Integration analysis of cis- and trans-regulatory long non-coding RNAs associated with immune-related pathways in non-small cell lung cancer

IF 2.3 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biochemistry and Biophysics Reports Pub Date : 2024-10-28 DOI:10.1016/j.bbrep.2024.101832

Yinqiang Liu , Hongjv Yang , Guoli Lv, Jin Duan, Wei Zhao, Yunfei Shi, Youming Lei

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引用次数: 0

Abstract

Background

Long non-coding RNAs (lncRNAs) are importantly involved in the initiation and progression of non-small cell lung cancer (NSCLC). However, the classification and mechanisms of lncRNAs remain largely elusive.

Aim

Hence, we addressed this through bioinformatics analysis.

Methods and results

We utilized microarray technology to analyze lncRNAs and mRNAs in twenty paired NSCLC tumor tissues and adjacent normal tissues. Gene set enrichment analysis, Kyoto Encyclopedia of Genes and Genomes, and Gene Ontology were conducted to discern the biological functions of identified differentially expressed transcripts. Additionally, networks of lncRNA-mRNA co-expression, including cis-regulation, lncRNA-transcription factor (TF)-mRNA, trans-regulation, and lncRNA-miRNA-mRNA interactions were explored. Furthermore, the study examined differentially expressed transcripts and their prognostic values in a large RNA-seq dataset of 1016 NSCLC tumors and normal tissues extracted from the Cancer Genome Atlas (TCGA). The analysis revealed 391 lncRNAs and 344 mRNAs with differential expression in NSCLC tumor tissues compared to adjacent normal tissues. Subsequently, 43,557 co-expressed lncRNA-mRNA pairs were identified, including 27 lncRNA-mRNA pairs in cis, 9 lncRNA-TF-mRNA networks, 34 lncRNA-mRNA pairs in trans, and 8701 lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) networks. Notably, these lncRNAs were found to be involved in immune-related pathways. Six significant transcripts, including NTF4, PTPRD-AS, ITGA11, HID1-AS1, RASGRF2-AS1, and TBX2-AS1, were identified within the ceRNA network and trans-regulation.

Conclusion

This study brings important insights into the regulatory roles of lncRNAs in NSCLC, providing a fresh perspective on lncRNA research in tumor biology.

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非小细胞肺癌中与免疫相关通路有关的顺式和反式调控长非编码 RNA 的整合分析

背景长非编码RNA（lncRNA）在非小细胞肺癌（NSCLC）的发生和发展过程中起着重要作用。方法与结果我们利用芯片技术分析了20个配对的NSCLC肿瘤组织和邻近正常组织中的lncRNA和mRNA。我们利用基因组富集分析、京都基因和基因组百科全书以及基因本体论来鉴定差异表达转录本的生物学功能。此外，还探讨了lncRNA-mRNA共表达网络，包括顺式调控、lncRNA-转录因子（TF）-mRNA、反式调控和lncRNA-miRNA-mRNA相互作用。此外，研究还检测了从癌症基因组图谱（TCGA）中提取的1016个NSCLC肿瘤和正常组织的大型RNA-seq数据集中的差异表达转录本及其预后价值。分析发现，与邻近的正常组织相比，391个lncRNA和344个mRNA在NSCLC肿瘤组织中有差异表达。随后，共鉴定出43557对共同表达的lncRNA-mRNA，包括27对顺式lncRNA-mRNA、9个lncRNA-TF-mRNA网络、34对反式lncRNA-mRNA和8701个lncRNA-miRNA-mRNA竞争内源性RNA（ceRNA）网络。值得注意的是，这些lncRNA被发现参与了免疫相关通路。在ceRNA网络和反式调控中发现了6个重要的转录本，包括NTF4、PTPRD-AS、ITGA11、HID1-AS1、RASGRF2-AS1和TBX2-AS1。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Biochemistry and Biophysics Reports Biochemistry, Genetics and Molecular Biology-Biophysics

CiteScore

4.60

自引率

0.00%

发文量

191

审稿时长

59 days

期刊介绍： Open access, online only, peer-reviewed international journal in the Life Sciences, established in 2014 Biochemistry and Biophysics Reports (BB Reports) publishes original research in all aspects of Biochemistry, Biophysics and related areas like Molecular and Cell Biology. BB Reports welcomes solid though more preliminary, descriptive and small scale results if they have the potential to stimulate and/or contribute to future research, leading to new insights or hypothesis. Primary criteria for acceptance is that the work is original, scientifically and technically sound and provides valuable knowledge to life sciences research. We strongly believe all results deserve to be published and documented for the advancement of science. BB Reports specifically appreciates receiving reports on: Negative results, Replication studies, Reanalysis of previous datasets.