lncRNA-mRNA Co-Expression and Regulation Analysis in Lung Fibroblasts from Idiopathic Pulmonary Fibrosis.

IF 3.6 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY Non-Coding RNA Pub Date : 2024-04-17 DOI:10.3390/ncrna10020026

Armando López-Martínez, Jovito Cesar Santos-Álvarez, Juan Manuel Velázquez-Enríquez, Alma Aurora Ramírez-Hernández, V. R. Vásquez-Garzón, Rafael Baltiérrez-Hoyos

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Abstract

Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease marked by abnormal accumulation of extracellular matrix (ECM) due to dysregulated expression of various RNAs in pulmonary fibroblasts. This study utilized RNA-seq data meta-analysis to explore the regulatory network of hub long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in IPF fibroblasts. The meta-analysis unveiled 584 differentially expressed mRNAs (DEmRNA) and 75 differentially expressed lncRNAs (DElncRNA) in lung fibroblasts from IPF. Among these, BCL6, EFNB1, EPHB2, FOXO1, FOXO3, GNAI1, IRF4, PIK3R1, and RXRA were identified as hub mRNAs, while AC008708.1, AC091806.1, AL442071.1, FAM111A-DT, and LINC01989 were designated as hub lncRNAs. Functional characterization revealed involvement in TGF-β, PI3K, FOXO, and MAPK signaling pathways. Additionally, this study identified regulatory interactions between sequences of hub mRNAs and lncRNAs. In summary, the findings suggest that AC008708.1, AC091806.1, FAM111A-DT, LINC01989, and AL442071.1 lncRNAs can regulate BCL6, EFNB1, EPHB2, FOXO1, FOXO3, GNAI1, IRF4, PIK3R1, and RXRA mRNAs in fibroblasts bearing IPF and contribute to fibrosis by modulating crucial signaling pathways such as FoxO signaling, chemical carcinogenesis, longevity regulatory pathways, non-small cell lung cancer, and AMPK signaling pathways.

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特发性肺纤维化肺成纤维细胞中 lncRNA-mRNA 的共表达和调控分析

特发性肺纤维化（IPF）是一种进行性肺部疾病，其特征是细胞外基质（ECM）的异常积聚，其原因是肺成纤维细胞中各种 RNA 的表达失调。本研究利用RNA-seq数据荟萃分析来探索IPF成纤维细胞中枢长非编码RNA（lncRNA）和信使RNA（mRNA）的调控网络。荟萃分析揭示了IPF肺成纤维细胞中584个差异表达的mRNA（DEmRNA）和75个差异表达的lncRNA（DElncRNA）。其中，BCL6、EFNB1、EPHB2、FOXO1、FOXO3、GNAI1、IRF4、PIK3R1和RXRA被确定为中枢mRNA，而AC008708.1、AC091806.1、AL442071.1、FAM111A-DT和LINC01989被指定为中枢lncRNA。功能表征显示，这些基因参与了 TGF-β、PI3K、FOXO 和 MAPK 信号通路。此外，这项研究还发现了中枢 mRNA 序列与 lncRNA 之间的调控相互作用。总之，研究结果表明，AC008708.1、AC091806.1、FAM111A-DT、LINC01989 和 AL442071.1 lncRNAs可调控IPF成纤维细胞中的BCL6、EFNB1、EPHB2、FOXO1、FOXO3、GNAI1、IRF4、PIK3R1和RXRA mRNAs，并通过调控FoxO信号、化学致癌、长寿调控通路、非小细胞肺癌和AMPK信号通路等关键信号通路促进纤维化。

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

Non-Coding RNA Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

6.70

自引率

4.70%

发文量

审稿时长

10 weeks

期刊介绍： Functional studies dealing with identification, structure-function relationships or biological activity of: small regulatory RNAs (miRNAs, siRNAs and piRNAs) associated with the RNA interference pathway small nuclear RNAs, small nucleolar and tRNAs derived small RNAs other types of small RNAs, such as those associated with splice junctions and transcription start sites long non-coding RNAs, including antisense RNAs, long ''intergenic'' RNAs, intronic RNAs and ''enhancer'' RNAs other classes of RNAs such as vault RNAs, scaRNAs, circular RNAs, 7SL RNAs, telomeric and centromeric RNAs regulatory functions of mRNAs and UTR-derived RNAs catalytic and allosteric (riboswitch) RNAs viral, transposon and repeat-derived RNAs bacterial regulatory RNAs, including CRISPR RNAS Analysis of RNA processing, RNA binding proteins, RNA signaling and RNA interaction pathways: DICER AGO, PIWI and PIWI-like proteins other classes of RNA binding and RNA transport proteins RNA interactions with chromatin-modifying complexes RNA interactions with DNA and other RNAs the role of RNA in the formation and function of specialized subnuclear organelles and other aspects of cell biology intercellular and intergenerational RNA signaling RNA processing structure-function relationships in RNA complexes RNA analyses, informatics, tools and technologies: transcriptomic analyses and technologies development of tools and technologies for RNA biology and therapeutics Translational studies involving long and short non-coding RNAs: identification of biomarkers development of new therapies involving microRNAs and other ncRNAs clinical studies involving microRNAs and other ncRNAs.

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