Exploration of molecular biomarkers in ankylosing spondylitis transcriptomics.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39759509", "kind": "science-record", "revision": 3, "content_hash": "sha256:3f8048258fa2b2676b14ed1ab7d8624f709a1e812ba6ae8a8d41765f8f398fa6", "created_at": "2026-11-01T20:30:05Z", "updated_at": "2026-11-01T22:13:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploration of molecular biomarkers in ankylosing spondylitis transcriptomics.", "doi": "10.3389/fimmu.2024.1480492", "pmid": "39759509", "authors": ["Yuanpiao Ni", "Linrui Zhong", "Yanhui Li", "Zeng Zhang", "Bin Ming", "Yufeng Qing", "Quanbo Zhang"], "journal": "Frontiers in immunology", "year": 2024, "abstract": "Background: Inflammation of the spine and sacroiliac joints is a hallmark of the chronic, progressive inflammatory illness known as ankylosing spondylitis (AS). The insidious onset and non-specific early symptoms of AS often lead to delays in diagnosis and treatment, which may result in the onset of disability. It is therefore imperative to identify new biomarkers.\nMethods: In this study, datasets GSE73754 and GSE25101 were derived from the Gene Expression Omnibus (GEO). Key genes were identified through differential expression analysis and weighted gene co-expression network analysis (WGCNA). A model was then established using LASSO regression, and then it was subjected to the receiver operating characteristic (ROC) curve analysis for evaluation of the diagnostic accuracy of the genes. Subsequently, immune infiltration analysis was conducted to demonstrate the immune infiltration status of the samples and the correlation between key genes and immune infiltration. Finally, the expression levels of key genes in peripheral blood mononuclear cells (PBMCs) and their correlation with clinical indicators were validated via RT-qPCR assay.\nResults: Through WGCNA and differential expression analysis, 6 genes were identified. Ultimately, five key genes (ACSL1, SLC40A1, GZMM, TRIB1, XBP1) were determined using LASSO regression. The area under the ROC curve (AUC) for these genes was greater than 0.7, indicating favorable diagnostic performance. Immune infiltration analysis showed that AS was associated with infiltration levels of various immune cells. RT-qPCR validated that the expression of ACSL1, SLC40A1, GZMM, and XBP1 was consistent with the predictive model, whereas TRIB1 expression was contrary to the predictive model. Clinical correlation analysis of key genes revealed that ACSL1 was positively linked to hsCRP levels, GZMM was negatively linked to, hsCRP levels, and neutrophil absolute values, SLC40A1 was positively linked to ESR, hsCRP levels and neutrophil absolute values, and XBP1 was negatively linked to ESR, hsCRP levels, and neutrophil absolute values.\nConclusion: This study identified key genes that may reveal a potential association between AS and ferroptosis, demonstrating high diagnostic value. Furthermore, the expression levels of these genes in peripheral blood mononuclear cells (PBMCs) are strongly correlated with disease activity. These findings not only suggest potential biomarkers for the diagnosis of AS but also offer important references for exploring new therapeutic targets, highlighting their substantial clinical applicability.", "claims": [{"id": "claim-method", "statement": "Using LASSO regression to simplify the model ( Figures 5B, C ), 5 key genes (ACSL1, SLC40A1, GZMM, TRIB1, and XBP1) were identified.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39759509", "locator": "sections[14] \"Validation of the diagnostic model based on key genes\" paragraph 2", "quote": "Using LASSO regression to simplify the model ( Figures 5B, C ), 5 key genes (ACSL1, SLC40A1, GZMM, TRIB1, and XBP1) were identified."}], "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 authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39759509", "locator": "sections[21] \"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 authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Additionally, the ROC curve analysis showed that the overall AUC of the model was 0.807 ( Figure 6C ), indicating that the core genes have high diagnostic performance.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39759509", "locator": "sections[14] \"Validation of the diagnostic model based on key genes\" paragraph 2", "quote": "Additionally, the ROC curve analysis showed that the overall AUC of the model was 0.807 ( Figure 6C ), indicating that the core genes have high diagnostic performance."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Additionally, the ROC curve analysis showed that the overall AUC of the model was 0.807 ( Figure 6C ), indicating that the core genes have high diagnostic performance.", "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:39759509"], "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:GSE25101"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_mann_whitney", "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:GSE25101"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_mann_whitney"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39759509", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fimmu.2024.1480492", "sha256": "sha256:fcd3972d72f398a11b5c4331a31a3448d6ecce5715ab031ddfe028208cd5538c", "bytes": 46617, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fimmu.2024.1480492", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11695275", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE25101", "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=GSE25101", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25101", "version": null, "note": "The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/supplementary material. 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Further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/supplementary material. 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Results: Through WGCNA and differenti", "infiltration levels of various immune cells. RT-qPCR validated that the expression of ACSL1, SLC4", "th clinical indicators were validated via RT-qPCR assay. Results: Through WGCNA and differenti", "iltration levels of various immune cells. RT-qPCR validated that the expression of ACSL1, SLC4"], "order_basis": "paper_text_order:1170", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Mann-Whitney"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}