MicroRNA-125b and chemokine CCL4 expression are associated with calcific aortic valve disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26203686", "kind": "science-record", "revision": 3, "content_hash": "sha256:2e764ef0d2004836903aab5b1a45c132db664f3fdfbd17dbf317d4b5604aaf8d", "created_at": "2026-11-01T15:01:41Z", "updated_at": "2026-11-01T16:36:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "pdf-sci-2026-11-01"}, "paper": {"state": "partial", "title": "MicroRNA-125b and chemokine CCL4 expression are associated with calcific aortic valve disease.", "doi": "10.3109/07853890.2015.1059955", "pmid": "26203686", "authors": null, "journal": "Annals of medicine", "year": 2015, "abstract": "Calcific aortic valve disease (CAVD) is a progressive pathological condition with no effective pharmacological therapy. To identify novel molecular pathways as potential targets for pharmacotherapy, we studied microRNA (miRNA) profiles of heavily stenotic aortic valves (AS). One of the most upregulated miRNAs in AS valves compared to control valves was miR-125b (1.4-fold; P < 0.05). To identify CAVD-related changes in gene expression, DNA microarray analysis was performed, including an intermediate fibro(sclero)tic stage of the disease. This revealed changes especially in genes related to inflammation and immune response, including chemokine (C-C motif) ligand 3 (CCL3) and 4 (CCL4). CCL3 mRNA level was increased 3.9-fold (P < 0.05) when AS valves were compared to control valves, and a 2.5-fold increase (P < 0.05) in CCL4 gene expression was observed when fibro(sclero)tic valves were compared to control valves. Both CCL3 and CCL4 localized to macrophages by immunofluorescence. To identify chemokine-miRNA target pairs, data from miRNA target prediction databases were combined with valvular miRNA and mRNA expression profiles. MiR-125b was computationally predicted to target CCL4, as confirmed experimentally in cultured human THP-1 macrophages. Collectively, miR-125b and CCL4 appear to be involved in the progression of CAVD and may offer novel therapeutic and diagnostic strategies related to this disease.", "claims": [{"id": "claim-method", "statement": "Genes were defined as differentially expressed if the change was at least 2.0-fold and statistically significant (P<0.05, One-way ANOVA and Benjamini and Hochberg false discovery rate).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26203686", "locator": "sections[5] \"DNA microarray analysis\" paragraph 2", "quote": "Genes were defined as differentially expressed if the change was at least 2.0-fold and statistically significant (P<0.05, One-way ANOVA and Benjamini and Hochberg false discovery rate)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "CCL3 mRNA level was increased 3.9-fold (P < 0.05) when AS valves were compared to control valves, and a 2.5-fold increase (P < 0.05) in CCL4 gene expression was observed when fibro(sclero)tic valves were compared to control valves.", "kind": "quantitative", "target": {"value": null, "unit": null, "tolerance": null, "source": "CCL3 mRNA level was increased 3.9-fold (P < 0.05) when AS valves were compared to control valves, and a 2.5-fold increase (P < 0.05) in CCL4 gene expression was observed when fibro(sclero)tic valves were compared to control valves."}, "evidence": [{"asset": "source:pmid:26203686", "locator": "abstract paragraph 1", "quote": "CCL3 mRNA level was increased 3.9-fold (P < 0.05) when AS valves were compared to control valves, and a 2.5-fold increase (P < 0.05) in CCL4 gene expression was observed when fibro(sclero)tic valves were compared to control valves."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The complete data sets are available from the NCBI’s Gene Expression Omnibus (GEO) database and gene expression profiling data comply with the Minimum Information About a Microarray Experiment (MIAME) standard. 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The data can be obtained from the GEO database with the accession numbers GSE51472."}], "state": "complete"}, {"id": "claim-target-ccl3-as-vs-control", "statement": "CCL3 (205114_s_at) was 7.32-fold in aortic stenosis vs control in the DNA microarray analysis.", "kind": "quantitative", "target": {"value": 7.32, "unit": "fold change (aortic stenosis vs control)", "tolerance": null, "source": "205114_s_at Chemokine (C-C motif) ligand 3 NM_002983 7.32"}, "evidence": [{"asset": "source:pmid:26203686", "locator": "sections[18] \"Supplementary Table 5. Differentially expressed genes between aortic stenosis group and\" paragraph 7", "quote": "205114_s_at Chemokine (C-C motif) ligand 3 NM_002983 7.32"}], "state": "complete"}, {"id": "claim-target-ccl4-as-vs-control", "statement": "CCL4 (204103_at) was 3.81-fold in aortic stenosis vs control in the DNA microarray analysis.", "kind": "quantitative", "target": {"value": 3.81, "unit": "fold change (aortic stenosis vs control)", "tolerance": null, "source": "204103_at Chemokine (C-C motif) ligand 4 NM_002984 3.81"}, "evidence": [{"asset": "source:pmid:26203686", "locator": "sections[18] \"Supplementary Table 5. Differentially expressed genes between aortic stenosis group and\" paragraph 