Integrative analysis of miRNA–mRNA network in high altitude retinopathy by bioinformatics analysis

Su, Tong; Gu, Chufeng; Draga, Deji; Zhou, Chuandi; Lhamo, Thashi; Zheng, Zhi; Qiu, Qinghua

doi:10.1042/bsr20200776

Cited by 9 publications

(6 citation statements)

References 49 publications

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“…Abnormal VEGF and disrupted angiogenesis are described in lung tissues of infants that died of severe BPD [64]. In addition, miR-1255b-5p is downregulated in hypoxia-induced lung A549 cells [65] as well as in models of high altitude retinopathy [66], and colorectal cancer, where it also regulates telomerase activity and suppresses EMT [67]. Notably, hypoxic stress in the presence of hyperoxia results in altering alveologenesis in mouse models of neonatal BPD [68].…”

Section: Discussionmentioning

confidence: 99%

Tracheal Aspirate miRNA Signatures in Preterm Infants with Severe Bronchopulmonary Dysplasia

Siddaiah¹,

Oji‐Mmuo²,

Montes³

et al. 2021

Preprint

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Bronchopulmonary dysplasia (BPD) is a form of chronic lung disease that develops in neonates as a consequence of preterm birth and arrested fetal lung development. The incidence of BPD remains on the rise, as a result of increasing survival of extremely preterm infants. Severe BPD contributes to significant health care costs and is associated with prolonged hospitalizations, respiratory infections, and neurodevelopmental deficits. In this study, we aimed to detect novel biomarkers of severe BPD. We collected tracheal aspirates (TA) from preterm babies with mild/moderate (n = 8) and severe (n = 17) BPD, and we profiled the expression of 1048 miRNAs using a PCR array. Associations with biological pathways were determined with the Ingenuity Pathway Analysis (IPA) software. We found 31 miRNAs differentially expressed between the two disease groups (2-fold change, FDR &lt; 0.05). Of these, 4 miRNAs displayed significantly higher expression levels, and 27 miRNAs had significantly lower expression levels in the severe BPD vs. the mild/moderate BPD group. IPA identified cell signaling and inflammation pathways associated with miRNA signatures. We conclude that TAs of extreme premature infants contain miRNA signatures associated with severe BPD. These signatures may serve as biomarkers of disease severity in infants with BPD.

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Section: Discussionmentioning

confidence: 99%

Tracheal Aspirate miRNA Signatures in Preterm Infants with Severe Bronchopulmonary Dysplasia

Siddaiah¹,

Oji‐Mmuo²,

Montes³

et al. 2021

Preprint

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“…The DAVID software ( ; accessed on 1 March 2022) was used for GO and KEGG enrichment analyses of pyroptosis-related DEGs [ 22 ]. The DEGs were characterized, and key pathways were examined.…”

Section: Methodsmentioning

confidence: 99%

Key Genes Associated with Pyroptosis in Gout and Construction of a miRNA-mRNA Regulatory Network

