Expression of CCL2, FOS, and JUN May Help to Distinguish Patients With IgA Nephropathy From Healthy Controls.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35464092", "kind": "science-record", "revision": 4, "content_hash": "sha256:4eb5ef79fc975611ad0da3c9aaa9c036892bf4e479de43a360e2c65f932f16ef", "created_at": "2026-11-01T18:14:19Z", "updated_at": "2026-11-01T22:06:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Expression of CCL2, FOS, and JUN May Help to Distinguish Patients With IgA Nephropathy From Healthy Controls.", "doi": "10.3389/fphys.2022.840890", "pmid": "35464092", "authors": ["Xue Zhou", "Ning Wang", "Yuefeng Zhang", "Pei Yu"], "journal": "Frontiers in physiology", "year": 2022, "abstract": "Background: IgA nephropathy (IgAN), the most common type of glomerulonephritis worldwide, can only be diagnosed mainly by renal biopsy owing to lack of effective biomarkers. It is urgent to explore and identify the potential diagnostic biomarkers through assessing the gene expression profiles of patients with IgAN.\nMethods: Two datasets were obtained from the Gene Expression Omnibus (GEO) database, including GSE115857 (55 IgAN, 7 living healthy donors) and GSE35487 (25 IgAN, 6 living healthy donors), then underwent differentially expressed genes (DEGs) and function enrichment analyses utilizing R packages. The common gene list was screened out between DEGs and immune-associated genes by Venn diagram, then performed gene-gene interaction, protein-protein interaction (PPI) and function enrichment analyses. Top three immune-associated hub genes were selected by Maximal Clique Centrality (MCC) method, then the expression and diagnostic value of these hub genes were determined. Consensus clustering algorithm was applied to conduct the unsupervised cluster analysis of the immune-associated hub gene list in IgAN. Finally, the Nephroseq V5 tool was applied to identify the expression level of CCL2, FOS, JUN in kidney diseases, as well as the correlation between CCL2, FOS, JUN expression and renal function in the patients with IgAN.\nResults: A total of 129 DEGs were obtained through comparing IgAN with healthy controls via the GSE115857 and GSE35487 datasets. Then, we screened out 24 immune-associated IgAN DEGs. CCL2, JUN, and FOS were identified as the top three hub genes, and they were all remarkably downregulated in IgAN. More importantly, CCL2, JUN, and FOS had a high accuracy [area under the curve (AUC) reached almost 1] in predicting IgAN, which could easily distinguish between IgAN patients and healthy individuals. Three distinct subgroups of IgAN were determined based on 24 immune-associated DEGs, with significant differences in the expression of CCL2, JUN, and FOS genes. Finally, CCL2, FOS, JUN were manifested a meaningful association with proteinuria, glomerular filtration rate (GFR), and serum creatinine level.\nConclusion: In summary, our study comprehensively uncovers that CCL2, JUN, and FOS may function as promising biomarkers for diagnosis of IgAN.", "claims": [{"id": "claim-method", "statement": "The receiver operating characteristic (ROC) curve was applied to evaluate the diagnostic value of the three hub genes in IgAN, which was plotted via the “pROC” package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35464092", "locator": "sections[9] \"Diagnostic Value Analysis\" paragraph 2", "quote": "The receiver operating characteristic (ROC) curve was applied to evaluate the diagnostic value of the three hub genes in IgAN, which was plotted via the “pROC” package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: Two datasets (GSE115857 and GSE35487) from the Gene Expression Omnibus GEO database (http://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35464092", "locator": "sections[21] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: Two datasets (GSE115857 and GSE35487) from the Gene Expression Omnibus GEO database (http://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "CCL2, JUN, and FOS were remarkably downregulated in IgAN and had high diagnostic accuracy, with their combination reaching an AUC of almost 1 for distinguishing IgAN patients from healthy individuals.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35464092", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "More importantly, CCL2, JUN, and FOS had a high accuracy [area under the curve (AUC) reached almost 1] in predicting IgAN, which could easily distinguish between IgAN patients and healthy individuals."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "CCL2, JUN, and FOS were remarkably downregulated in IgAN and had high diagnostic accuracy, with their combination reaching an AUC of almost 1 for distinguishing IgAN patients from healthy individuals.", "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:35464092"], "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:GSE115857"], "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:GSE115857"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35464092", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fphys.2022.840890", "sha256": "sha256:c3adf005c707762c57f047f28600b7fb48cd41a23a5eed9f92b7c985a14af230", "bytes": 28029, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fphys.2022.840890", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9021889", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE115857", "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=GSE115857", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE115857", "version": null, "note": "Publicly available datasets were analyzed in this study. 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