Differentially Expressed Genes in Nasopharyngeal Carcinoma Tissues and Their Correlation with Recurrence and Metastasis of Nasopharyngeal Carcinoma.

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The GSE61218 microarray dataset obtained from the Gene Expression Omnibus Database (GEO) was used. The limma R package was used to screen differentially expressed genes (DEGs) between NPC and normal nasopharyngeal (NP) tissues. KEGG functional enrichment was performed on these selected DEGs. Protein-protein interaction (PPI) networks were constructed using Cytoscape software to identify key node proteins. The NPC-metastasis microarray dataset GSE103611 was obtained from GEO to analyze the expression of DEGs in NPC metastasis. A total of 239 DEGs were identified. DEGs were mainly enriched in oocyte maturation-related pathways, cytokine-related pathways, cell cycle-related pathways, cancer-related pathways, and homologous recombination-related pathways. In addition, the top 10 nodes with the higher degree in the DEG PPI network were as follows: CDK1, CCNB2, BUB1, CCNA2, AURKB, BUB1B, MAD2L1, NDC80, BIRC5, and CENPF. The results indicated that DEGs may be involved in the pathogenesis of NPC by regulating cell cycle and mitosis, which can be used as molecular biomarkers for the diagnosis of NPC. In addition, we identified 87 DEGs with FC > 2 and P < 0.01 from the metastasis spectrum of NPC. The intersection gene between DEGs of NPC and normal NP tissue samples and those of the metastatic spectrum of NPC was identified to be VRK2. The expression of VRK2 in NPC samples was significantly higher than that in normal NP tissue, and similarly, VRK2 expression was significantly upregulated in metastatic samples compared with nonmetastatic samples (P < 0.05). Therefore, VRK2 may be a biomarker for predicting the metastasis of NPC patients after treatment.", "claims": [{"id": "claim-method", "statement": "The R software limma package [15] was used to set the filter condition as the |Fold Change| > 2 times and adjust P < 0.01 (FC > 2 and adjust P < 0.01).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35509856", "locator": "sections[5] \"2.3. Extraction and Screening of DEGs between NPC and Normal NP Tissues\" paragraph 2", "quote": "The R software limma package [15] was used to set the filter condition as the |Fold Change| > 2 times and adjust P < 0.01 (FC > 2 and adjust P < 0.01)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are available from the corresponding authors upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35509856", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are available from the corresponding authors upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "VRK2 was the sole intersection between DEGs in NPC versus normal NP tissue and DEGs in the metastatic spectrum of NPC, was significantly upregulated in both NPC and metastatic samples, and may serve as a biomarker for predicting post-treatment NPC metastasis.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "The expression of VRK2 in NPC samples was significantly higher than that in normal NP tissue, and similarly, VRK2 expression was significantly upregulated in metastatic samples compared with nonmetastatic samples (P < 0.05)."}, "evidence": [{"asset": "source:pmid:35509856", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The intersection gene between DEGs of NPC and normal NP tissue samples and those of the metastatic spectrum of NPC was identified to be VRK2."}, {"asset": "source:pmid:35509856", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The expression of VRK2 in NPC samples was significantly higher than that in normal NP tissue, and similarly, VRK2 expression was significantly upregulated in metastatic samples compared with nonmetastatic samples (P < 0.05)."}, {"asset": "source:pmid:35509856", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Therefore, VRK2 may be a biomarker for predicting the metastasis of NPC patients after treatment."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "VRK2 was the sole intersection between DEGs in NPC versus normal NP tissue and DEGs in the metastatic spectrum of NPC, was significantly upregulated in both NPC and metastatic samples, and may serve as a biomarker for predicting post-treatment NPC metastasis.", "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:35509856"], "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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