Identification and validation of glomerulotubular crosstalk genes mediating IgA nephropathy by integrated bioinformatics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35418061", "kind": "science-record", "revision": 3, "content_hash": "sha256:1c0c7b973193d299831beda3bcfa9ae1277bf210d8fc170f9a0ef56318a6d51d", "created_at": "2026-11-01T18:14:14Z", "updated_at": "2026-11-01T21:27:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of glomerulotubular crosstalk genes mediating IgA nephropathy by integrated bioinformatics.", "doi": "10.1186/s12882-022-02779-7", "pmid": "35418061", "authors": ["Yawen Bai", "Yajing Li", "Yali Xi", "Chunjie Ma"], "journal": "BMC nephrology", "year": 2022, "abstract": "BACKGROUND: IgA nephropathy (IgAN), which has been reported as the most prevalent glomerulonephritis globally, is the major contributor to end-stage renal diseases. This bioinformatics study aimed to explore glomerulotubular crosstalk genes and dysregulated pathways relating to the pathogenesis of IgAN.\nMETHODS: The microarray datasets from the Gene Expression Omnibus (GEO) database were searched. Weighted gene co-expression network analysis (WGCNA) and differentially expressed genes (DEGs) of both glomeruli and tubulointerstitium were conducted individually. The co-expression gene modules of glomeruli and tubulointerstitium were compared via gene function enrichment analysis. Subsequently, the crosstalk co-expression network was constructed via the STRING database and key genes were mined from the crosstalk network. Finally, key genes were validated using another GEO dataset (GSE99340) containing RNA-seq data of IgAN and lupus nephritis, and their potential diagnostic values were shown using receiver operating characteristic (ROC) analysis.\nRESULTS: Five hundred eighty-three DEGs and eight modules were identified in glomerular samples, while 272 DEGs and four modules were in tubulointerstitial samples. There were 119 overlapping DEGs between the two groups. Among the distinctive modules, four modules in glomeruli and one module in tubulointerstitium were positively associated with IgAN. While four modules in glomeruli and two modules in tubulointerstitium were negatively associated with IgAN. The top ten key genes screened by CytoHubba were ITGAM, ALB, TYROBP, ITGB2, CYBB, HCK, CSF1R, LAPTM5, FN1, and CTSS. Compared with lupus nephritis, there were significant differences in the expression levels of CYBB, CTSS and TYROBP (P < 0.05), while other key genes showed no significant difference. Meanwhile, CYBB, CTSS, and TYROBP demonstrated possible diagnostic significance.\nCONCLUSIONS: The crosstalk genes confirmed in this study may provide novel insight into the pathogenesis of IgAN. Immune-related pathways are associated with both glomerular and tubulointerstitial injuries in IgAN. The glomerulotubular crosstalk might perform a role in the pathogenesis of IgAN.", "claims": [{"id": "claim-method", "statement": "As a bioinformatics approach, WGCNA was utilized to create a scale-free network according to gene expression profiles [13].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35418061", "locator": "sections[6] \"Co-expression gene modules constructing\" paragraph 2", "quote": "As a bioinformatics approach, WGCNA was utilized to create a scale-free network according to gene expression profiles [13]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "These data were derived from the following resources available in the public domain: Gene Expression Omnibus (GEO) database http://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35418061", "locator": "sections[24] \"Availability of data and materials\" paragraph 2", "quote": "These data were derived from the following resources available in the public domain: Gene Expression Omnibus (GEO) database http://www.ncbi.nlm.nih.gov/geo/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Five hundred eighty-three DEGs and eight modules were identified in glomerular samples, while 272 DEGs and four modules were in tubulointerstitial samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35418061", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Five hundred eighty-three DEGs and eight modules were identified in glomerular samples, while 272 DEGs and four modules were in tubulointerstitial samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Five hundred eighty-three DEGs and eight modules were identified in glomerular samples, while 272 DEGs and four modules were in tubulointerstitial samples.", "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:35418061"], "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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