鉴定和验证关键 lnc-TRIM28-14 和促进胃癌腹膜转移的枢纽基因。
Identification and validation of crucial lnc-TRIM28-14 and hub genes promoting gastric cancer peritoneal metastasis.
机构信息
Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
出版信息
BMC Cancer. 2023 Jan 23;23(1):76. doi: 10.1186/s12885-023-10544-8.
BACKGROUND
Gastric cancer peritoneal metastasis (GCPM) is an important cause of cancer-related deaths worldwide. Long non-coding RNAs (lncRNAs) play a key role in the regulation of GCPM, but the underlying mechanisms have not been elucidated.
METHODS
High-throughput RNA sequencing (RNA-seq) was performed on four groups of clinical specimens (non-metastatic gastric cancer primary tumor, adjacent normal gastric mucosal tissue, gastric cancer primary tumor with peritoneal metastasis and adjacent normal gastric mucosal tissue). After sequencing, many lncRNAs and mRNAs were screened for further Weighted Gene Co-expression Network Analysis (WGCNA). GCPM-related hub lncRNAs and genes were identified by cytoHubba and validated by Quantitative real-time PCR (qRT-PCR), Receiver operating characteristic curve (ROC) analysis and Kaplan-Meier survival analysis. GO, KEGG and GSEA showed GCPM-related pathways. Correlation analysis revealed the potential relationship between hub lncRNAs and genes.
RESULTS
By analyzing lncRNA expression data by WGCNA, we found that blue module was highly correlated with GCPM (r = 0.44, p = 0.04) and six lncRNAs involved in this module (DNM3OS, lnc-MFAP2-53, lnc-PPIAL4C-4, lnc-RFNG-1, lnc-TRIM28-14 and lnc-YARS2-4) were identified. We then performed qRT-PCR validation of gastric cancer specimens and found that the expression of lnc-RFNG-1 and lnc-TRIM28-14 was significantly increased in gastric cancer tissues with peritoneal metastasis. Kaplan-Meier survival analysis showed shorter overall survival time (OS) for gastric cancer patients with high expression of lnc-TRIM28-14. Receiver operating characteristic curve (ROC) analysis showed that lnc-TRIM28-14 could improve the sensitivity and specificity of GCPM diagnosis. In addition, we identified three key mRNAs (CD93, COL3A1 and COL4A1) associated with gastric cancer peritoneal metastasis through WGCNA analysis and clinical specimen validation. Moreover, there was a positive correlation between lnc-TRIM28-14 and the expression of CD93 and COL4A1 in gastric cancer peritoneal metastasis, suggesting a regulatory relationship between them. Subsequent GO, KEGG and GSEA analysis suggested that ECM-receptor interaction and focal adhesion were the hub pathways of GCPM.
CONCLUSION
In summary, lnc-RFNG-1, lnc-TRIM28-14, CD93, COL3A1 and COL4A1 could be novel tumor biomarkers and potential therapeutic targets for GCPM.
背景
胃癌腹膜转移（GCPM）是全球癌症相关死亡的重要原因。长链非编码 RNA（lncRNA）在 GCPM 的调控中起着关键作用，但潜在机制尚未阐明。
方法
对四组临床标本（非转移性胃癌原发肿瘤、邻近正常胃黏膜组织、胃癌原发肿瘤伴腹膜转移和邻近正常胃黏膜组织）进行高通量 RNA 测序（RNA-seq）。测序后，通过加权基因共表达网络分析（WGCNA）筛选出许多 lncRNA 和 mRNAs。通过 cytoHubba 鉴定与 GCPM 相关的 hub lncRNA 和基因，并通过定量实时 PCR（qRT-PCR）、受试者工作特征曲线（ROC）分析和 Kaplan-Meier 生存分析进行验证。GO、KEGG 和 GSEA 显示了与 GCPM 相关的通路。相关性分析揭示了 hub lncRNA 和基因之间的潜在关系。
结果
通过 WGCNA 分析 lncRNA 表达数据，我们发现蓝色模块与 GCPM 高度相关（r=0.44，p=0.04），并且该模块中涉及六个 lncRNA（DNM3OS、lnc-MFAP2-53、lnc-PPIAL4C-4、lnc-RFNG-1、lnc-TRIM28-14 和 lnc-YARS2-4）。然后，我们对胃癌标本进行 qRT-PCR 验证，发现 lnc-RFNG-1 和 lnc-TRIM28-14 在伴腹膜转移的胃癌组织中的表达明显增加。Kaplan-Meier 生存分析显示 lnc-TRIM28-14 高表达的胃癌患者总生存时间（OS）较短。ROC 分析表明，lnc-TRIM28-14 可提高 GCPM 诊断的灵敏度和特异性。此外，我们通过 WGCNA 分析和临床标本验证，确定了与胃癌腹膜转移相关的三个关键 mRNAs（CD93、COL3A1 和 COL4A1）。此外，lnc-TRIM28-14 与胃癌腹膜转移中 CD93 和 COL4A1 的表达呈正相关，提示它们之间存在调节关系。随后的 GO、KEGG 和 GSEA 分析表明，ECM-受体相互作用和焦点粘附是 GCPM 的关键通路。
结论
综上所述，lnc-RFNG-1、lnc-TRIM28-14、CD93、COL3A1 和 COL4A1 可能是 GCPM 的新型肿瘤标志物和潜在治疗靶点。
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