Analysis of necroptosis-related prognostic genes and immune infiltration in idiopathic pulmonary fibrosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37051233", "kind": "science-record", "revision": 3, "content_hash": "sha256:c1a4ea7f499448f6f9d3578fbb1db3f7cd0f9c95a59e2b1eb034a93002c659fd", "created_at": "2026-11-01T19:01:42Z", "updated_at": "2026-11-01T22:09:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of necroptosis-related prognostic genes and immune infiltration in idiopathic pulmonary fibrosis.", "doi": "10.3389/fimmu.2023.1119139", "pmid": "37051233", "authors": ["Hongzuo Chen", "Zhenkun Xia", "Bei Qing", "Wei Wang", "Linguo Gu", "Ying Chen", "Juan Wang", "Yunchang Yuan"], "journal": "Frontiers in immunology", "year": 2023, "abstract": "Background: IPF is an undetermined, progressive lung disease. Necroptosis is a type of programmed apoptosis, which involved in the pathogenesis of lung diseases like COPD and ARDS. However, necroptosis in IPF have not been adequately studied. This study aimed to investigate the necroptosis in IPF and the relationship between necroptosis and immune infiltration, to construct a prognostic prediction model of IPF based on necroptosis-related genes.\nMethods: GSE110147 was downloaded from the GEO database and utilized to analyze the expression of necroptosis-related differentially expressed genes (NRDEGs). Then NRDEGs were used to construct protein-protein interaction (PPI) networks in the STRING database, and Cytoscape software was used to identify and visualize hub genes. Necroptosis-related prognosticgenes were explored in GSE70866, and a prognostic prediction model was constructed. The ImmuCellAI algorithm was utilized to analyze the landscape of immune infiltration in GSE110147. The single-cell RNA sequencing dataset GSE122960 was used to explore the association between necroptosis and type II alveolar epithelial cells (AT II) in IPF. The GSE213001 and GSE93606 were used for external validation. The expression of prognostic genes was quantified using RT-qPCRin the IPF A549 cell model, and was further verified by western blotting in the bleomycin-induced pulmonary fibrosis mouse model.\nResults: It was observed that necroptosis-related signaling pathways were abundantly enriched in IPF. 29 NRDEGs were screened, of which 12 showed consistent expression trends in GSE213001. Spearman correlation analysis showed that the expression of NRDEGs was positively correlated with the infiltration of proinflammatory immune cells, and negatively correlated with the infiltration of anti-inflammatory immune cells. NRDEGs, including MLKL, were highly expressed in AT II of fibrotic lung tissue. A necroptosis-related prediction model was constructed based on 4 NRDEGsby the cox stepwise regression. In the validation dataset GSE93606, the prognostic prediction model showed good applicability. The verification results of RT-qPCR and western blotting showed the reliability of most of the conclusions.\nConclusions: This study revealed that necroptosis existed in IPF and might occur in AT II. Necroptosis was associated with immune infiltration, suggesting that necroptosis of AT II might involve in IPF by activating immune infiltration and immune response.", "claims": [{"id": "claim-method", "statement": "Subsequently, the Cox stepwise regression method was used to screen the important genes from hub genes and establish a necroptosis-related prediction model.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37051233", "locator": "sections[8] \"Identification of prognostic hub genes and construction of prediction model\" paragraph 2", "quote": "Subsequently, the Cox stepwise regression method was used to screen the important genes from hub genes and establish a necroptosis-related prediction model."}], "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:37051233", "locator": "sections[23] \"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": "A necroptosis-related prediction model was constructed based on 4 NRDEGs by the cox stepwise regression.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37051233", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A necroptosis-related prediction model was constructed based on 4 NRDEGsby the cox stepwise regression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A necroptosis-related prediction model was constructed based on 4 NRDEGs by the cox stepwise regression.", "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:37051233"], "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:GSE110147"], "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:GSE110147"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37051233", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2023.1119139", "sha256": "sha256:1042c62603374356af07ec7064e7198cf865f85f945d4733dcb2a17155aa66f7", "bytes": 37915, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2023.1119139", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10083386", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE110147", "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=GSE110147", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE110147", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE110147", "GSE70866", "GSE122960", "GSE213001", "GSE93606"], "resolved_accessions": ["GSE110147", "GSE70866", "GSE122960", "GSE213001", "GSE93606"], "statements": ["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."], "basis": "The paper names GSE110147, GSE70866, GSE122960, GSE213001, GSE93606 in GEO and the accession resolves in the repository. 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Necroptosis is a type of programmed apoptosis, which involved in the pathogenesis of lung"], "order_basis": "paper_text_order:160", "id": "assay:1"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ape of immune infiltration in GSE110147. The single-cell RNA sequencing dataset GSE122960 was used to explore the as"], "order_basis": "paper_text_order:1060", "id": "assay:2"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["e infiltration in GSE110147. The single-cell RNA sequencing dataset GSE122960 was used to explore the as"], "order_basis": "paper_text_order:1072", "id": "assay:3"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["genes was quantified using RT-qPCRin the IPF A549 cell model, and was further verified by west"], "order_basis": "paper_text_order:1351", "id": "assay:4"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["A549 cell model, and was further verified by western blotting in the bleomycin-induced pulmonary fibrosis", "ity. The verification results of RT-qPCR and western blotting showed the reliability of most of the conclu"], "order_basis": "paper_text_order:1396", "id": "assay:5"}, {"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": ["in the bleomycin-induced pulmonary fibrosis mouse model. Results: It was observed that necroptosis-r", "in the bleomycin-induced pulmonary fibrosis mouse model. Results: It was observed that necropt"], "order_basis": "paper_text_order:1458", "id": "assay:6"}, {"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": ["d applicability. The verification results of RT-qPCR and western blotting showed the reliability", "pplicability. The verification results of RT-qPCR and western blotting showed the reliability"], "order_basis": "paper_text_order:2197", "id": "assay:7"}, {"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": 0.7, "evidence": ["Spearman correlation"], "order_basis": "consumes_earlier_output", "id": "assay:8"}]}