NET-Related Gene as Potential Diagnostic Biomarkers for Diabetic Tubulointerstitial Injury.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38766319", "kind": "science-record", "revision": 4, "content_hash": "sha256:8bc4b6edd749689a83217e7882f8ceefd75be1b21aa1d1a59d24566cbd50ef24", "created_at": "2026-11-01T19:20:43Z", "updated_at": "2026-11-01T22:54:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "NET-Related Gene as Potential Diagnostic Biomarkers for Diabetic Tubulointerstitial Injury.", "doi": "10.1155/2024/4815488", "pmid": "38766319", "authors": ["Yufeng Liang", "Jiaqun Lin", "Binsan Huang", "Mengjie Weng", "Tingting Zhen", "Liyan Yang", "Yongping Chen", "Qiu Li", "Jianxin Wan"], "journal": "Journal of diabetes research", "year": 2024, "abstract": "Background: Tubulointerstitial injury plays a pivotal role in the progression of diabetic kidney disease (DKD), yet the link between neutrophil extracellular traps (NETs) and diabetic tubulointerstitial injury is still unclear. Methods: We analyzed microarray data (GSE30122) from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs) associated with DKD's tubulointerstitial injury. Functional and pathway enrichment analyses were conducted to elucidate the involved biological processes (BP) and pathways. Weighted gene coexpression network analysis (WGCNA) identified modules associated with DKD. LASSO regression and random forest selected NET-related characteristic genes (NRGs) related to DKD tubulointerstitial injury. Results: Eight hundred ninety-eight DEGs were identified from the GSE30122 dataset. A significant module associated with diabetic tubulointerstitial injury overlapped with 15 NRGs. The hub genes, CASP1 and LYZ, were identified as potential biomarkers. Functional enrichment linked these genes with immune cell trafficking, metabolic alterations, and inflammatory responses. NRGs negatively correlated with glomerular filtration rate (GFR) in the Neph v5 database. Immunohistochemistry (IHC) validated increased NRGs in DKD tubulointerstitial injury. Conclusion: Our findings suggest that the CASP1 and LYZ genes may serve as potential diagnostic biomarkers for diabetic tubulointerstitial injury. Furthermore, NRGs involved in diabetic tubulointerstitial injury could emerge as prospective targets for the diagnosis and treatment of DKD.", "claims": [{"id": "claim-method", "statement": "The DEGs between renal tubular interstitial tissues of DKD patients and healthy controls were calculated using the R software limma package with adjusted p values of 0.05 and log FC (fold change) greater than 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38766319", "locator": "sections[4] \"2.2. Data Processing and Identification of Differential Expression\" paragraph 2", "quote": "The DEGs between renal tubular interstitial tissues of DKD patients and healthy controls were calculated using the R software limma package with adjusted p values of 0.05 and log FC (fold change) greater than 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38766319", "locator": "sections[26] \"Data Availability Statement\" paragraph 2", "quote": "The data that support the findings of this study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In GSE30122, CASP1 and LYZ were upregulated in DKD tubulointerstitial injury samples and achieved diagnostic AUC values of 0.921 and 0.954, respectively.", "kind": "quantitative", "target": {"value": 0.01, "unit": "p-value", "tolerance": null, "source": "Boxplots showed upregulated CASP1 and LYZ mRNA expression (p < 0.01) in patient samples (Figures 4(a) and 4(b))."}, "evidence": [{"asset": "source:pmid:38766319", "locator": "sections[20] \"3.5. The Diagnostic Efficacy Evaluation and Validation of Feature Genes\" paragraph 2", "quote": "Boxplots showed upregulated CASP1 and LYZ mRNA expression (p < 0.01) in patient samples (Figures 4(a) and 4(b))."}, {"asset": "source:pmid:38766319", "locator": "sections[20] \"3.5. The Diagnostic Efficacy Evaluation and Validation of Feature Genes\" paragraph 2", "quote": "Receiver operating characteristic analysis demonstrated high area under the curve (AUC) values of 0.921 and 0.954 for CASP1 and LYZ, respectively (Figures 4(c) and 4(d)), indicating excellent diagnostic performance."}, {"asset": "source:pmid:38766319", "locator": "sections[20] \"3.5. The Diagnostic Efficacy Evaluation and Validation of Feature Genes\" paragraph 3", "quote": "Evaluating the performance of signature genes within GSE30122."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In GSE30122, CASP1 and LYZ were upregulated in DKD tubulointerstitial injury samples and achieved diagnostic AUC values of 0.921 and 0.954, respectively.", "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:38766319"], "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:GSE30122"], "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:GSE30122"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38766319", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2024/4815488", "sha256": "sha256:c2eeadb06ff08164234cb61df830e8f826b90956f9d6596b7181ecca0ce6d19d", "bytes": 41447, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2024/4815488", "version": null, "note": "Full article fetched from PMC; 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Methods: We analyzed microarray data (GSE30122) from the Gene Expression Omn", "e S2: DEGs identified in the gene expression microarray study. Table S3: GO enrichment analysis of D"], "order_basis": "paper_text_order:296", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ltration rate (GFR) in the Neph v5 database. Immunohistochemistry (IHC) validated increased NRGs in DKD tubulo", "the Neph v5 database. Immunohistochemistry (IHC) validated increased NRGs in DKD tubulointer"], "order_basis": "paper_text_order:1276", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["mal Preparation Seven-week-old male C57BL/6J mice were purchased from Gempharmatech Co., Ltd (Jiang", "Ltd (Jiangsu, China). At 8 weeks of age, the mice were intraperitoneally injected with multiple low"], "order_basis": "paper_text_order:3591", "id": "assay:3"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The DEGs between renal tubular interstitial tissues of DKD patients and healthy controls were calculated using the R software limma package with adjusted p values of 0.05 and log FC (fold change) greater than 1."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}