7", "quote": "204103_at Chemokine (C-C motif) ligand 4 NM_002984 3.81"}], "state": "complete"}, {"id": "claim-target-ccl3-as-vs-fibro", "statement": "CCL3 (205114_s_at) was 5.66-fold in aortic stenosis vs fibro(sclerosis) in the DNA microarray analysis.", "kind": "quantitative", "target": {"value": 5.66, "unit": "fold change (aortic stenosis vs fibro(sclerosis))", "tolerance": null, "source": "205114_s_at Chemokine (C-C motif) ligand 3 NM_002983 5.66"}, "evidence": [{"asset": "source:pmid:26203686", "locator": "sections[19] \"Supplementary Table 6. Differentially expressed genes between aortic stenosis group and fibro(sclerotic)\" paragraph 5", "quote": "205114_s_at Chemokine (C-C motif) ligand 3 NM_002983 5.66"}], "state": "complete"}, {"id": "claim-target-ccl4-as-vs-fibro", "statement": "CCL4 (204103_at) was 3.03-fold in aortic stenosis vs fibro(sclerosis) in the DNA microarray analysis.", "kind": "quantitative", "target": {"value": 3.03, "unit": "fold change (aortic stenosis vs fibro(sclerosis))", "tolerance": null, "source": "204103_at Chemokine (C-C motif) ligand 4 NM_002984 3.03"}, "evidence": [{"asset": "source:pmid:26203686", "locator": "sections[19] \"Supplementary Table 6. Differentially expressed genes between aortic stenosis group and fibro(sclerotic)\" paragraph 7", "quote": "204103_at Chemokine (C-C motif) ligand 4 NM_002984 3.03"}], "state": "complete"}], "gaps": ["authors"]}, "experiment": {"state": "complete", "objective": "DNA microarray analysis of human aortic valve tissue identified differentially expressed genes in calcific aortic valve disease, using a ≥2-fold change with one-way ANOVA and Benjamini–Hochberg false discovery rate (P<0.05); the data are available in the NCBI GEO database under accession GSE51472, and CCL3 and CCL4 showed reported expression increases of 3.9-fold in aortic stenosis versus control valves and 2.5-fold in fibro(sclero)tic versus control valves, respectively.", "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:26203686"], "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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For miRNA-array and DNA microarray analyses, the samples were matched for all p"], "order_basis": "paper_text_order:493", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["th CCL3 and CCL4 localized to macrophages by immunofluorescence. To identify chemokine-miRNA target pairs, d", "the area of the tissue sections. Factor VIII immunohistochemical staining was used to visualize density of bl", "in aortic valve cusps was also confirmed by immunohistochemical staining. Specific antibodies for CCL3/MIP-1"], "order_basis": "paper_text_order:1021", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["nufacturer’s instructions and verified using qPCR (Supplementary Fig. 4). The cells and cell c", "cell culture supernatants were collected for qPCR and ELISA analyses. In qPCR, the average miR", "re collected for qPCR and ELISA analyses. In qPCR, the average miRNA- 125b expression of cells", "gen, Hilden, Germany). The quantification of real-time quantitative PCR results was done using the ѐѐCT method. Smal"], "order_basis": "paper_text_order:3945", "id": "assay:3"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["Collection (Manassas, VA; cat. TIB-202) and cultured in RPMI 1640 supplemented with 2 mM L- glutamin"], "order_basis": "paper_text_order:4838", "id": "assay:4"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["a- Aldrich, St. Louis, MO) for 24 hours. The transfection mixtures were prepared according to the manu", "UAACUUGUGA) mimics (by Ambion, Austin, USA). Transfection reagent was 1.4% Lipofectamin (Invitrogen) i", "were washed with PBS and incubated with the transfection reagents in THP-1 medium in the presence of", "the average miRNA- 125b expression of cells transfected with miRNA-125b was 170-fold (P<0.001) as co"], "order_basis": "paper_text_order:5182", "id": "assay:5"}, {"role": "data_generation", "definition_id": "elisa", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ure supernatants were collected for qPCR and ELISA analyses. In qPCR, the average miRNA- 125b e", "ed from cell culture media with a commercial ELISA kit (R&D Systems, Minneapolis, MN, USA) acco"], "order_basis": "paper_text_order:6022", "id": "assay:6"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["econdary antibody (Alexa Fluor 594 goat anti-mouse IgG3 (red), 1:100) was incubated for 1 hour", "dary antibodies (Alexa Fluor 488 donkey anti-mouse IgG1 (green) for CCL3 and Alexa Fluor 488 go", "s were carried out by substituting nonimmune mouse or rabbit serum for the primary antibodies.", "s were carried out by substituting nonimmune mouse or goat serum for the primary 9 antibodies."], "order_basis": "paper_text_order:8563", "id": "assay:7"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_comparison_anova", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Genes were defined as differentially expressed if the change was at least 2.0-fold and statistically significant (P<0.05, One-way ANOVA and Benjamini and Hochberg false discovery rate)."], "order_basis": "consumes_earlier_output", "id": "assay:8"}]}