Mitophagy and immune cell interaction: insights into pathogenesis and potential targets for necrotizing enterocolitis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40115463", "kind": "science-record", "revision": 4, "content_hash": "sha256:660797d08f1406dad903d38045998437fdddcc70b968291f0ede47ec3f9de229", "created_at": "2026-11-01T20:30:19Z", "updated_at": "2026-11-01T22:56:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Mitophagy and immune cell interaction: insights into pathogenesis and potential targets for necrotizing enterocolitis.", "doi": "10.21037/tp-24-441", "pmid": "40115463", "authors": ["Xinyun Jin", "Wenqiang Sun", "Yihui Li", "Xueping Zhu"], "journal": "Translational pediatrics", "year": 2025, "abstract": "Background: Neonatal necrotizing enterocolitis (NEC) is a fatal disease in early life characterized by an inflammatory response or even necrosis of the bowel wall. NEC is one of the leading causes of preterm infant mortality. The pathogenesis of NEC is intricate and involves mitochondrial damage to intestinal cells and infiltration of immune cells. However, the specific functions of mitophagy and its association with immune cells in NEC remain unclear. The aim of this study was to explore the pivotal roles of mitophagy and the immune microenvironment in NEC and their potential interactions.\nMethods: Microarray data (GSE46619) associated with NEC were obtained from the Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI). Differentially expressed genes (DEGs) were screened by GEO2R. Mitophagy gene data were downloaded from the Pathway Unification database and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Consequently, mitophagy-related differentially expressed genes (MRDEGs) were obtained. To identify hub MRDEGs that are closely associated with NEC, we used CytoHubba, Molecular Complex Detection (MCODE) and Comparative Toxicogenomics Database (CTD) scores. Cytoscape and miRWalk databases were used to predict the transcription factors (TFs) and target microRNAs (miRNAs) of hub MRDEGs, respectively, and a regulatory network was established. The ImmuCellAI was used to analyze the pattern of immune infiltration, and the Spearman correlation was used to investigate the relationship between the hub MRDEGs and the abundance of infiltrating immune cells. Finally, the expression levels of the hub MRDEGs were verified by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting in NEC animal model.\nResults: A total of 14 up-regulated and 22 down-regulated MRDEGs were identified, these genes exhibited enrichment in mitophagy, and inflammation-related pathways. Furthermore, 13 hub MRDEGs closely related to NEC were identified. The increased presence of immune cells such as neutrophils, M1 macrophages, and activated mast cells were observed while adaptive immune cells including B cells and various T-cell subsets exhibited reduced infiltration. Furthermore, up-regulated MRDEGs were positively correlated with the proinflammatory immune cell infiltration, and the down-regulated MRDEGs were positively correlated with the anti-inflammatory immune cell infiltration. In vivo experiments demonstrated that the expressions of four genes Hif-1a, Acsl4, Pck2, and Aifm1 were consistent with the bioinformatics analysis results.\nConclusions: The potential interplay of mitophagy and immune cells is crucial in the onset and progression of NEC. This perspective opens the door for deeper investigations into NEC pathogenesis, presenting a possible target for disease intervention.", "claims": [{"id": "claim-method", "statement": "R package “limma” was used to retrieve DEGs from each microarray. all identified DEGs met P<0.05 and |log2fold change (FC)| ≥1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40115463", "locator": "sections[6] \"Microarray data acquisition and identification of differentially expressed genes (DEGs)\" paragraph 2", "quote": "R package “limma” was used to retrieve DEGs from each microarray. all identified DEGs met P<0.05 and |log2fold change (FC)| ≥1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Available at https://tp.amegroups.com/article/view/10.21037/tp-24-441/dss 10.21037/tp-24-441", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40115463", "locator": "sections[31] \"Data Sharing Statement\" paragraph 2", "quote": "Available at https://tp.amegroups.com/article/view/10.21037/tp-24-441/dss 10.21037/tp-24-441"}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 14 up-regulated and 22 down-regulated MRDEGs were identified, and these genes exhibited enrichment in mitophagy and inflammation-related pathways.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40115463", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 14 up-regulated and 22 down-regulated MRDEGs were identified, these genes exhibited enrichment in mitophagy, and inflammation-related pathways."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 14 up-regulated and 22 down-regulated MRDEGs were identified, and these genes exhibited enrichment in mitophagy and inflammation-related pathways.", "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:40115463"], "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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Methods: Microarray data (GSE46619) associated with NEC were obt"], "order_basis": "paper_text_order:681", "id": "assay:1"}, {"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": ["time polymerase chain reaction (qRT-PCR) and Western blotting in NEC animal model. Results: A total of 14", "AIFM1, and PPARGC1A within the two groups by Western blotting. In agreement with the mRNA results, protein", "hub MRDEGs in two groups. (G) Representative Western blotting picture showing the expression of HIF-1α, AC"], "order_basis": "paper_text_order:1867", "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": ["anti-inflammatory immune cell infiltration. In vivo experiments demonstrated that the expression", "f animals. Six-day-old C57BL/6 neonatal male mice were bought from JOINN Laboratories [Suzhou, Chin", "ith some modifications (10,11). The neonatal mice were randomly divided into the NEC (10 mice) and", "EC group’s modeling conditions were: (I) the mice were exposed to a hypoxic environment (95% N2 + 5"], "order_basis": "paper_text_order:2578", "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": ["R package “limma” was used to retrieve DEGs from each microarray. all identified DEGs met P<0.05 and |log2fold change (FC)| ≥1."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}