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pmid:38515458
Validation of CDC45 as a novel biomarker for diagnosis and prognosis of gastric cancer.
Lihua Wu · Gan Gao · Hui Mi · Zhou Luo · Zheng Wang · Yongdong Liu · Liangyan Wu · Haihua Long · Yongqi Shen
PeerJ · 2024 doi:10.7717/peerj.17130
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, the clinical significance of CDC45 in gastric cancer (GC) remains unreported.\nMethod: In this study, we employed the TCGA database and the TCGA & GTEx dataset to compare the mRNA expression levels of CDC45 between gastric cancer tissues and adjacent or normal tissues (p < 0.05 was considered statistically significant), which was further validated in multiple datasets including GSE13911, GSE29272, GSE118916, GSE66229, as well as RT-qPCR. Furthermore, we harnessed the Human Protein Atlas (HPA) to evaluate the protein expression of CDC45, which was subsequently verified through immunohistochemistry (IHC). To ascertain the diagnostic utility of CDC45, receiver operating characteristic (ROC) curves and the area under the ROC curve (AUC) were calculated in TCGA database, and further validated it in TCGA & GTEx and GSE66229 datasets. The Kaplan-Meier method was used to reveal the prognostic importance of CDC45 in The Cancer Genome Atlas (TCGA) database and authenticated through the GSE66229, GSE84433, and GSE84437 datasets. Through cBioPortal, we identified co-expressed genes of CDC45, and pursued enrichment analysis. Additionally, we availed gene set enrichment analysis (GSEA) to annotate the biological functions of CDC45.\nResults: Differential expression analysis revealed that CDC45 was significantly upregulated at both the mRNA and protein levels in GC (all p < 0.05). Remarkably, CDC45 emerged as a promising prognostic indicator and a novel diagnostic biomarker for GC. In a comprehensive the drug susceptibility analysis, we found that patients with high expression of CDC45 had high sensitivity to various chemotherapeutic agents, among which 5-fluorouracil, docetaxel, cisplatin, and elesclomol were most evident. Furthermore, our findings suggested a plausible association between CDC45 and immune cell infiltration. Enrichment analysis revealed that CDC45 and its associated genes may play crucial roles in muscle biofunction, whereas GSEA demonstrated significant enrichment of gene sets pertaining to G protein-coupled receptor ligand binding and G alpha (i) signaling events.\nConclusion: Our study elucidates that upregulation of CDC45 is intricately associated with immune cell infiltration and holds promising potential as a favorable prognostic marker and a novel diagnostic biomarker for GC.", "claims": [{"id": "claim-method", "statement": "To ascertain the diagnostic utility of CDC45, receiver operating characteristic (ROC) curves and the area under the ROC curve (AUC) were calculated in TCGA database, and further validated it in TCGA & GTEx and GSE66229 datasets. The Kaplan–Meier method was used to reveal the prognostic importance of CDC45 in The Cancer Genome Atlas (TCGA) database and authenticated through the GSE66229, GSE84433, and GSE84437 datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38515458", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "To ascertain the diagnostic utility of CDC45, receiver operating characteristic (ROC) curves and the area under the ROC curve (AUC) were calculated in TCGA database, and further validated it in TCGA & GTEx and GSE66229 datasets. The Kaplan–Meier method was used to reveal the prognostic importance of CDC45 in The Cancer Genome Atlas (TCGA) database and authenticated through the GSE66229, GSE84433, and GSE84437 datasets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data are available in the Supplemental Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38515458", "locator": "sections[30] \"Data Availability\" paragraph 2", "quote": "The raw data are available in the Supplemental Files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "CDC45 exhibited strong diagnostic capability for gastric cancer in the TCGA cohort, with an AUC of 0.911 (95% CI [0.873–0.948]).", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "This was evidenced by the receiver operating characteristic (ROC) analysis, which yielded an impressive area under the curve (AUC) value of 0.911 (95% CI [0.873–0.948]) (Fig. 3A)."}, "evidence": [{"asset": "source:pmid:38515458", "locator": "sections[14] \"Potential significance of CDC45 in GC diagnosis and prognosis\" paragraph 2", "quote": "This was evidenced by the receiver operating characteristic (ROC) analysis, which yielded an impressive area under the curve (AUC) value of 0.911 (95% CI [0.873–0.948]) (Fig. 3A)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "CDC45 exhibited strong diagnostic capability for gastric cancer in the TCGA cohort, with an AUC of 0.911 (95% CI [0.873–0.948]).", "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:38515458"], "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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