Identification and Functional Analysis of Long Non-coding RNAs in Human Pulmonary Microvascular Endothelial Cells Subjected to Cyclic Stretch

Wang, Dong; Dai, Chenyang; Zhang, Xiaoning; Gu, Chao; Liu, Mengjie; Liu, Huan; Yang, Fan; Wu, Haifeng; Wang, Yuelan

doi:10.3389/fphys.2021.655971

Cited by 4 publications

(2 citation statements)

References 47 publications

(37 reference statements)

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“…As transmode RNAs, lncRNAs influence gene expression by binding to proteins, DNA, and other RNAs far from the main transcription sites [ 37 ]. In this study, lncRNA XR_359945.3 was predicted to transregulate Zfyve27 , KSR1 , ELK4 , Gfi1 , and Apaf-1 .…”

Section: Discussionmentioning

confidence: 99%

Expression Profiles of Long Noncoding RNAs and Messenger RNAs in a Rat Model of Spinal Cord Injury

Cao

Tang²,

Tan

et al. 2023

Computational and Mathematical Methods in Medicine

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Spinal cord injury (SCI) is a serious disorder of the central nervous system with a high disability rate. Long noncoding RNAs (lncRNAs) are reported to mediate many biological processes. The aim of this study was to explore lncRNA and mRNA expression profiles and functional networks after SCI. Differentially expressed genes between SCI model rats and sham controls were identified by microarray assays and analyzed by functional enrichment. Key lncRNAs were identified using a support vector machine- (SVM-) recursive feature elimination (RFE) algorithm. A trans and cis regulation model was used to analyze the regulatory relationships between lncRNAs and their targets. An lncRNA-related ceRNA network was established. We identified 5465 differentially expressed lncRNAs (DE lncRNAs) and 8366 differentially expressed mRNAs (DE mRNAs) in the SCI group compared with the sham group ( fold change > 2.0 , p < 0.05 ). Four genes were confirmed by qRT-PCR which were consistent with the microarray data. GSEA analysis showed that most marked changes occurred in pathways related to immune inflammation and nerve cell function, including cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and GABAergic synapse. Enrichment analysis identified 30 signaling pathways, including those associated with immune inflammation response. A total of 40 key lncRNAs were identified using the SVM-RFE algorithm. A key lncRNA-mRNAs coexpression network was generated for 230 951 lncRNA-mRNA pairs with half showing positive correlations. Several key DE lncRNAs were predicted to have “cis”- or “trans”-regulated target genes. The transcription factors, Sp1, JUN, and SOX10, may regulate the interaction between XR_001837123.1 and ETS 1. In addition, five pairs of ceRNA regulatory sequences were constructed. Many mRNAs and lncRNAs were found to be dysregulated after SCI. Bioinformatic analysis showed that DE lncRNAs may play crucial roles in SCI. It is anticipated that these findings will provide new insights into the underlying mechanisms and potential therapeutic targets for SCI.

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Section: Discussionmentioning

confidence: 99%

Expression Profiles of Long Noncoding RNAs and Messenger RNAs in a Rat Model of Spinal Cord Injury

Cao

Tang²,

Tan

et al. 2023

Computational and Mathematical Methods in Medicine

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“…In lung endothelial dysfunction, cyclic stretch induces HDAC6 activation and is downregulated in endothelial cells (EC) and results in a-tubulin deacetylation[ 29 ]. However, instead of changes in tubulin modification, HDAC4 translocation from the cytoplasm to the nucleus in murine chondrocytes after stretch repressed RUNX-2 expression [ 30 ]. In chondrocytes, cyclic stretch also stimulates the expression of ADAMTS-5 which could induce osteoarthritis.…”

Section: Mechanical Strainmentioning

confidence: 99%

Mechanical Cues Regulate Histone Modifications and Cell Behavior

Zhou

Wang

et al. 2022

Stem Cells International

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Change of biophysical factors in tissue microenvironment is an important step in a chronic disease development process. A mechanical and biochemical factor from cell living microniche can regulate cell epigenetic decoration and, therefore, further induce change of gene expression. In this review, we will emphasize the mechanism that biophysical microenvironment manipulates cell behavior including gene expression and protein decoration, through modifying histone amino acid residue modification. The influence given by different mechanical forces, including mechanical stretch, substrate surface stiffness, and shear stress, on cell fate and behavior during chronic disease development including tumorigenesis will also be teased out. Overall, the recent work summarized in this review culminates on the hypothesis that a mechanical factor stimulates the modification on histone which could facilitate disease detection and potential therapeutic target.

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Vascular mechanotransduction

Davis

Earley

et al. 2023

Physiological Reviews

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This review aims to survey the current state of mechanotransduction in vascular smooth muscle cells (VSMCs) and endothelial cells (ECs), including their sensing of mechanical stimuli and transduction of mechanical signals that result in the acute functional modulation and longer-term transcriptomic and epigenetic regulation of blood vessels. The mechanosensors discussed include ion channels, plasma membrane associated structures and receptors, and junction proteins. The mechanosignaling pathways presented include the cytoskeleton, integrins, extracellular matrix and intracellular signaling molecules. These are followed by discussions on mechanical regulation of transcriptome and epigenetics, relevance of mechanotransduction to health and disease, and interactions between ECs and VSMCs. Throughout this review, we offer suggestions for specific topics that require further understanding. In the closing section on Conclusions and Perspectives, we summarize what is known and point out the need to treat the vasculature as a system, including not only ECs and VSMCs, but also the extracellular matrix and other types of cells such as resident macrophages and pericytes, so that we can fully understand the physiology and pathophysiology of the blood vessel as a whole, thus enhancing the comprehension, diagnosis, treatment, and prevention of vascular diseases.

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Identification and Functional Analysis of Long Non-coding RNAs in Human Pulmonary Microvascular Endothelial Cells Subjected to Cyclic Stretch

Cited by 4 publications

References 47 publications

Expression Profiles of Long Noncoding RNAs and Messenger RNAs in a Rat Model of Spinal Cord Injury

Expression Profiles of Long Noncoding RNAs and Messenger RNAs in a Rat Model of Spinal Cord Injury

Mechanical Cues Regulate Histone Modifications and Cell Behavior

Vascular mechanotransduction

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