Exploring the common mechanism of vascular dementia and inflammatory bowel disease: a bioinformatics-based study.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38736878", "kind": "science-record", "revision": 4, "content_hash": "sha256:32aafe1d0539ba96af88d2f0098b8eba99826762a70dff6355158bd0235750dd", "created_at": "2026-11-01T19:20:41Z", "updated_at": "2026-11-01T22:54:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the common mechanism of vascular dementia and inflammatory bowel disease: a bioinformatics-based study.", "doi": "10.3389/fimmu.2024.1347415", "pmid": "38736878", "authors": ["Yujiao Wang", "Daojun Xie", "Shijia Ma", "Nan Shao", "Xiaoyan Zhang", "Xie Wang"], "journal": "Frontiers in immunology", "year": 2024, "abstract": "Objective: Emerging evidence has shown that gut diseases can regulate the development and function of the immune, metabolic, and nervous systems through dynamic bidirectional communication on the brain-gut axis. However, the specific mechanism of intestinal diseases and vascular dementia (VD) remains unclear. We designed this study especially, to further clarify the connection between VD and inflammatory bowel disease (IBD) from bioinformatics analyses.\nMethods: We downloaded Gene expression profiles for VD (GSE122063) and IBD (GSE47908, GSE179285) from the Gene Expression Omnibus (GEO) database. Then individual Gene Set Enrichment Analysis (GSEA) was used to confirm the connection between the two diseases respectively. The common differentially expressed genes (coDEGs) were identified, and the STRING database together with Cytoscape software were used to construct protein-protein interaction (PPI) network and core functional modules. We identified the hub genes by using the Cytohubba plugin. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied to identify pathways of coDEGs and hub genes. Subsequently, receiver operating characteristic (ROC) analysis was used to identify the diagnostic ability of these hub genes, and a training dataset was used to verify the expression levels of the hub genes. An alternative single-sample gene set enrichment (ssGSEA) algorithm was used to analyze immune cell infiltration between coDEGs and immune cells. Finally, the correlation between hub genes and immune cells was analyzed.\nResults: We screened 167 coDEGs. The main articles of coDEGs enrichment analysis focused on immune function. 8 shared hub genes were identified, including PTPRC, ITGB2, CYBB, IL1B, TLR2, CASP1, IL10RA, and BTK. The functional categories of hub genes enrichment analysis were mainly involved in the regulation of immune function and neuroinflammatory response. Compared to the healthy controls, abnormal infiltration of immune cells was found in VD and IBD. We also found the correlation between 8 shared hub genes and immune cells.\nConclusions: This study suggests that IBD may be a new risk factor for VD. The 8 hub genes may predict the IBD complicated with VD. Immune-related coDEGS may be related to their association, which requires further research to prove.", "claims": [{"id": "claim-method", "statement": "Based on the bioinformatics analysis tools in Xiantao Academic website, we used the package “limma” by implementing the R software to normalize the data obtained from GEO.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38736878", "locator": "sections[5] \"Differential expression genes identification between VD and UC\" paragraph 2", "quote": "Based on the bioinformatics analysis tools in Xiantao Academic website, we used the package “limma” by implementing the R software to normalize the data obtained from GEO."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original data used in this study are all publicly available. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/ under the accession numbers GSE122063, GSE47908, and GSE479285.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38736878", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "The original data used in this study are all publicly available. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/ under the accession numbers GSE122063, GSE47908, and GSE479285."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 8 shared hub genes—PTPRC, ITGB2, CYBB, IL1B, TLR2, CASP1, IL10RA, and BTK—as potential predictors of IBD complicated with VD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38736878", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "8 shared hub genes were identified, including PTPRC, ITGB2, CYBB, IL1B, TLR2, CASP1, IL10RA, and BTK."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 8 shared hub genes—PTPRC, ITGB2, CYBB, IL1B, TLR2, CASP1, IL10RA, and BTK—as potential predictors of IBD complicated with VD.", "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:38736878"], "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:GSE122063"], "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:GSE122063"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38736878", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2024.1347415", "sha256": "sha256:602f99d1af2cca9489123f2249edd6ce7ed685f1ad871295a646505641023463", "bytes": 74927, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2024.1347415", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11084673", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE122063", "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=GSE122063", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE122063", "version": null, "note": "The original data used in this study are all publicly available. 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