Gene expression profile analyses to identify potential biomarkers for myopia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35610360", "kind": "science-record", "revision": 5, "content_hash": "sha256:c05d16afe9eb11beb61fc1fcffb6f8dbf368a8ff6c40ba3e645c63e57bdc3168", "created_at": "2026-11-01T18:14:31Z", "updated_at": "2026-11-01T22:49:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profile analyses to identify potential biomarkers for myopia.", "doi": "10.1038/s41433-022-02013-6", "pmid": "35610360", "authors": ["Yao Ni", "Lili Wang", "Chang Liu", "Zuohong Li", "Jing Yang", "Junwen Zeng"], "journal": "Eye (London, England)", "year": 2023, "abstract": "PURPOSE: Increasing evidence suggests myopia is not a simple refractive error, many other factors might also be involved. Here, we assessed myopic and normal corneas' gene expression profiles to identify possible diagnostic and therapeutic biomarkers for myopia.\nMATERIALS AND METHODS: We obtained the expression profile of ten patients and seven normal control samples from the GSE112155 and GSE151631 datasets based on the Gene Expression Omnibus (GEO) database. We used the \"limma\" R package to determine the differentially expressed genes (DEGs) between myopic and normal corneas. Weighted gene co-expression network analysis (WGCNA) was used to identify critical co-expressed modules related to myopia, and enrichment analyses were used to annotate the function of genes encompassed in the compulsory module. We also validated these findings in two external datasets (GSE24641 and GSE136701).\nRESULTS: We identified that the DEGs were significantly enriched in ultraviolet (UV) response, TNF-α signaling via NFκB, Angiogenesis, Myogenesis pathways, etc. We used 2095 genes to construct the co-expression gene modules and found five interesting modules because the eigengene expression of these modules was significantly differentially expressed between myopic and normal corneas. Notably, the enrichment analysis found that the genes encompassed in lightgreen module were significantly enriched in immune-related pathways. These findings were proved by subsequent analysis based on Xcell software. We found the component of B cells, CD4+ memory T cells, CD8+ central memory T cells, plasmacytoid dendritic cells, T helper 2 (Th2) cells, regulatory T cells (Tregs), etc. were significantly increased in myopic corneas, while CD8+ T cells, CD4+ T central memory cells, natural killer T (NKT) cells, and T helper 1 (Th1) cells were significantly decreased.\nCONCLUSION: Our findings identified some markers that might detect diagnosis and treatment for myopia from cornea aspect. Future studies are warranted to verify the functional role of immune-related pathways in cornea during the pathogenesis or progression of myopia.", "claims": [{"id": "claim-method", "statement": "We used the “limma” R package to determine the differentially expressed genes (DEGs) between myopic and normal corneas.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35610360", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We used the “limma” R package to determine the differentially expressed genes (DEGs) between myopic and normal corneas."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We obtained the expression profile of ten patients and seven normal control samples from the GSE112155 and GSE151631 datasets based on the Gene Expression Omnibus (GEO) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35610360", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We obtained the expression profile of ten patients and seven normal control samples from the GSE112155 and GSE151631 datasets based on the Gene Expression Omnibus (GEO) database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified differentially expressed genes enriched in UV response, TNF-α signaling via NFκB, angiogenesis, and myogenesis, and found myopic corneas to have altered immune-cell components.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35610360", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified that the DEGs were significantly enriched in ultraviolet (UV) response, TNF-α signaling via NFκB, Angiogenesis, Myogenesis pathways, etc."}, {"asset": "source:pmid:35610360", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We found the component of B cells, CD4+ memory T cells, CD8+ central memory T cells, plasmacytoid dendritic cells, T helper 2 (Th2) cells, regulatory T cells (Tregs), etc. were significantly increased in myopic corneas, while CD8+ T cells, CD4+ T central memory cells, natural killer T (NKT) cells, and T helper 1 (Th1) cells were significantly decreased."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified differentially expressed genes enriched in UV response, TNF-α signaling via NFκB, angiogenesis, and myogenesis, and found myopic corneas to have altered immune-cell components.", "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:35610360"], "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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