Bai

Liu

Abudukerimu

et al. 2022

Cells

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This study aimed to analyze key hub genes related to pyroptosis in gout and construct a miRNA-mRNA regulatory network using bioinformatic tools to elucidate the pathogenesis of gout and offer novel ideas to develop targeted therapeutic strategies for gout. Methods: The GSE160170 dataset was downloaded from the GEO database. The expression data extracted from the dataset were used to screen for differentially expressed genes (DEGs), which intersected with pyroptosis-related genes. These DEGs were analyzed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, and a protein–protein interaction (PPI) network was constructed to identify pyroptosis-related hub DEGs. The relationship between upstream miRNAs and the hub genes was analyzed, miRNA-mRNA networks belonging to gout disease were constructed and samples from patients with gout were used for experimental verification. The CTDbase tool was used to analyze the identified hub genes and construct a molecular docking model. Results: A total of 943 DEGs (380 upregulated and 563 downregulated) were identified by analyzing the data of patients with early-stage gout and healthy control individuals in the GSE160170 dataset. DEGs and pyroptosis-related genes were intersected to obtain 17 pyroptosis-related DEGs associated with gout; of which, 12 were upregulated, and five were downregulated. The results of GO and KEGG analyses revealed that the DEGs were enriched in inflammatory and immune signaling pathways. Additionally, the DEGs were found to regulate inflammatory responses and were associated with apoptosis. TNF, IL-1β, NLRP3, CXCL8, PTGS2, NFE2L2, CASP8, and CD274 were identified as key hub genes in the PPI network, and a miRNA-mRNA network was constructed, which had 16 edges. Experimental validation revealed that PTGS2 and NFE2L2 were significantly upregulated, and CASP8 and CD274 were significantly downregulated in gout. In addition, miR-128-3p, miR-16-5p, miR-155-5p, and miR-20a-5p (associated with the miRNA-mRNA regulatory network) were significantly downregulated in gout. Five potential therapeutic drugs with stable PTGS2 binding were selected to develop a molecular docking model. Conclusion: A miRNA-mRNA potential regulatory network was constructed based on pyroptosis-related DEGs associated with gout. miR-16-5p, miR-128-3p, miR-20a-5p, and miR-155-5p can potentially influence pyroptosis and the occurrence and development of gout by affecting the expression of the PTGS2, CASP8, NFE2L2, and CD274 genes. Screening of celecoxib and resveratrol and other targeted drugs with stable binding. The findings of this study offer valuable insights into the regulatory mechanisms of gout and may help to identify Biomarkers and develop targeted therapeutic strategies for gout.

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“…We mainly focused on the two miRNAs (miR-424 and miR-346) whose expression was significantly up-regulated with the increase of high glucose concentration. Previous studies have reported the involvement of miR-424 in retina-associated diseases [35][36] , while miR-346 has not been investigated yet. Therefore, miR-346 was selected for further investigations.…”

Section: Expression Of Mirnas In Human Retinal Pigmentmentioning

confidence: 99%

Bioinformatics and in vitro study reveal the roles of microRNA-346 in high glucose-induced human retinal pigment epithelial cell damage

Li,

Liu,

2023

Int J Ophthalmol

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AIM: To study microRNAs (miRNAs) and their potential effects in high glucose-induced human retinal pigment epithelial cell damage. METHODS: We screened the GSE52233 miRNA expression dataset for differentially expressed miRNAs (DEMs). The target genes of the top 10 DEMs were predicted using miRWalk 2.0 database, followed by function enrichment and protein-protein interaction analysis. miRNA expression was determined in the human retinal pigment epithelial cell line ARPE-19 treated with high glucose (HG) by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Cell proliferation was determined using cell counting kit (CCK)-8 assay. Cell cycle, apoptosis, and reactive oxygen species (ROS) levels were determined by flow cytometry. The direct interaction between miRNA and targets was validated using dual-luciferase reporter assay. RESULTS: Thirty-nine DEMs were screened, and we predicted 125 miRNA-mRNA pairs for the top 10 DEMs, including 119 target genes of seven DEMs such as miR-346, which was upregulated in diabetic retinopathy (DR). miR-346 target genes were substantially enriched in the regulation of intracellular transport and retinoic acid-inducible gene I (RIG-I)-like receptor signaling pathway. Expression of three upregulated and downregulated miRNAs were verified by qRT-PCR in HG-treated ARPE-19 cells. Expression of miR-346 was elevated in HG treated ARPE-19 cells in a dose-dependent manner. HG inhibited cell proliferation and induced apoptosis, which were partly reversed by transfecting an miR-346 inhibitor, which even decreased the ROS levels elevated due to HG. Argonaute 2 (AGO2) was a target of miR-346. CONCLUSION: miR-346 is a key miRNA and plays an important role in HG-induced damage in human retinal pigment epithelial cells.

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Integrative analysis of miRNA–mRNA network in high altitude retinopathy by bioinformatics analysis

Cited by 9 publications

References 49 publications

Tracheal Aspirate miRNA Signatures in Preterm Infants with Severe Bronchopulmonary Dysplasia

Tracheal Aspirate miRNA Signatures in Preterm Infants with Severe Bronchopulmonary Dysplasia

Key Genes Associated with Pyroptosis in Gout and Construction of a miRNA-mRNA Regulatory Network

Bioinformatics and in vitro study reveal the roles of microRNA-346 in high glucose-induced human retinal pigment epithelial cell damage

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