Targeting MSR1 to Facilitate Efferocytosis: A Novel Strategy for Immune Homeostasis Regulation in Irreversible Pulpitis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41138691", "kind": "science-record", "revision": 2, "content_hash": "sha256:836ad38fcb6a6a51487051b07ff3f5dfbe01b55e55a12438b8a7630f040b8db8", "created_at": "2026-11-01T20:31:11Z", "updated_at": "2026-11-01T21:35:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Targeting MSR1 to Facilitate Efferocytosis: A Novel Strategy for Immune Homeostasis Regulation in Irreversible Pulpitis.", "doi": "10.1016/j.identj.2025.103968", "pmid": "41138691", "authors": ["Sitong Liu", "Longrui Dang", "Xiaolan Guo", "Kailun Wu", "Xiaofei Qu", "Jing Xu", "Buling Wu", "Zhao Chen"], "journal": "International dental journal", "year": 2025, "abstract": "AIM: To investigate the role of macrophage-mediated efferocytosis in resolution of inflammation during irreversible pulpitis, with a focus on the functional relevance of macrophage scavenger receptor 1 (MSR1).\nMETHODS: Whole-transcriptome sequencing was performed on pulp tissue from 3 healthy individuals and 3 with pulpitis, integrated with Gene Expression Omnibus (GEO) datasets (GSE77459, GSE92681; total n = 30). After batch correction, differentially expressed genes (DEGs) were identified (|Fold Change|>1.5, P < .05) and analyzed by Gene Ontology (GO) / Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, CIBERSORT immune cell deconvolution, and machine learning. Efferocytosis activity was validated by immunofluorescence, Quantitative real-time polymerase chain reaction (qRT-PCR), and Western blot (WB). MSR1 was selected for in vivo validation via small interfering RNA (siRNA) knockdown in a rat pulpitis model.\nRESULTS: A total of 467 differentially expressed genes were identified, which were enriched in immune response and phagosome-related pathways. Macrophage infiltration was significantly increased in pulpitis tissues, accompanied by upregulation of efferocytosis markers. Immunofluorescence showed that MER proto-oncogene tyrosine kinase (MERTK)-positive macrophages in human inflammatory dental pulp could phagocytize apoptotic cells positive for caspase 3 (CASP3) and poly(ADP-ribose) polymerase (PARP). MSR1 is regarded as a key regulatory factor. Knockdown of Msr1 in rats can impair the clearance of apoptotic cells, reduce the expression of Mertk, and aggravate inflammation.\nCONCLUSION: MSR1 maintains immune homeostasis in the dental pulp by promoting macrophage efferocytosis, providing a theoretical basis for targeted vital pulp therapy.", "claims": [{"id": "claim-method", "statement": "Batch effects were corrected using the SVA algorithm, and PCA plots were generated to visualize batch correction (Figure 2A-B).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41138691", "locator": "sections[18] \"Identification of differentially expressed genes in pulpitis tissues\" paragraph 3", "quote": "Batch effects were corrected using the SVA algorithm, and PCA plots were generated to visualize batch correction (Figure 2A-B)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available in Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/, reference numbers GSE77459 and GSE92681. These data were derived from the following resources available in the public domain: GSE77459 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77459) and GSE92681 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92681).\n\nThe data that support the findings of this study are openly available in NCBI SRA at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1140404, reference number PRJNA1140404.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41138691", "locator": "sections[28] \"Data availability\" paragraphs 1-3", "quote": "The data that support the findings of this study are available in Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/, reference numbers GSE77459 and GSE92681. These data were derived from the following resources available in the public domain: GSE77459 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77459) and GSE92681 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92681).\n\nThe data that support the findings of this study are openly available in NCBI SRA at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1140404, reference number PRJNA1140404."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 467 differentially expressed genes were identified, which were enriched in immune response and phagosome-related pathways.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41138691", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 467 differentially expressed genes were identified, which were enriched in immune response and phagosome-related pathways."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 467 differentially expressed genes were identified, which were enriched in immune response and phagosome-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:41138691"], "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:GSE77459"], "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:GSE77459"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41138691", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.identj.2025.103968", "sha256": "sha256:f9fa2371602f802cc208f4645deafb57132997fac92f7ce43db6cf3c407d2336", "bytes": 56658, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.identj.2025.103968", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12593554", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE77459", "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=GSE77459", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE77459", "version": null, "note": "The data that support the findings of this study are available in Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/, reference numbers GSE77459 and GSE92681. 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These data were derived from the following resources available in the public domain: GSE77459 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77459) and GSE92681 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92681).\n\nThe data that support the findings of this study are openly available in NCBI SRA at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1140404, reference number PRJNA1140404.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2052371", "GSM2052372", "GSM2052373", "GSM2052374", "GSM2052375", "GSM2052376", "GSM2052377", "GSM2052378", "GSM2052379", "GSM2052380", "GSM2052381", "GSM2052382"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "17692", "taxon": "Homo sapiens", "title": "Gene Expression Profile of Pulpitis", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE92681", "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=GSE92681", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE92681", "version": null, "note": "The data that support the findings of this study are available in Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/, reference numbers GSE77459 and GSE92681. These data were derived from the following resources available in the public domain: GSE77459 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77459) and GSE92681 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92681).\n\nThe data that support the findings of this study are openly available in NCBI SRA at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1140404, reference number PRJNA1140404.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available in Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/, reference numbers GSE77459 and GSE92681. These data were derived from the following resources available in the public domain: GSE77459 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77459) and GSE92681 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92681).\n\nThe data that support the findings of this study are openly available in NCBI SRA at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1140404, reference number PRJNA1140404.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2434473", "GSM2434474", "GSM2434475", "GSM2434476", "GSM2434477", "GSM2434478", "GSM2434479", "GSM2434480", "GSM2434481", "GSM2434482", "GSM2434483", "GSM2434484"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "16956", "taxon": "Homo sapiens", "title": "Differential Expression of LncRNAs and mRNAs in normal and inflamed human pulp", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:PRJNA1140404", "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=PRJNA1140404", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PRJNA1140404", "version": null, "note": "The data that support the findings of this study are available in Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/, reference numbers GSE77459 and GSE92681. These data were derived from the following resources available in the public domain: GSE77459 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77459) and GSE92681 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92681).\n\nThe data that support the findings of this study are openly available in NCBI SRA at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1140404, reference number PRJNA1140404.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data that support the findings of this study are available in Gene Expression Omnibus (GEO) at https://www.ncbi.nlm.nih.gov/geo/, reference numbers GSE77459 and GSE92681. 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