RNA 测序分析结直肠癌中长链非编码 RNA 和信使 RNA 的转录组谱和共表达网络。
Transcriptome profiling and co-expression network analysis of lncRNAs and mRNAs in colorectal cancer by RNA sequencing.
机构信息
Department of Clinical Laboratory, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, 361102, China.
Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou, 350001, China.
出版信息
BMC Cancer. 2022 Jul 16;22(1):780. doi: 10.1186/s12885-022-09878-6.
BACKGROUND
Long non-coding RNAs (lncRNAs) are widely involved in the pathogenesis of cancers. However, biological roles of lncRNAs in occurrence and progression of colorectal cancer (CRC) remain unclear. The current study aimed to evaluate the expression pattern of lncRNAs and messenger RNAs (mRNAs).
METHODS
RNA sequencing (RNA-Seq) in CRC tissues and adjacent normal tissues from 6 CRC patients was performed and functional lncRNA-mRNA co-expression network was constructed afterwards. Gene enrichment analysis was demonstrated using DAVID 6.8 tool. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to validate the expression pattern of differentially expressed lncRNAs. Pearson correlation analysis was applied to evaluate the relationships between selected lncRNAs and mRNAs.
RESULTS
One thousand seven hundred and sixteenth differentially expressed mRNAs and 311 differentially expressed lncRNAs were screened out. Among these, 568 mRNAs were up-regulated while 1148 mRNAs down-regulated, similarly 125 lncRNAs were up-regulated and 186 lncRNAs down-regulated. In addition, 1448 lncRNA-mRNA co-expression pairs were screened out from 940,905 candidate lncRNA-mRNA pairs. Gene enrichment analysis revealed that these lncRNA-related mRNAs are associated with cell adhesion, collagen adhesion, cell differentiation, and mainly enriched in ECM-receptor interaction and PI3K-Akt signaling pathways. Finally, RT-qPCR results verified the expression pattern of lncRNAs, as well as the relationships between lncRNAs and mRNAs in 60 pairs of CRC tissues.
CONCLUSIONS
In conclusion, these results of the RNA-seq and bioinformatic analysis strongly suggested that the dysregulation of lncRNA is involved in the complicated process of CRC development, and providing important insight regarding the lncRNAs involved in CRC.
背景
长链非编码 RNA（lncRNA）广泛参与癌症的发病机制。然而，lncRNA 在结直肠癌（CRC）发生和进展中的生物学作用尚不清楚。本研究旨在评估 lncRNA 和信使 RNA（mRNA）的表达模式。
方法
对 6 例 CRC 患者的 CRC 组织和相邻正常组织进行 RNA 测序（RNA-Seq），构建功能 lncRNA-mRNA 共表达网络。使用 DAVID 6.8 工具进行基因富集分析。采用逆转录定量聚合酶链反应（RT-qPCR）验证差异表达 lncRNA 的表达模式。应用 Pearson 相关分析评估选定 lncRNA 和 mRNA 之间的关系。
结果
筛选出 1716 个差异表达的 mRNA 和 311 个差异表达的 lncRNA。其中，568 个 mRNA 上调，1148 个 mRNA 下调，同样上调 125 个 lncRNA，下调 186 个 lncRNA。此外，从 940905 个候选 lncRNA-mRNA 对中筛选出 1448 个 lncRNA-mRNA 共表达对。基因富集分析表明，这些与 lncRNA 相关的 mRNAs 与细胞黏附、胶原黏附、细胞分化有关，主要富集在 ECM 受体相互作用和 PI3K-Akt 信号通路中。最后，RT-qPCR 结果验证了 60 对 CRC 组织中 lncRNA 的表达模式以及 lncRNA 与 mRNA 之间的关系。
结论
综上所述，RNA-seq 和生物信息学分析的结果强烈表明，lncRNA 的失调参与了结直肠癌的复杂发展过程，并为涉及 CRC 的 lncRNA 提供了重要的见解。
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