PI3 as a Common Hub Gene Linking Atopic Dermatitis and Ulcerative Colitis Through Immune Cell Recruitment Mechanisms.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40901026", "kind": "science-record", "revision": 4, "content_hash": "sha256:240a60ae57c75f6672f075d1b04f14f7e96c6ddbfe9954cb16f8cc72bdac5385", "created_at": "2026-11-01T20:31:00Z", "updated_at": "2026-11-01T22:57:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PI3 as a Common Hub Gene Linking Atopic Dermatitis and Ulcerative Colitis Through Immune Cell Recruitment Mechanisms.", "doi": "10.2147/JIR.S527507", "pmid": "40901026", "authors": ["Dan Jian", "Jian Chen", "Jinping Yuan", "Kunwar Namrata", "Dan Su", "Bingxue Bai"], "journal": "Journal of inflammation research", "year": 2025, "abstract": "Background: Atopic dermatitis (AD) and ulcerative colitis (UC) are increasingly prevalent, and growing evidence suggests a potential link between them. However, the shared pathogenesis remains unclear. This study aims to identify the hub genes and immunological features underlying the connection between AD and UC.\nMethods: In this study, we downloaded the GSE121212 and GSE75214 datasets from the GEO database. Differentially expressed genes (DEGs) were identified through DESeq2 and limma R packages, revealing enrichment in immune-related pathways such as neutrophil migration and chemokine signaling. Subsequently, weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network analysis were performed to identify common candidate genes. Three machine learning algorithms were employed to select the hub gene, and single-cell RNA sequencing was used to validate the findings.\nResults: Seven common candidate genes (CXCL1, CCL20, CXCL2, ZC3H12A, PI3, CXCL3, LCN2) were identified, showing significant expression differences in both diseases and associations with immune cell infiltration. Among them, PI3 emerged as the hub gene with strong diagnostic potential (AUC > 0.95) based on three machine learning models. Single-cell RNA sequencing supported high PI3 expression in UC intestinal epithelial cells and AD keratinocytes, with correlations to certain CCL and CXCL chemokines. These chemokines play overlapping roles in recruiting M1 macrophages, CD4 T cells, and neutrophils, thereby regulating inflammation in both AD and UC.\nConclusion: Our study uncovers shared immune cell recruitment mechanisms in both diseases, suggesting that CCR1 may serve as a potential common target. Additionally, PI3 is identified as a potential biomarker for both AD and UC, providing new insights into the mechanisms and potential connections between these diseases.", "claims": [{"id": "claim-method", "statement": "Subsequently, we employed |FC|>2 and p-adjust<0.05 as the filtration conditions using the “DESeq2” R package and “limma” R package to isolate the differentially expressed genes (DEGs) in the two datasets independently.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40901026", "locator": "sections[3] \"Data Preprocessing and Differential Expression\" paragraph 2", "quote": "Subsequently, we employed |FC|>2 and p-adjust<0.05 as the filtration conditions using the “DESeq2” R package and “limma” R package to isolate the differentially expressed genes (DEGs) in the two datasets independently."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets used for analysis (GSE121212, GSE75214, GSE16161, GSE87466, GSE214695, GSE197023 and GSE153760) were derived from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) database, a publicly available dataset.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40901026", "locator": "sections[27] \"Data Sharing Statement\" paragraph 2", "quote": "All datasets used for analysis (GSE121212, GSE75214, GSE16161, GSE87466, GSE214695, GSE197023 and GSE153760) were derived from the Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/) database, a publicly available dataset."}], "state": "complete"}, {"id": "claim-target-result", "statement": "PI3 was identified as a shared diagnostic biomarker with an AUC exceeding 0.95 in both atopic dermatitis and ulcerative colitis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40901026", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Among them, PI3 emerged as the hub gene with strong diagnostic potential (AUC > 0.95) based on three machine learning models."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "PI3 was identified as a shared diagnostic biomarker with an AUC exceeding 0.95 in both atopic dermatitis and ulcerative colitis.", "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:40901026"], "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:GSE121212"], "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:GSE121212"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40901026", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/JIR.S527507", "sha256": 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