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pmid:39951446
miR-455-3p has superior diagnostic potential to PSA in peripheral blood for prostate cancer.
Yi Cen · Shourui Feng · Yuyu Xu · Churuo Zhang · Xiangjin Lin · Xuan Ye · Zeyu Zha · Haiyan Wang · Guangbin Zhu
PloS one · 2025 doi:10.1371/journal.pone.0317385
Paper
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Experiment
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Data
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Analysis
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Execution
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Complete file
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However, PSA detection is susceptible to changes in the physiologic environment, which may lead to some misdiagnosis. Thus, it is crucial to find a novel diagnostic marker.\nMETHODS: We accessed microRNA (miRNA) expression datasets (GSE206793 and GSE112264) from the GEO database, analyzing peripheral blood samples from PCa patients. Differentially expressed miRNAs (DEmiRNAs) were identified using GEO2R. A specific miRNA, miR-455-3p, was pinpointed through rigorous analysis of clinical correlations and ROC curves. Peripheral blood samples from healthy individuals and PCa patients were subjected to qRT-PCR validation, aligning results with the GSE206793 dataset. The miRWalk database was utilized to predict downstream genes, while STRING facilitated the construction of a protein-protein interaction (PPI) network. KEGG pathway analysis enriched our understanding of potential molecular pathways.\nRESULTS: We found that miR-455-3p was highly expressed in the peripheral blood of PCa patients with Gleason score (GS) ≥ 8, while independent of T stage, age and PSA. ROC analysis revealed a favorable diagnostic efficacy of miR-455-3p and AUC for the two datasets was respectively 0.943 and 0.847. The qRT-PCR assay also revealed consistent results. Interestingly, the PSA levels of P1 (GS = 5 + 4) and P6 (GS = 3 + 3) were respectively 3.38 and 4.45 ng/ml, while miR-455-3p was highly expressed in both, suggesting its low misdiagnosis. The speculation was validated in GSE206793 dataset. Finally, 9 potential targets of miR-455-3p were predicted. PPI network revealed PPP2R2A, ITGB1 and CDKN1A as key nodes. KEGG pathway analysis revealed that they were enriched in various cancers, biological processes and molecular signals.\nCONCLUSION: Our study identifies miR-455-3p as a promising diagnostic marker for PCa, outperforming PSA in terms of specificity and sensitivity. The robustness of miR-455-3p, coupled with its potential downstream targets and associated pathways, highlights its clinical significance for improved PCa diagnosis and management.", "claims": [{"id": "claim-method", "statement": "To validate the diagnostic efficacy of miR-455-3p, ROC analysis was performed on both datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39951446", "locator": "sections[16] \"miR-455-3p has high diagnostic efficacy for PCa\" paragraph 2", "quote": "To validate the diagnostic efficacy of miR-455-3p, ROC analysis was performed on both datasets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE206793 dataset included 5 healthy individuals, 40 low-risk, 16 medium-risk and 91 high-risk PCa patients with clinical informations (including age, Gleason score (GS) and PSA).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39951446", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "GSE206793 dataset included 5 healthy individuals, 40 low-risk, 16 medium-risk and 91 high-risk PCa patients with clinical informations (including age, Gleason score (GS) and PSA)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "miR-455-3p showed favorable diagnostic efficacy for prostate cancer, with AUC values of 0.943 and 0.847 in the GSE206793 and GSE112264 datasets, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39951446", "locator": "sections[16] \"miR-455-3p has high diagnostic efficacy for PCa\" paragraph 2", "quote": "The results indicated that miR-455-3p had favorable diagnostic efficacy in GSE206793 and GSE112264 datasets, with AUC values of 0.943 and 0.847, respectively (Fig 3D and 3E)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "miR-455-3p showed favorable diagnostic efficacy for prostate cancer, with AUC values of 0.943 and 0.847 in the GSE206793 and GSE112264 datasets, 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:39951446"], "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:GSE112264"], "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:GSE112264"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39951446", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0317385", "sha256": 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