CXCL10-based gene cluster model serves as a potential diagnostic biomarker for premature ovarian failure.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38107572", "kind": "science-record", "revision": 4, "content_hash": "sha256:72f8fd839ccbcecba03efdf535bfa929d4ef6b7701d60ad095a9d53739394382", "created_at": "2026-11-01T19:03:02Z", "updated_at": "2026-11-01T22:10:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CXCL10-based gene cluster model serves as a potential diagnostic biomarker for premature ovarian failure.", "doi": "10.7717/peerj.16659", "pmid": "38107572", "authors": ["Ying Qin", "Canliang Wen", "Huijiao Wu"], "journal": "PeerJ", "year": 2023, "abstract": "Objective: Premature ovarian failure (POF) is a disease with high clinical heterogeneity. Subsequently, its diagnosis is challenging. CXCL10 which is a small signaling protein involved in immune response and inflammation may have diagnostic potential in detection of premature ovarian insufficiency. Therefore, this study aimed to investigate CXCL10 based diagnostic biomarkers for POF.\nMethods: Transcriptome data for POF was obtained from the Gene Expression Omnibus (GEO) database (GSE39501). Principal component analysis (PCA) assessed CXCL10 expression in patients with POF. The receiver operating characteristic (ROC) curve, analyzed using PlotROC, demonstrated the diagnostic potential of CXCL10 and CXCL10-based models for POF. Differentially expressed genes (DEGs) in the control group of POF were identified using DEbylimma. PlotVenn was used to determine the overlap between the POF-control group and the high-/low-expression CXCL10 groups. QuadrantPlot was employed to detect CXCL10-dysregulated genes in POF. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were conducted on DEGs using RunMulti Group cluster Profiler. A POF model was induced with cisplatin (DDP) using KGN cells. RT-qPCR and Western blot were used to measure the expression of CXCL10, apoptosis-related proteins, and peroxisome proliferator-activated receptor (PPAR) signaling pathway-related proteins in this model, following siRNA-mediated silencing of CXCL10. Flow cytometry was employed to assess the apoptosis of KGN cells after CXCL10 downregulation.\nResults: The expression of CXCL10 is dysregulated in POF, and it shows promising diagnostic potential for POF, as evidenced by an area under the curve value of 1. In POF, we found 3,362 up-regulated and 3,969 down-regulated DEGs compared to healthy controls, while the high- and low-expression groups of POF (comprising samples above and below the median CXCL10 expression) exhibited 1,304 up-regulated and 1,315 down-regulated DEGs. Among these, 786 DEGs consistently displayed dysregulation in POF due to CXCL10 influence. Enrichment analysis indicated that the PPAR signaling pathway was activated by CXCL10 in POF. The CXCL10-based model (including CXCL10, Itga2, and Raf1) holds potential as a diagnostic biomarker for POF. Additionally, in the DDP-induced KGN cell model, interfering with CXCL10 expression promoted the secretion of estradiol, and reduced apoptosis. Furthermore, CXCL10 silencing led to decreased expression levels of PPARβ and long-chain acyl-CoA synthetase 1 compared to the Si-NC group. These results suggest that CXCL10 influences the progression of POF through the PPAR signaling pathway.\nConclusion: The CXCL10-based model, demonstrating perfect diagnostic accuracy for POF and comprising CXCL10, Itga2, and Raf1, holds potential as a valuable diagnostic biomarker. Thus, the expression levels of these genes may collectively provide valuable diagnostic information for POF.", "claims": [{"id": "claim-method", "statement": "ROC analysis was performed to assess the optimum cutoff value, sensitivity, specificity, and AUC with a 95% confidence interval (CI). We utilized Baiyin Cloud to implement RunLASSO for selecting feature genes impacted by CXCL10 in POF with diagnostic potential.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38107572", "locator": "sections[5] \"Receiver operating characteristic (ROC) curve\" paragraph 2", "quote": "ROC analysis was performed to assess the optimum cutoff value, sensitivity, specificity, and AUC with a 95% confidence interval (CI)."}, {"asset": "source:pmid:38107572", "locator": "sections[5] \"Receiver operating characteristic (ROC) curve\" paragraph 3", "quote": "We utilized Baiyin Cloud to implement RunLASSO for selecting feature genes impacted by CXCL10 in POF with diagnostic potential."}], "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:38107572", "locator": "sections[23] \"Additional Information and Declarations\" paragraph 4", "quote": "The following information was supplied regarding data availability:The raw measurements are available in the Supplemental Files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The CXCL10-based model comprising CXCL10, ITGA2, and RAF1 achieved an AUC of 1 for POF diagnosis in the training set.", "kind": "quantitative", "target": {"value": 1.0, "unit": "auc", "tolerance": null, "source": "Finally, the ROC curve (Fig. 5C) demonstrates that the CXCL10-based model possesses excellent diagnostic efficiency (AUC = 1) for POF in the training set, serving as a potential diagnostic biomarker for POF."}, "evidence": [{"asset": "source:pmid:38107572", "locator": "sections[18] \"Diagnostic efficacy of CXCL10-based clinical model\" paragraph 2", "quote": "Finally, the ROC curve (Fig. 5C) demonstrates that the CXCL10-based model possesses excellent diagnostic efficiency (AUC = 1) for POF in the training set, serving as a potential diagnostic biomarker for POF."