Identification of mitochondria-related genes associated with anesthetics in patients undergoing off-pump coronary artery bypass grafting surgery.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40703433", "kind": "science-record", "revision": 4, "content_hash": "sha256:f9123041237d5ce0632eb8eb772cb9c98baf437986b73228c43a2e320915045b", "created_at": "2026-11-01T20:30:48Z", "updated_at": "2026-11-01T22:56:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of mitochondria-related genes associated with anesthetics in patients undergoing off-pump coronary artery bypass grafting surgery.", "doi": "10.3389/fsurg.2025.1515732", "pmid": "40703433", "authors": ["Yuhu Zhang", "Xinjian Li", "Tingru Sun"], "journal": "Frontiers in surgery", "year": 2025, "abstract": "Background: Anesthetics have been reported to play a protective role in the heart during surgery. This study aimed to identify mitochondrial-related genes (Mito-RGs) involved in sevoflurane- and propofol-induced anesthesia in patients undergoing off-pump coronary artery bypass grafting (OPCABG) surgery.\nMethods: The GSE4386 dataset, which contains atrial samples obtained from patients receiving sevoflurane or propofol during OPCABG, was downloaded from GEO database for differential expression analysis and immune cell infiltration analysis between the pre-operative and post-surgery groups. Furthermore, to model the ischemia-reperfusion injury encountered during cardiac surgery, we established an in vitro hypoxia/reoxygenation (H/R) model and investigated the effects of sevoflurane and propofol on the expression of hub genes in cardiomyocytes subjected to H/R injury.\nResults: In this study, we identified a total of 11 common Mito-RGs that were influenced by sevoflurane and propofol during OPCABG. Furthermore, a PPI network of these genes was constructed using STRING, followed by the application of the MCODE and cytoHubba plug-ins to further identify hub genes within the network. Our analysis revealed that MCL1, RGS2, PPP1R15A, and MAFF may be the hub Mito-RGs associated with anesthetics. In the post-surgery group, the levels of these genes were negatively correlated with pro-inflammatory M1 macrophages. Notably, compared to pre-OPCABG levels, both sevoflurane and propofol significantly upregulated the expressions of these four hub genes in atrial samples following OPCABG. Furthermore, RT-qPCR and western blot analyses validated that both sevoflurane and propofol can upregulate the expression of Maff, Ppp1r15a, Rgs2, and Mcl1 in H9C2 cardiomyocytes following H/R injury.\nConclusion: Collectively, these four genes may be linked to the potential cardioprotective effects of anesthetics during OPCABG, which could facilitate further research into the underlying mechanisms and contribute to the development of a more comprehensive and effective anesthesia protocol.", "claims": [{"id": "claim-method", "statement": "Using the limma package (version 3.56.2) in R language, the expression data were presented as log transformed fold-change (log2FC) (26). Meanwhile, the false discovery rate (FDR, Benjamini-Hochberg method) method was employed to adjust p-values for multiple hypothesis testing.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40703433", "locator": "sections[4] \"Differential expression analysis\" paragraph 2", "quote": "Using the limma package (version 3.56.2) in R language, the expression data were presented as log transformed fold-change (log2FC) (26). Meanwhile, the false discovery rate (FDR, Benjamini-Hochberg method) method was employed to adjust p-values for multiple hypothesis testing."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40703433", "locator": "sections[26] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 11 common mitochondrial-related genes affected by sevoflurane and propofol during OPCABG, with MCL1, RGS2, PPP1R15A, and MAFF identified as the hub genes and experimentally validated as upregulated in H/R-injured cardiomyocytes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40703433", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In this study, we identified a total of 11 common Mito-RGs that were influenced by sevoflurane and propofol during OPCABG."}, {"asset": "source:pmid:40703433", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Our analysis revealed that MCL1, RGS2, PPP1R15A, and MAFF may be the hub Mito-RGs associated with anesthetics."}, {"asset": "source:pmid:40703433", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Furthermore, RT-qPCR and western blot analyses validated that both sevoflurane and propofol can upregulate the expression of Maff, Ppp1r15a, Rgs2, and Mcl1 in H9C2 cardiomyocytes following H/R injury."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study identified 11 common mitochondrial-related genes affected by sevoflurane and propofol during OPCABG, with MCL1, RGS2, PPP1R15A, and MAFF identified as the hub genes and experimentally validated as upregulated in H/R-injured cardiomyocytes.", "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:40703433"], "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:GSE4386"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE4386"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40703433", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fsurg.2025.1515732", "sha256": "sha256:045f63755206f340482b27e95903786e2bb52c06f90f2e13a830dc93df2ec909", "bytes": 41988, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fsurg.2025.1515732", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12283725", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE4386", "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=GSE4386", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE4386", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM99229", "GSM99235", "GSM99239", "GSM99241", "GSM99244", "GSM99246", "GSM99247", "GSM99249", "GSM99252", "GSM99253", "GSM99255", "GSM99257", "GSM99258", "GSM99259", "GSM99261", "GSM99265", "GSM99268", "GSM99271", "GSM99274", "GSM99277", "GSM99280", "GSM99282", "GSM99285", "GSM99287", "GSM99289", "GSM99290", "GSM99291", "GSM99292", "GSM99293", "GSM99294", "GSM99295", "GSM99296", "GSM99298", "GSM99299", "GSM99301", "GSM99302", "GSM99303", "GSM99304", "GSM99305", "GSM99306"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Transcriptomics in cardiac surgery", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE4386 not downloaded", "asset:data:geo:GSE4386 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Using the limma package (version 3.56.2) in R language, the expression data were presented as log transformed fold-change (log2FC) (26). 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Furthermore, RT-qPCR and western blot analyses validated that bot", "al samples following OPCABG. Furthermore, RT-qPCR and western blot analyses validated that bot"], "order_basis": "paper_text_order:1711", "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": 0.93, "evidence": ["s following OPCABG. Furthermore, RT-qPCR and western blot analyses validated that both sevoflurane and"], "order_basis": "paper_text_order:1723", "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": 0.642, "evidence": ["gorithm. Cell culture and treatment The H9C2 rat embryo cardiomyocyte cell line was maintaine"], "order_basis": "paper_text_order:2652", "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": 0.99, "evidence": ["treatment The H9C2 rat embryo cardiomyocyte cell line was maintained in DMEM medium supplemented with 10% fetal b", "larbio) or 25 µmol/L propofol (Solarbio) and cultured in standard conditions for 1 h prior to H/R. 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