基于基因芯片的结肠癌预后相关差异表达LncRNAs的筛选及临床验证-东南大学学报医学版

基于基因芯片的结肠癌预后相关差异表达LncRNAs的筛选及临床验证

单位：1. 河北北方学院附属第一医院肿瘤内科, 河北张家口 075000;
2. 陆军第八十一集团军医院肿瘤内科, 河北张家口 075000

分类号：R735.3

出版年·卷·期（页码）：2025·44·第三期（370-378）

摘要：

目的: 基于基因芯片技术筛选结肠癌预后相关差异表达长链非编码核糖核酸(LncRNAs),并进行临床验证。方法: 选取2020年6月至2023年6月于医院就诊的321例结肠癌患者,其中34例用于筛选差异表达LncRNAs,287例用于验证。34例患者术后1年有9例预后不良,纳入A组,其余25例纳入B组。采用基因芯片技术检测A、B组肿瘤组织中差异表达LncRNAs;构建结肠癌预后竞争性内源核糖核酸(ceRNA)网络,并进行基因本体论(GO)及京都基因和基因组百科全书(KEGG)富集分析;经LASSO回归模型筛选结肠癌预后相关LncRNAs,将LASSO回归筛选出的变量纳入多因素Cox回归模型,分析结肠癌预后的影响因素。结果: 筛选出A、B组肿瘤组织样本中差异表达的LncRNAs共227个,其中上调LncRNAs 162个,下调LncRNAs 65个;构建的ceRNA网络共包括181个节点(93个LncRNA节点、29个miRNA节点、59个mRNA节点)和603个边缘;GO富集分析显示,差异表达LncRNA的功能集中在细胞对化学应激、氧化应激和外部刺激的反应,包括转录调节复合物、RNA聚合酶Ⅱ转录调节复合物和核外膜,DNA结合转录因子的结合位点、R-SMAD结合和Ⅱ型RNA聚合酶激活的转录因子结合;KEGG富集分析差异表达LncRNA的功能主要集中在白介素-17(IL-17)信号通路、肿瘤坏死因子(TNF)信号通路、催产素信号通路和核转录因子-κB(NF-κB)信号通路;LASSO回归筛选出11个与结肠癌预后相关的变量,分别为LncRNA NEAT1、LncRNA PCAT1、LncRNA CASC11、LncRNA CCAT1、LncRNA PCAT6、LncRNA ZEB1-AS1、LncRNA PSMA3-AS1、LncRNA AC005062.1、LncRNA GAS5、LncRNA MEG3、LncRNA USP30-AS1;Cox回归分析结果显示,TNM分期、LncRNA CASC11、LncRNA CCAT1、LncRNA PCAT6是结肠癌预后的危险因素(P＜0.05),LncRNA GAS5、LncRNA MEG3是保护因素(P＜0.05)。结论: 在结肠癌不同预后患者中筛选出差异表达的Lnc RNAs共227个,成功构建ceRNA网络,GO富集主要集中在细胞对化学应激、氧化应激和外部刺激的反应等,KEGG富集主要集中在IL-17信号通路、TNF信号通路、催产素信号通路和NF-κB信号通路,经临床验证LncRNA CASC11、LncRNA CCAT1、LncRNA PCAT6是结肠癌预后的危险因素,LncRNA GAS5、LncRNA MEG3是保护因素。

Objective: To screen and clinically validate prognosis-related differentially expressed long non-coding RNAs(LncRNAs) in colon cancer using gene chip technology. Methods: A cohort of 321 colon cancer patients treated between June 2020 and June 2023 was selected for this study. Among them, 34 patients were used for screening differentially expressed LncRNAs, while 287 patients were used for subsequent validation. Of the 34 patients, 9 who experienced poor prognosis one year post-surgery were categorized into Group A, with the remaining 25 patients were assigned to Group B. Gene chip technology was employed to detect differentially expressed LncRNAs in the tumor tissues of Groups A and B. A competing endogenous RNA(ceRNA) network was constructed, followed by Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment analyses. Prognosis-related LncRNAs were screened using the LASSO regression model, and the variables identified were included in a multivariate Cox regression model to analyze factors affecting the prognosis of colon cancer. Results: A total of 227 differentially expressed LncRNAs were screened between Groups A and B, with 162 upregulated and 65 downregulated LncRNAs. The constructed ceRNA network comprised 181 nodes(93 LncRNA nodes, 29 miRNA nodes, and 59 mRNA nodes) and 603 edges. GO enrichment analysis revealed that the differentially expressed LncRNAs were primarily involved in cellular responses to chemical stress, oxidative stress, and external stimuli, including transcriptional regulatory complexes, RNA polymerase Ⅱ transcription regulatory complexes, and the nuclear outer membrane. These LncRNAs were also involved in DNA-binding transcription factor binding, R-SMAD binding, and RNA polymerase Ⅱ-activated transcription factor binding. KEGG enrichment analysis indicated that the differentially expressed LncRNAs were mainly concentrated in the IL-17 signaling pathway, TNF signaling pathway, oxytocin signaling pathway, and NF-κB signaling pathway. LASSO regression identified 11 variables associated with colon cancer prognosis, including LncRNA NEAT1, LncRNA PCAT1, LncRNA CASC11, LncRNA CCAT1, LncRNA PCAT6, LncRNA ZEB1-AS1, LncRNA PSMA3-AS1, LncRNA AC005062.1, LncRNA GAS5, LncRNA MEG3, and LncRNA USP30-AS1. Cox regression analysis revealed that TNM stage, LncRNA CASC11, LncRNA CCAT1, and LncRNA PCAT6 were risk factors for colon cancer prognosis(P<0.05), whereas LncRNA GAS5 and LncRNA MEG3 were protective factors(P<0.05). Conclusion: This study identify 227 differentially expressed LncRNAs in colon cancer patients with varying prognoses. A ceRNA network is successfully constructed, with GO enrichment analysis highlights cellular responses to chemical stress, oxidative stress, and external stimuli, while KEGG enrichment analysis points to significant involvement in the IL-17, TNF, oxytocin, and NF-κB signaling pathways. Clinical validation indicates that LncRNA CASC11, LncRNA CCAT1, and LncRNA PCAT6 are risk factors for colon cancer prognosis, while LncRNA GAS5 and LncRNA MEG3 serve as protective factors.

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