Identification and validation of the diagnostic biomarker MFAP5 for CAVD with type 2 diabetes by bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39749331", "kind": "science-record", "revision": 4, "content_hash": "sha256:92fd89ac79328179c47e005da7883b27b8c711a7a448c217239315bbc8b1f60f", "created_at": "2026-11-01T20:30:05Z", "updated_at": "2026-11-01T22:55:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of the diagnostic biomarker MFAP5 for CAVD with type 2 diabetes by bioinformatics analysis.", "doi": "10.3389/fimmu.2024.1506663", "pmid": "39749331", "authors": ["Qiang Shen", "Lin Fan", "Chen Jiang", "Dingyi Yao", "Xingyu Qian", "Fuqiang Tong", "Zhengfeng Fan", "Zongtao Liu", "Nianguo Dong", "Chao Zhang", "Jiawei Shi"], "journal": "Frontiers in immunology", "year": 2024, "abstract": "Introduction: Calcific aortic valve disease (CAVD) is increasingly prevalent among the aging population, and there is a notable lack of drug therapies. Consequently, identifying novel drug targets will be of utmost importance. Given that type 2 diabetes is an important risk factor for CAVD, we identified key genes associated with diabetes - related CAVD via various bioinformatics methods, which provide further potential molecular targets for CAVD with diabetes.\nMethods: Three transcriptome datasets related to CAVD and two related to diabetes were retrieved from the Gene Expression Omnibus (GEO) database. To distinguish key genes, differential expression analysis with the \"Limma\" package and WGCNA was applied. Machine learning (ML) algorithms were employed to screen potential biomarkers. The receiver operating characteristic curve (ROC) and nomogram were then constructed. The CIBERSORT algorithm was utilized to investigate immune cell infiltration in CAVD. Lastly, the association between the hub genes and 22 types of infiltrating immune cells was evaluated.\nResults: By intersecting the results of the \"Limma\" and WGCNA analyses, 727 and 190 CAVD - related genes identified from the GSE76717 and GSE153555 datasets were obtained. Then, through differential analysis and interaction, 619 genes shared by the two diabetes mellitus datasets were acquired. Next, we intersected the differential genes and module genes of CAVD with the differential genes of diabetes, and the obtained genes were used for subsequent analysis. ML algorithms and the PPI network yielded a total of 12 genes, 10 of which showed a higher diagnostic value. Immune cell infiltration analysis revealed that immune dysregulation was closely linked to CAVD progression. Experimentally, we have verified the gene expression differences of MFAP5, which has the potential to serve as a diagnostic biomarker for CAVD.\nConclusion: In this study, a multi-omics approach was used to identify 10 CAVD-related biomarkers (COL5A1, COL5A2, THBS2, MFAP5, BTG2, COL1A1, COL1A2, MXRA5, LUM, CD34) and to develop an exploratory risk model. Western blot (WB) and immunofluorescence experiments revealed that MFAP5 plays a crucial role in the progression of CAVD in the context of diabetes, offering new insights into the disease mechanism.", "claims": [{"id": "claim-method", "statement": "The R package “limma” was used to detect differentially expressed genes (DEGs) between various subtypes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39749331", "locator": "sections[4] \"Data processing and identification of differentially expressed genes\" paragraph 2", "quote": "The R package “limma” was used to detect differentially expressed genes (DEGs) between various subtypes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author/s.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39749331", "locator": "sections[28] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author/s."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In this study, a multi-omics approach was used to identify 10 CAVD-related biomarkers (COL5A1, COL5A2, THBS2, MFAP5, BTG2, COL1A1, COL1A2, MXRA5, LUM, CD34) and to develop an exploratory risk model.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39749331", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "In this study, a multi-omics approach was used to identify 10 CAVD-related biomarkers (COL5A1, COL5A2, THBS2, MFAP5, BTG2, COL1A1, COL1A2, MXRA5, LUM, CD34) and to develop an exploratory risk model."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In this study, a multi-omics approach was used to identify 10 CAVD-related biomarkers (COL5A1, COL5A2, THBS2, MFAP5, BTG2, COL1A1, COL1A2, MXRA5, LUM, CD34) and to develop an exploratory risk model.", "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:39749331"], "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:GSE148219"], "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:GSE148219"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39749331", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2024.1506663", "sha256": "sha256:eb77915c1518803a6c2ded53ef955f210c31219b9d41f187d32e83bd54c8e6d4", "bytes": 40449, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2024.1506663", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11693595", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE148219", "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=GSE148219", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE148219", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . 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Western blot (WB) and immunofluorescence experiments reve", "n disease. MFAP5 was selected for subsequent Western blot (WB) and immunofluorescence experiments. The", "fied aortic valve tissue. (C) Representative Western blot (WB) analysis and quantification of MFAP5 pr"], "order_basis": "paper_text_order:2186", "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": ["xploratory risk model. Western blot (WB) and immunofluorescence experiments revealed that MFAP5 plays a cruc", "elected for subsequent Western blot (WB) and immunofluorescence experiments. The results of WB and immunoflu", "orescence experiments. The results of WB and immunofluorescence demonstrated that the levels of MFAP5 in the", "ative mRNA levels were detected by qPCR. (B) Immunofluorescence analysis showed increased MFAP5 expression i"], "order_basis": "paper_text_order:2208", "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": ["verified in human aortic valve tissue using qPCR ( Figure 11A ). Compared to normal valve tis", "e. (A) Relative mRNA levels were detected by qPCR. (B) Immunofluorescence analysis showed incr"], "order_basis": "paper_text_order:5403", "id": "assay:3"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The R package “limma” was used to detect differentially expressed genes (DEGs) between various subtypes."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}