Identification of pyroptosis-related genes and potential drugs in diabetic nephropathy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37480090", "kind": "science-record", "revision": 4, "content_hash": "sha256:1babf468216271ea8772840d86478468ee8403a6fbac377d929d2581b3c23330", "created_at": "2026-11-01T19:02:15Z", "updated_at": "2026-11-01T22:52:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of pyroptosis-related genes and potential drugs in diabetic nephropathy.", "doi": "10.1186/s12967-023-04350-w", "pmid": "37480090", "authors": ["Meng Yan", "Wenwen Li", "Rui Wei", "Shuwen Li", "Yan Liu", "Yuqian Huang", "Yunye Zhang", "Zihao Lu", "Qian Lu"], "journal": "Journal of translational medicine", "year": 2023, "abstract": "BACKGROUND: Diabetic nephropathy (DN) is one of the serious microvascular complications of diabetes mellitus (DM). A growing body of research has demonstrated that the inflammatory state plays a critical role in the incidence and development of DN. Pyroptosis is a new way of programmed cell death, which has the particularity of natural immune inflammation. The inhibition of inflammatory cytokine expression and regulation of pathways related to pyroptosis may be a novel strategy for DN treatment. The aim of this study is to identify pyroptosis-related genes and potential drugs for DN.\nMETHODS: DN differentially expressed pyroptosis-related genes were identified via bioinformatic analysis Gene Expression Omnibus (GEO) dataset GSE96804. Dataset GSE30528 and GSE142025 were downloaded to verify pyroptosis-related differentially expressed genes (DEGs). Least absolute shrinkage and selection operator (LASSO) regression analysis was used to construct a pyroptosis-related gene predictive model. A consensus clustering analysis was performed to identify pyroptosis-related DN subtypes. Subsequently, Gene Set Variation Analysis (GSVA), Gene Ontology (GO) function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted to explore the differences between DN clusters. A protein-protein interaction (PPI) network was used to select hub genes and DGIdb database was utilized to screen potential therapeutic drugs/compounds targeting hub genes.\nRESULTS: A total of 24 differentially expressed pyroptosis-related genes were identified in DN. A 16 gene predictive model was conducted via LASSO regression analysis. According to the expression level of these 16 genes, DN cases were divided into two subtypes, and the subtypes are mainly associated with inflammation, activation of immune response and cell metabolism. In addition, we identified 10 hub genes among these subtypes, and predicted 65 potential DN therapeutics that target key genes.\nCONCLUSION: We identified two pyroptosis-related DN clusters and 65 potential therapeutical agents/compounds for DN, which might shed a light on the treatment of DN.", "claims": [{"id": "claim-method", "statement": "Pyroptosis-related genes that were differentially expressed in GSE96804 dataset were identified using the “limma” R package with P < 0.05 and |logFC| > 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37480090", "locator": "sections[4] \"Identification of differentially expressed pyroptosis-related genes\" paragraph 2", "quote": "Pyroptosis-related genes that were differentially expressed in GSE96804 dataset were identified using the “limma” R package with P < 0.05 and |logFC| > 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA expression data could be download at https://www.ncbi.nlm.nih.gov/geo/ and all data generated during this study are included in this article and its Additional files. All data are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37480090", "locator": "sections[29] \"notes\" paragraph 1", "quote": "The RNA expression data could be download at https://www.ncbi.nlm.nih.gov/geo/ and all data generated during this study are included in this article and its Additional files. All data are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Two pyroptosis-related diabetic nephropathy clusters and 65 potential therapeutic agents or compounds for diabetic nephropathy were identified.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37480090", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "We identified two pyroptosis-related DN clusters and 65 potential therapeutical agents/compounds for DN, which might shed a light on the treatment of DN."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Two pyroptosis-related diabetic nephropathy clusters and 65 potential therapeutic agents or compounds for diabetic nephropathy were identified.", "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:37480090"], "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:GSE142025"], "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:GSE142025"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37480090", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12967-023-04350-w", "sha256": "sha256:e7d2ff1f65aaa23011483c3428045588ab17232bab46b2bc79206e3f356ba6f0", "bytes": 40959, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12967-023-04350-w", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10360355", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE142025", "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=GSE142025", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE142025", "version": null, "note": "The RNA expression data could be download at https://www.ncbi.nlm.nih.gov/geo/ and all data generated during this study are included in this article and its Additional files. All data are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA expression data could be download at https://www.ncbi.nlm.nih.gov/geo/ and all data generated during this study are included in this article and its Additional files. 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All data are available from the corresponding author on reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA expression data could be download at https://www.ncbi.nlm.nih.gov/geo/ and all data generated during this study are included in this article and its Additional files. 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