Identification and Validation of Aging-Related Genes in IgA Nephropathy in the Asian Population.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40671964", "kind": "science-record", "revision": 4, "content_hash": "sha256:77edbf055df909c5b03c8786566caf9502f5eb051165805c5d5f0f77547c68e4", "created_at": "2026-11-01T20:30:46Z", "updated_at": "2026-11-01T22:56:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Validation of Aging-Related Genes in IgA Nephropathy in the Asian Population.", "doi": "10.2147/IJGM.S530953", "pmid": "40671964", "authors": ["Jinlian Shu", "He Li", "Hairong Li"], "journal": "International journal of general medicine", "year": 2025, "abstract": "Background: IgA nephropathy (IgAN) is the most common primary glomerulonephritis worldwide. Aging is a major risk factor for progression of IgAN to end-stage renal disease. The purpose of this study was to identify and verify aging-related genes associated with IgAN through bioinformatics analysis.\nMethods: Microarray datasets of GSE93798 and GSE37460 were downloaded from the Gene Expression Omnibus (GEO) database. The aging-related DEGs (AR-DEGs) associated with IgAN were analyzed using R programming software, and then Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed. The PPI network of AR-DEGs was then constructed, and hub genes were ranked using five methods of the cytoHubba plugin in Cytoscape software. CIBERSORT algorithm was used to evaluate immune infiltration and its relationship with hub genes. Next, Nephroseq V5 online platform was used to verify and analyze the mRNA expression patterns of hub genes in IgAN patients and normal controls.\nResults: A total of 372 differentially expressed genes (DEGs) were identified, of which 158 were upregulated and 214 were downregulated. GO and KEGG enrichment analyses mainly focused on regulation of macrophage-derived foam cell differentiation and PI3K-Akt signaling pathway. Based on the results of PPI network analysis, eight hub genes were identified, including AGT, ALB, CD36, EGF, KDR, LPL, MYC, and PPARGC1A. Immune infiltration analysis indicated that CD36 was closely related to immune cell infiltration. Furthermore, the expression levels of these hub genes were validated using the Nephroseq V5 online platform. Further clinical samples confirmed that CD36 was highly expressed in renal tissues of IgAN patients.\nConclusion: These findings provide new insights into potential aging-related genes associated with IgAN, which may contribute to better understanding the pathogenesis of IgAN. CD36 may have diagnostic value for aging-related IgAN.", "claims": [{"id": "claim-method", "statement": "The differentially expressed genes (DEGs) between IgAN and control group in combined GEO datasets were selected using the limma R package. The cut-off criteria was set as adjusted P-value < 0.05 and |logFC| > 0.5 in the combined datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40671964", "locator": "sections[4] \"Identification of Aging-Related Differentially Expressed Genes in IgAN\" paragraph 2", "quote": "The differentially expressed genes (DEGs) between IgAN and control group in combined GEO datasets were selected using the limma R package. The cut-off criteria was set as adjusted P-value < 0.05 and |logFC| > 0.5 in the combined datasets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Summary statistics can be downloaded from the appropriate website (see Materials and methods for details). Further inquiries and requests can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40671964", "locator": "sections[28] \"Data Sharing Statement\" paragraph 2", "quote": "Summary statistics can be downloaded from the appropriate website (see Materials and methods for details). Further inquiries and requests can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 372 differentially expressed genes, including 158 upregulated and 214 downregulated genes, and 20 differentially expressed aging-related genes in IgAN.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "After the microarray results were normalized, totally 372 DEGs involved in IgAN were identified by limma package (adj.p < 0.05, |logFC| > 0.5), of which 158 genes were up-regulated and 214 genes were down-regulated."}, "evidence": [{"asset": "source:pmid:40671964", "locator": "sections[15] \"Identification of DEGs and AR-DEGs in IgAN\" paragraph 2", "quote": "After the microarray results were normalized, totally 372 DEGs involved in IgAN were identified by limma package (adj.p < 0.05, |logFC| > 0.5), of which 158 genes were up-regulated and 214 genes were down-regulated."}, {"asset": "source:pmid:40671964", "locator": "sections[15] \"Identification of DEGs and AR-DEGs in IgAN\" paragraph 2", "quote": "Subsequently, 20 AR-DEGs were obtained by intersection of DEGs involved in IgAN with 355 aging-related genes, namely ABCB1, AGT, AGTR1, ALB, ARG2, C3, CD36, CDKN1A, COL1A1, CX3CR1, EG, GHR, HBB, HLA-DQB1, KDR, LPL, MYC, PPARGC1A, SERPINE1, and TWIST1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 372 differentially expressed genes, including 158 upregulated and 214 downregulated genes, and 20 differentially expressed aging-related genes in IgAN.", "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:40671964"], "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:GSE37460"], "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:GSE37460"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40671964", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/IJGM.S530953", "sha256": "sha256:4e5830137598ffe773f8fd1d7d74c4c223d875cbaa4d3327e66d8ad31105c2e0", "bytes": 57010, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/IJGM.S530953", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12266244", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE37460", "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=GSE37460", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE37460", "version": null, "note": "Summary statistics can be downloaded from the appropriate website (see Materials and methods for details). Further inquiries and requests can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Summary statistics can be downloaded from the appropriate website (see Materials and methods for details). 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Further inquiries and requests can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Summary statistics can be downloaded from the appropriate website (see Materials and methods for details). Further inquiries and requests can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2462533", "GSM2462534", "GSM2462535", "GSM2462536", "GSM2462537", "GSM2462538", "GSM2462539", "GSM2462540", "GSM2462541", "GSM2462542", "GSM2462543", "GSM2462544", "GSM2462545", "GSM2462546", "GSM2462547", "GSM2462548", "GSM2462549", "GSM2462550", "GSM2462551", "GSM2462552", "GSM2462553", "GSM2462554", "GSM2462555", "GSM2462556", "GSM2462557", "GSM2462558", "GSM2462559", "GSM2462560", "GSM2462561", "GSM2462562", "GSM2462563", "GSM2462564", "GSM2462565", "GSM2462566", "GSM2462567", "GSM2462568", "GSM2462569", "GSM2462570", "GSM2462571", "GSM2462572", "GSM2462573", "GSM2462574"], "sample_count": 42, "group_sizes": null, "group_sizes_basis": null, "platform": "22945", "taxon": "Homo sapiens", "title": "Transcriptomic and proteomic profiling reveal insights of mesangial cell function in patients with IgA Nephropathy", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE37460 not downloaded", "asset:data:geo:GSE37460 licence not read", "asset:data:geo:GSE93798 not downloaded", "asset:data:geo:GSE93798 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The differentially expressed genes (DEGs) between IgAN and control group in combined GEO datasets were selected using the limma R package. 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A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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