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The CXCL10-based model comprising CXCL10, ITGA2, and RAF1 achieved an AUC of 1 for POF diagnosis in the training set.", "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:38107572"], "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:GSE39501"], "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:GSE39501"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38107572", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.16659", "sha256": "sha256:c29efcaa7bab55d4bd08a0b07e51a013b59e22c09e007885c6bc71ee50607108", "bytes": 36871, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.16659", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10725173", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE39501", "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=GSE39501", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39501", "version": null, "note": "The following information was supplied regarding data availability:The raw measurements are available in the Supplemental Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:The raw measurements are available in the Supplemental Files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM970248", "GSM970249", "GSM970250", "GSM970251", "GSM970252", "GSM970253", "GSM970254", "GSM970255", "GSM970256"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "6887", "taxon": "Mus musculus", "title": "Genomic profiling of SSCs (spermatogonial stem cells) transplanted recipients (SSCTR), premature ovarian failure (POF) and wild-type (WT) control ovaries.", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE39501 not downloaded", "asset:data:geo:GSE39501 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "Principal component analysis"}}, {"id": "method-3", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 0.8, "band": "high", "quote": "ROC analysis"}}, {"id": "method-4", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "χ2"}}, {"id": "method-5", "family": null, "specific": null, "label": "Receiver operating characteristic (ROC) curve analysis and Least Absolute Shrinkage and Selection Operator (LASSO) regression", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "ROC analysis was performed to assess the optimum cutoff value, sensitivity, specificity, and AUC with a 95% confidence interval (CI). We utilized Baiyin Cloud to implement RunLASSO for selecting feature genes impacted by CXCL10 in POF with diagnostic potential."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "bootstrap_mean_difference", "expected_value": 1.0, "unit": "auc", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE39501"], "resolved_accessions": ["GSE39501"], "statements": ["The following information was supplied regarding data availability:The raw measurements are available in the Supplemental Files."], "basis": "The paper names GSE39501 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:38107572", "data:geo:GSE39501"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE39501"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:02:54Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10600, "completion_tokens": 1333, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38107572", "type": "paper", "label": "pmid:38107572"}, {"id": "source:pmid:38107572", "type": "manuscript", "label": "PMID 38107572 full text"}, {"id": "data:geo:GSE39501", "type": "dataset", "label": "GEO GSE39501"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38107572", "type": "paper", "label": "pmid:38107572"}, {"id": "source:pmid:38107572", "type": "manuscript", "label": "PMID 38107572 full text"}, {"id": "data:geo:GSE39501", "type": "dataset", "label": "GEO GSE39501"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38107572", "type": "extraction", "used": ["source:pmid:38107572"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE39501", "type": "accession_resolution", "used": ["data:geo:GSE39501"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:38107572", "parent_hash": "sha256:f9f87f6605ac05a1063c629ba54daea6a0ab8ddcd5be75f58ecab0b13ee83054", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE39501 licence not read", "asset:data:geo:GSE39501 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["nduced with cisplatin (DDP) using KGN cells. RT-qPCR and Western blot were used to measure the ex", "ced with cisplatin (DDP) using KGN cells. RT-qPCR and Western blot were used to measure the ex"], "order_basis": "paper_text_order:1315", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["cisplatin (DDP) using KGN cells. RT-qPCR and Western blot were used to measure the expression of CXCL1"], "order_basis": "paper_text_order:1327", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["re used to measure the expression of CXCL10, apoptosis-related proteins, and peroxisome proliferato", "0. Flow cytometry was employed to assess the apoptosis of KGN cells after CXCL10 downregulation. Re", "oted the secretion of estradiol, and reduced apoptosis. Furthermore, CXCL10 silencing led to decrea"], "order_basis": "paper_text_order:1387", "id": "assay:3"}, {"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": ["ay-related proteins in this model, following siRNA-mediated silencing of CXCL10. Flow cytometry", "Materials and Methods Cell culture and transfection Human ovarian granulosa cells (KGN cells) we", ", and 80 μg/mL) for 24 or 48 h. The utilized siRNA sequences were as follows: Si-CXCL10, 5′-GCC"], "order_basis": "paper_text_order:1529", "id": "assay:4"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ollowing siRNA-mediated silencing of CXCL10. Flow cytometry was employed to assess the apoptosis of KGN"], "order_basis": "paper_text_order:1565", "id": "assay:5"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["analysis of variance"], "order_basis": "consumes_earlier_output", "id": "assay:6"}]}