Single-cell sequencing reveals an important role of SPP1 and microglial activation in age-related macular degeneration.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38259505", "kind": "science-record", "revision": 3, "content_hash": "sha256:bdc766af37286a8b38beb5a9d02acb97b9fa92cf60292eb53dd3d010cdcb48cc", "created_at": "2026-11-01T19:20:10Z", "updated_at": "2026-11-01T22:11:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Single-cell sequencing reveals an important role of SPP1 and microglial activation in age-related macular degeneration.", "doi": "10.3389/fncel.2023.1322451", "pmid": "38259505", "authors": ["Shizhen Lei", "Mang Hu", "Zhongtao Wei"], "journal": "Frontiers in cellular neuroscience", "year": 2023, "abstract": "Purpose: To investigate the role of senescence-related cytokines (SRCs) in the pathophysiology of age-related macular degeneration (AMD).\nDesign: The whole study is based on single-cell and bulk tissue transcriptomic analysis of the human neuroretinas with or without AMD. The transcriptomic data of human neuroretinas was obtained from Gene-Expression Omnibus (GEO) database.\nMethods: For single-cell transcriptomic analysis, the gene expression matrix goes through quality control (QC) filtering, being normalized, scaled and integrated for downstream analysis. The further analyses were performed using Seurat R package and CellChat R package. After cell type annotation, the expression of phenotype and functional markers of microglia was investigated and cell-cell communication analysis was performed. For bulk tissue transcriptomic analysis, GSE29801 dataset contains the transcriptomic data of human macular neuroretina (n = 118) from control group and AMD patients. The expression of SPP1 in control and AMD subtypes were compared by Student's t-test. In addition, the AMD macular neuroretina were classified into SPP1-low and SPP1-high groups according to the expression level of SPP1. The differentially expressed genes between these two groups were subsequently identified and the pathway enrichment analysis for these genes was further conducted.\nResults: Secreted phosphoprotein 1, as an SRC, was revealed to be highly expressed in microglia of AMD neuroretina and the SPP1-receptor signaling was highly activated in AMD neuroretina. In addition, SPP1 signaling was associated with the pro-inflammatory phenotype and phagocytic state of microglia. SPP1 expression was elevated in macular neuroretina with late dry and wet AMD and the inflammatory pathways were found to be activated in SPP1-high AMD macular neuroretina.\nConclusion: Our findings indicated that SPP1 and microglial activation might play an important role in the pathophysiology of AMD. Therefore, SPP1 might serve as a potential therapeutic target for AMD. More in vitro and in vivo studies are required to confirm the results and the therapeutic effect of SPP1-targeting strategy.", "claims": [{"id": "claim-method", "statement": "The expression of SPP1 in control and AMD subtypes were compared by Student’s t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38259505", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The expression of SPP1 in control and AMD subtypes were compared by Student’s t-test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in this study are included in this article/Supplementary material, further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38259505", "locator": "sections[10] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in this study are included in this article/Supplementary material, further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Secreted phosphoprotein 1, as an SRC, was revealed to be highly expressed in microglia of AMD neuroretina and the SPP1-receptor signaling was highly activated in AMD neuroretina.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38259505", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Secreted phosphoprotein 1, as an SRC, was revealed to be highly expressed in microglia of AMD neuroretina and the SPP1-receptor signaling was highly activated in AMD neuroretina."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Secreted phosphoprotein 1, as an SRC, was revealed to be highly expressed in microglia of AMD neuroretina and the SPP1-receptor signaling was highly activated in AMD neuroretina.", "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:38259505"], "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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