatics-Gene Expression Omnibus (NCBI-GEO). The GSE48350 consisted of mRNA microarray data from 55 normal controls (aged 20-99 years) and 26 AD cases (aged 74-99 years) obtained, from four brain regions: entorhinal cortex (EC) HC, post-central gyrus (PCG), and superior frontal gyrus (SFG).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37065298", "locator": "sections[2] \"Materials and methods\" paragraph 3", "quote": "The AD gene expression dataset was obtained from National Center for Bioinformatics-Gene Expression Omnibus (NCBI-GEO). The GSE48350 consisted of mRNA microarray data from 55 normal controls (aged 20-99 years) and 26 AD cases (aged 74-99 years) obtained, from four brain regions: entorhinal cortex (EC) HC, post-central gyrus (PCG), and superior frontal gyrus (SFG)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "SOX9 was significantly upregulated in AD tissue compared to control cases.", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "SOX9 was significantly upregulated (p<0.001) in AD tissue compared to control cases."}, "evidence": [{"asset": "source:pmid:37065298", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "SOX9 was significantly upregulated (p<0.001) in AD tissue compared to control cases."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "SOX9 was significantly upregulated in AD tissue compared to control cases.", "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:37065298"], "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:GSE48350"], "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:GSE48350"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37065298", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7759/cureus.36129", "sha256": "sha256:3e44a35ad3370ab9f65fdf0b3858424098ec5ad94a982e9650f22595d6419269", "bytes": 23731, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7759/cureus.36129", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10100190", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE48350", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48350", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48350", "version": null, "note": "The AD gene expression dataset was obtained from National Center for Bioinformatics-Gene Expression Omnibus (NCBI-GEO). 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