Identification of Genetic Signature Associated With Aging in Pulmonary Fibrosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34746180", "kind": "science-record", "revision": 5, "content_hash": "sha256:cb060e27644cfb670b7aa206ec0511c7c5b7b6b900e36a55c628057734f0b7f0", "created_at": "2026-11-01T17:36:26Z", "updated_at": "2026-11-01T22:47:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Genetic Signature Associated With Aging in Pulmonary Fibrosis.", "doi": "10.3389/fmed.2021.744239", "pmid": "34746180", "authors": ["Yanjiao Lu", "Jinkun Chen", "Shanshan Wang", "Zhen Tian", "Yan Fan", "Meijia Wang", "Jianping Zhao", "Kun Tang", "Jungang Xie"], "journal": "Frontiers in medicine", "year": 2021, "abstract": "Background: Aging is a strong risk factor and an independent prognostic factor in idiopathic pulmonary fibrosis (IPF). In this study, we aimed to conduct a comprehensive analysis based on gene expression profiles for the role of aging in pulmonary fibrosis. Method: Four datasets (GSE21411, GSE24206, GSE47460, and GSE101286) for patients with clinical IPF and one dataset for bleomycin (BLM)-induced pulmonary fibrosis (BIPF) mouse model (GSE123293) were obtained from Gene Expression Omnibus (GEO). According to different age ranges, both patients with IPF and BIPF mice were divided into young and aged groups. The differently expressed genes (DEGs) were systemically analyzed using Gene Ontology (GO) functional, Kyoto Encyclopedia of Genes and Genomes (KEGG), and hub genes analysis. Finally, we verified the role of age and core genes associated with age in vivo. Results: Via the expression profile comparisons of aged and young patients with IPF, we identified 108 aging-associated DEGs, with 21 upregulated and 87 downregulated. The DEGs were associated with \"response to glucocorticoid,\" \"response to corticosteroid,\" and \"rhythmic process\" in GO biological process (BP). For KEGG analysis, the top three significantly enriched KEGG pathways of the DEGs included \"IL-17 signaling pathway,\" \"Mineral absorption,\" and \"HIF-1-signaling pathway.\" Through the comparisons of aged and young BIPF mice, a total number of 778 aging-associated DEGs were identified, with 453 genes increased and 325 genes decreased. For GO and KEGG analysis, the DEGs were enriched in extracellular matrix (ECM) and collagen metabolism. The common DEGs of patients with IPF and BIPF mice were enriched in the BP category, including \"induction of bacterial agglutination,\" \"hyaluronan biosynthetic process,\" and \"positive regulation of heterotypic cell-cell adhesion.\" We confirmed that aged BIPF mice developed more serious pulmonary fibrosis. Finally, the four aging-associated core genes (Slc2a3, Fga, Hp, and Thbs1) were verified in vivo. Conclusion: This study provides new insights into the impact of aging on pulmonary fibrosis. We also identified four aging-associated core genes (Slc2a3, Fga, Hp, and Thbs1) related to the development of pulmonary fibrosis.", "claims": [{"id": "claim-method", "statement": "A two-way analysis of variance (ANOVA) followed by Tukey's multiple comparison post-test was used.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34746180", "locator": "sections[6] \"Statistical Analysis\" paragraph 2", "quote": "A two-way analysis of variance (ANOVA) followed by Tukey's multiple comparison post-test was used."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34746180", "locator": "sections[13] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We confirmed that aged BIPF mice developed more serious pulmonary fibrosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34746180", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We confirmed that aged BIPF mice developed more serious pulmonary fibrosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We confirmed that aged BIPF mice developed more serious pulmonary fibrosis.", "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:34746180"], "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:GSE101286"], "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:GSE101286"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34746180", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmed.2021.744239", "sha256": "sha256:27e4185793ccff94d6a6fd3159675766331daf272250f998c504575209057e9e", "bytes": 39099, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmed.2021.744239", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8564051", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE101286", "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=GSE101286", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE101286", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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