Identifying Immune Cell Infiltration and Hub Genes During the Myocardial Remodeling Process After Myocardial Infarction.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37456781", "kind": "science-record", "revision": 5, "content_hash": "sha256:3f0102768e1c0163a87a3a07b38aeda456a3f37c5f33a6a28f9b68ef42835c20", "created_at": "2026-11-01T19:02:13Z", "updated_at": "2026-11-01T22:52:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying Immune Cell Infiltration and Hub Genes During the Myocardial Remodeling Process After Myocardial Infarction.", "doi": "10.2147/JIR.S416914", "pmid": "37456781", "authors": ["Yuan Tian", "Zilin Wang", "Feng Liang", "Yi Wang"], "journal": "Journal of inflammation research", "year": 2023, "abstract": "Purpose: Myocardial remodeling after myocardial infarction (MI) is a complex repair process following myocardial injury, characterized by the infiltration of multiple types of immune cells. However, the underlying molecular mechanism of myocardial remodeling after MI remains obscure. This study aimed to identify the hub differential expression genes (DEGs) of myocardial remodeling after MI and determine the distribution of immune cells infiltrating the pathology.\nMethods: We downloaded GSE132143, GSE151834, and GSE176092 data from the GEO database. The GSE132143 dataset was used to identify DEGs, perform functional annotation, and screen hub genes based on protein-protein interaction (PPI) analysis. The GSE151834 dataset was used to validate the expression of hub genes. CIBERSORTx analysis was performed to explore the immune microenvironment in myocardial remodeling after MI. After conducting a literature review, we selected P3H3 to confirm the expression by utilizing immunohistochemistry and qRT-PCR. Finally, the snRNA-seq data in dataset GSE176092 was used for clarifying the expression of these hub genes in various cell clusters.\nResults: We found 975 DEGs in myocardial remodeling after MI. Four hub genes (P3H3, COL15A1, COL16A1, COL27A1) were identified and were verified in the GSE151834 dataset. According to immune infiltration analysis, CD4+ naive T cells, regulatory T cells, monocytes, M2 macrophages, and neutrophils were involved in the pathological process of myocardial remodeling after MI. Additionally, in vitro experiments verified that P3h3 expression was significantly elevated in myocardial remodeling after MI. The snRNA-seq data analyzed that P3h3, Col15a1, Col16a1, and Col27a1 were highly expressed in fibroblasts of post-MI.\nConclusion: This study identified four hub genes P3H3, COL15A1, COL16A1, and COL27A1, particularly P3H3, as potential targets for targeted therapy in MI patients.", "claims": [{"id": "claim-method", "statement": "Next, DEGs in the post-MI myocardial remodeling were screened by using the “limma” R package21 with cut-off criteria of the false-discovery rate (FDR, Benjamini-Hochberg correction method) < 0.05 and |log fold change (FC)| > 1.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37456781", "locator": "sections[4] \"Processing of the Datasets and DEGs Screening\" paragraph 2", "quote": "Next, DEGs in the post-MI myocardial remodeling were screened by using the “limma” R package21 with cut-off criteria of the false-discovery rate (FDR, Benjamini-Hochberg correction method) < 0.05 and |log fold change (FC)| > 1.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data of bioinformatics analysis (GSE132143, GSE151834, and GSE176092) for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37456781", "locator": "sections[27] \"Data Sharing Statement\" paragraph 2", "quote": "The data of bioinformatics analysis (GSE132143, GSE151834, and GSE176092) for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified four hub genes—P3H3, COL15A1, COL16A1, and COL27A1—as potential targets for post-myocardial-infarction myocardial remodeling, with P3H3 further validated experimentally.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37456781", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "This study identified four hub genes P3H3, COL15A1, COL16A1, and COL27A1, particularly P3H3, as potential targets for targeted therapy in MI patients."}, {"asset": "source:pmid:37456781", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We found 975 DEGs in myocardial remodeling after MI. Four hub genes (P3H3, COL15A1, COL16A1, COL27A1) were identified and were verified in the GSE151834 dataset."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified four hub genes—P3H3, COL15A1, COL16A1, and COL27A1—as potential targets for post-myocardial-infarction myocardial remodeling, with P3H3 further validated experimentally.", "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:37456781"], "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:GSE132143"], "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": {"fdr_threshold": "y expressed genes, with FDR < 0"}, "inputs": ["data:geo:GSE132143"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37456781", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/JIR.S416914", "sha256": "sha256:d5db6e678530d36f245015d0b8f91dec12f41aa12c2ada596a182a52cb7a7673", "bytes": 39219, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/JIR.S416914", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10349602", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE132143", "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=GSE132143", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE132143", "version": null, "note": "The data of bioinformatics analysis (GSE132143, GSE151834, and GSE176092) for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data of bioinformatics analysis (GSE132143, GSE151834, and GSE176092) for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). 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Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4592088", "GSM4592089", "GSM4592090", "GSM4592091", "GSM4592092", "GSM4592093", "GSM4592094", "GSM4592095", "GSM4592096", "GSM4592097", "GSM4592098", "GSM4592099", "GSM4592100", "GSM4592101", "GSM4592102", "GSM4592103", "GSM4592104", "GSM4592105", "GSM4592106", "GSM4592107", "GSM4592108", "GSM4592109", "GSM4592110", "GSM4592111", "GSM4592112", "GSM4592113", "GSM4592114", "GSM4592115", "GSM4592116", "GSM4592117", "GSM4592118", "GSM4592119", "GSM4592120", "GSM4592121", "GSM4592122", "GSM4592123", "GSM4592124", "GSM4592125", "GSM4592126", "GSM4592127"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "21103", "taxon": "Mus musculus", "title": "Type V collagen in scar tissue regulates the size of scar after heart injury", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE176092", "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=GSE176092", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE176092", "version": null, "note": "The data of bioinformatics analysis (GSE132143, GSE151834, and GSE176092) for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/). 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Finally, the snRNA-seq data in", "esentative images and quantification of P3h3 immunohistochemical staining. Magnification 20×, scale bar = 100", "choose to validate the expression of P3h3 by IHC and qRT-PCR analyses. Figure 8A depicts echo"], "order_basis": "paper_text_order:1060", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["onary artery ligation was not performed. 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