Identification of biomarkers associated with clinical severity of chronic obstructive pulmonary disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33354437", "kind": "science-record", "revision": 7, "content_hash": "sha256:d34f411770bb27296031f5f852d704ab09413899ebb1ae3d2facd2e6bd94e6fd", "created_at": "2026-11-01T15:41:20Z", "updated_at": "2026-11-01T22:02:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of biomarkers associated with clinical severity of chronic obstructive pulmonary disease.", "doi": "10.7717/peerj.10513", "pmid": "33354437", "authors": ["Jie Zhang", "Changli Zhu", "Hong Gao", "Xun Liang", "Xiaoqian Fan", "Yulong Zheng", "Song Chen", "Yufeng Wan"], "journal": "PeerJ", "year": 2020, "abstract": "We sought to identify the biomarkers related to the clinical severity of stage I to stage IV chronic obstructive pulmonary disease (COPD). Gene expression profiles from the blood samples of COPD patients at each of the four stages were acquired from the Gene Expression Omnibus Database (GEO, accession number: GSE54837). Genes showing expression changes among the different stages were sorted by soft clustering. We performed functional enrichment, protein-protein interaction (PPI), and miRNA regulatory network analyses for the differentially expressed genes. The biomarkers associated with the clinical classification of COPD were selected from logistic regression models and the relationships between TLR2 and inflammatory factors were verified in clinical blood samples by qPCR and ELISA. Gene clusters demonstrating continuously rising or falling changes in expression (clusters 1, 2, and 7 and clusters 5, 6, and 8, respectively) from stage I to IV were defined as upregulated and downregulated genes, respectively, and further analyzed. The upregulated genes were enriched in functions associated with defense, inflammatory, or immune responses. The downregulated genes were associated with lymphocyte activation and cell activation. TLR2, HMOX1, and CD79A were hub proteins in the integrated network of PPI and miRNA regulatory networks. TLR2 and CD79A were significantly correlated with clinical classifications. TLR2 was closely associated with inflammatory responses during COPD progression. Functions associated with inflammatory and immune responses as well as lymphocyte activation may play important roles in the progression of COPD from stage I to IV. TLR2 and CD79A may serve as potential biomarkers for the clinical severity of COPD. TLR2 and CD79A may also serve as independent biomarkers in the clinical classification in COPD. TLR2 may play an important role in the inflammatory responses of COPD.", "claims": [{"id": "claim-method", "statement": "We analyzed the correlation between TLR2 expression levels and inflammatory factor levels in all detected samples using Pearson Correlation Analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33354437", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "We analyzed the correlation between TLR2 expression levels and inflammatory factor levels in all detected samples using Pearson Correlation Analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:The raw measurements are available in the Supplemental Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33354437", "locator": "sections[27] \"Data Availability\" paragraph 2", "quote": "The following information was supplied regarding data availability:The raw measurements are available in the Supplemental Files."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33354437"], "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:GSE54837"], "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:GSE54837"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33354437", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.10513", "sha256": 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of multivariate logistic regression analysis.", "structure": {"pmcid": "PMC7733647", "section_index": 9, "section_title": "Influencing factors of the clinical grade of COPD", "row_count": 7, "column_count": 3}, "table": {"label": "Table 5", "caption": "Results of multivariate logistic regression analysis.", "rows": [["Factor", "Coefficients", "P value"], ["Age", "0.1069", "0.4220"], ["TLR2", "0.6894", "0.0027**"], ["MMP9", "0.0374", "0.7310"], ["CCR1", "0.0282", "0.8695"], ["CD79A", "−0.1930", "0.0450*"], ["PLCG1", "−0.1267", "0.6488"]], "row_count": 7, "column_count": 3, "numeric_cells": 13, "header_rows": 1, "locator": "section[17]/table-wrap[2]#table-5"}}, {"id": "asset:table:pmid:33354437:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b0a4a77cd04ff2e9321f11c5c23cbe032718a9405d2dbe230137cdf826266d6c", "bytes": 1193, "access": "open", "state": "verified", "reader": "read_table", "reader_status": 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