Characterizing Chemokine Signaling Pathways and Hub Genes in Calcium Oxalate-Induced Kidney Stone Formation: Insights from Rodent Models.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39893356", "kind": "science-record", "revision": 4, "content_hash": "sha256:e0d820d0d27274a4406e88f3a3bd6ce907ad46f7c3c9a0e578c529f7443d7129", "created_at": "2026-11-01T20:30:10Z", "updated_at": "2026-11-01T22:56:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Characterizing Chemokine Signaling Pathways and Hub Genes in Calcium Oxalate-Induced Kidney Stone Formation: Insights from Rodent Models.", "doi": "10.1007/s10528-025-11036-z", "pmid": "39893356", "authors": ["Boqiang Wang", "Zhenkun Tan", "Wusheng She", "Xiang Wang", "Xiaofeng Guan", "Zhiwei Tao", "Fuyou Guo", "Hua Xu", "Yaoliang Deng"], "journal": "Biochemical genetics", "year": 2025, "abstract": "The predominant component of kidney stone is calcium oxalate monohydrate (COM), a fact widely acknowledged. Although rodent models are frequently used to induce calcium oxalate (CaOx) crystallization, further exploration of Randall's plaques (RPs) in these models is still needed. We first selected the GSE89028 and GSE75542 datasets from the Gene Expression Omnibus (GEO) database to identify commonly differentially expressed genes (co-DEGs). Based on co-DEGs, we conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to identify significantly enriched pathways. Additionally, we performed Gene Set Enrichment Analysis (GSEA) to validate the enriched pathways. In order to identify hub genes, we established a network of protein-protein interactions (PPI). Finally, we conducted real-time PCR and Western blot to validate the findings from the bioinformatics analysis. We selected 28 co-DEGs from two datasets. The enrichment analysis using GO, KEGG, and GSEA revealed significant enrichment of chemokine-related signaling pathways. The histogram analysis showed that three chemokine factor-related genes were involved in multiple pathways. We used Cytohubba to confirm the presence of three hub genes. Subsequently, analysis of external datasets and quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot demonstrated significant upregulation of CCL2, CXCL1, and CXCL2 in HK-2 cells following CaOx treatment compared to the control group (p < 0.05). Our study demonstrated that upon stimulation by CaOx, renal tubular epithelial cells release chemokines, including CCL2, CXCL1, and CXCL2. This release of chemokines is accompanied by the activation of signaling pathways such as TNF and IL-17. These findings may provide new directions for future research on Kidney Stone Disease.", "claims": [{"id": "claim-method", "statement": "We utilized the R language's limma package to identify DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39893356", "locator": "sections[5] \"Identification of Co-DEGs\" paragraph 2", "quote": "We utilized the R language's limma package to identify DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available on request from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39893356", "locator": "sections[24] \"Data Availability\" paragraph 2", "quote": "The data that support the findings of this study are available on request from the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We selected 28 co-DEGs from two datasets.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39893356", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We selected 28 co-DEGs from two datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We selected 28 co-DEGs from two datasets.", "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:39893356"], "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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