Identification of Key Biomarkers Associated with Immunogenic Cell Death and Their Regulatory Mechanisms in Severe Acute Pancreatitis Based on WGCNA and Machine Learning.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36769358", "kind": "science-record", "revision": 2, "content_hash": "sha256:276b6511e1a4407f3e6185b5eeee54fdeb7406c542d0833219aa9a074620dd11", "created_at": "2026-11-01T19:01:21Z", "updated_at": "2026-11-01T21:30:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Biomarkers Associated with Immunogenic Cell Death and Their Regulatory Mechanisms in Severe Acute Pancreatitis Based on WGCNA and Machine Learning.", "doi": "10.3390/ijms24033033", "pmid": "36769358", "authors": ["Zhengjian Wang", "Jin Liu", "Yuting Wang", "Hui Guo", "Fan Li", "Yinan Cao", "Liang Zhao", "Hailong Chen"], "journal": "International journal of molecular sciences", "year": 2023, "abstract": "Immunogenic cell death (ICD) is a form of programmed cell death with a strong sense of inflammatory detection, whose powerful situational awareness can cause the reactivation of aberrant immunity. However, the role of ICD in the pathogenesis of severe acute pancreatitis (SAP) has yet to be investigated. This study aims to explore the pivotal genes associated with ICD in SAP and how they relate to immune infiltration and short-chain fatty acids (SCFAs), in order to provide a theoretical foundation for further, in-depth mechanistic studies. We downloaded GSE194331 datasets from the Gene Expression Omnibus (GEO). The use of differentially expressed gene (DEG) analysis; weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression analysis allowed us to identify a total of three ICD-related hub genes (LY96, BCL2, IFNGR1) in SAP. Furthermore, single sample gene set enrichment analysis (ssGSEA) demonstrated that hub genes are closely associated with the infiltration of specific immune cells, the activation of immune pathways and the metabolism of SCFAs (especially butyrate). These findings were validated through the analysis of gene expression patterns in both clinical patients and rat animal models of SAP. In conclusion, the first concept of ICD in the pathogenesis of SAP was proposed in our study. This has important implications for future investigations into the pro-inflammatory immune mechanisms mediated by damage-associated molecular patterns (DAMPs) in the late stages of SAP.", "claims": [{"id": "claim-method", "statement": "The use of differentially expressed gene (DEG) analysis; weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression analysis allowed us to identify a total of three ICD-related hub genes (LY96, BCL2, IFNGR1) in SAP.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36769358", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The use of differentially expressed gene (DEG) analysis; weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression analysis allowed us to identify a total of three ICD-related hub genes (LY96, BCL2, IFNGR1) in SAP."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36769358", "locator": "sections[30] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The use of differentially expressed gene (DEG) analysis; weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression analysis allowed us to identify a total of three ICD-related hub genes (LY96, BCL2, IFNGR1) in SAP.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36769358", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The use of differentially expressed gene (DEG) analysis; weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression analysis allowed us to identify a total of three ICD-related hub genes (LY96, BCL2, IFNGR1) in SAP."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The use of differentially expressed gene (DEG) analysis; weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression analysis allowed us to identify a total of three ICD-related hub genes (LY96, BCL2, IFNGR1) in SAP.", "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:36769358"], "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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In conclusion, the fir", "mean ± standard error of the mean (SEM), and in vivo validation of clinical and animal specimens", "hub genes in pancreatic tissue using the SAP rat model. HE staining showed diffuse lobular wi", "histochemical plots showing hub genes in SAP rats and controls (original magnification ×100 an"], "order_basis": "paper_text_order:1382", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["in SAP, we collected and extracted PBMCs for RT-qPCR from 20 clinical SAP patients and healthy co", "SAP, we collected and extracted PBMCs for RT-qPCR from 20 clinical SAP patients and healthy co"], "order_basis": "paper_text_order:6116", "id": "assay:2"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["in the pancreas and lung tissue (Figure 9B). ELISA results demonstrated that serum amylase and", "ssional levels of α-amylase, IL-1β, TNF-α by ELISA. (F) Immunohistochemical plots showing hub g"], "order_basis": "paper_text_order:7034", "id": "assay:3"}, {"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": ["els of α-amylase, IL-1β, TNF-α by ELISA. (F) Immunohistochemical plots showing hub genes in SAP rats and cont", "miquantitative results of hub genes based on immunohistochemistry. (G) Immunohistochemical plots showing hub g", "hub genes based on immunohistochemistry. (G) Immunohistochemical plots showing hub genes in SAP rats and cont", "ure 9C–E). Interestingly, the results of the IHC were consistent with those of qRT-PCR, which"], "order_basis": "paper_text_order:7300", "id": "assay:4"}, {"role": "analysis", "definition_id": "correlation_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["spearman_rho"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Spearman rank correlation"], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}