Identification of key biomarkers of endothelial dysfunction in hypertension with carotid atherosclerosis based on WGCNA and the LASSO algorithm.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38984304", "kind": "science-record", "revision": 3, "content_hash": "sha256:ef689c011543384dd11ba61dfd8411369a2d99b1a2af07ee66e70850081b3327", "created_at": "2026-11-01T20:29:03Z", "updated_at": "2026-11-01T22:12:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key biomarkers of endothelial dysfunction in hypertension with carotid atherosclerosis based on WGCNA and the LASSO algorithm.", "doi": "10.1016/j.heliyon.2024.e32966", "pmid": "38984304", "authors": ["Yimin Wang", "Xinyang Shou", "Yuteng Wu", "Jun Chen", "Rui Zeng", "Qiang Liu"], "journal": "Heliyon", "year": 2024, "abstract": "Background: Endothelial dysfunction is the early stage of carotid atherosclerosis (CAS) in patients with hypertension. It is worth identifying the potential hub genes of endothelial dysfunction to elucidate pathological mechanism in the progression of the disease.\nMethod: We obtained gene expression profiles of GSE43292 from the Gene Expression Omnibus (GEO) database. Hub genes associated with CAS were identified through weighted gene correlation network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to explore potential biological mechanisms and signaling pathways. Finally, in vitro experiments on human umbilical vein endothelial cells (HUVECs) were conducted to validate these hub genes.\nResults: The microarray dataset GSE43292 included 32 CAS plaques samples and corresponding macroscopically intact tissues from patients with hypertension. A total of 161 differentially expressed genes were discovered. Through WGCNA analysis, the gray60 module emerged as the most significant module associated with clinical features. The GO and KEGG enrichment analyses of genes in the gray60 module highlighted the substantial involvement of immune response-related signaling pathways. Two key hub genes (CCR1 and NCKAP1L) were pinpointed via LASSO regression. We found a significant increase in the mRNA expression level of the hub genes in oxidized low density lipoprotein (ox-LDL) treated HUVECs.\nConclusions: Our study indicated that the hub genes related to immune responses are involved in the development of CAS. Two hub genes (CCR1 and NCKAP1L) of endothelial dysfunction were identified. These genes may provide a valuable therapeutic target of CAS in patients with hypertension.", "claims": [{"id": "claim-method", "statement": "Hub genes associated with CAS were identified through weighted gene correlation network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38984304", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Hub genes associated with CAS were identified through weighted gene correlation network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data for our study were sourced from the publicly available GEO database, and the processing methods along with the resulting data were detailed in the manuscript materials section and figures.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38984304", "locator": "sections[20] \"Data availability statement\" paragraph 2", "quote": "All the data for our study were sourced from the publicly available GEO database, and the processing methods along with the resulting data were detailed in the manuscript materials section and figures."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Two key hub genes (CCR1 and NCKAP1L) were pinpointed via LASSO regression.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38984304", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Two key hub genes (CCR1 and NCKAP1L) were pinpointed via LASSO regression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Two key hub genes (CCR1 and NCKAP1L) were pinpointed via LASSO regression.", "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:38984304"], "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:GSE43292"], "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:GSE43292"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38984304", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e32966", "sha256": "sha256:fd8aa9dbfa7ccf3798a1dbb00780ec9f7ae639164c833350a108e98dbf3051e9", "bytes": 31658, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2024.e32966", "version": null, "note": "Full article fetched from PMC; 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