The Encystment-Related MicroRNAs and Its Regulation Molecular Mechanism in Pseudourostyla cristata Revealed by High Throughput Small RNA Sequencing

Pan, Nan; Bhatti, Muhammad Zeeshan; Zhang, Haiyang; Ni, Bing; Fan, Xinpeng; Chen, Jiwu

doi:10.3390/ijms21072309

Cited by 5 publications

(4 citation statements)

References 51 publications

(55 reference statements)

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“…The threshold used to screen RNAs with |log 2 FC| >1 was P<0.05. |log 2 FC| >1 is to screen genes with multiples of difference >2 times ( 34 , 35 ). Gene Ontology (GO) analysis ( http://www.geneontology.org ) described the molecular function, cellular component and biological process of differentially expressed transcripts.…”

Section: Methodsmentioning

confidence: 99%

Characterization of novel lncRNAs in upper thoracic spinal cords of rats with myocardial ischemia‑reperfusion injuries

Wang

et al. 2021

Exp Ther Med

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Myocardial ischemia-reperfusion injury (MIRI) is a significant problem in clinical cardiology, and refers to a more serious myocardial injury caused by blood recanalization after a period of myocardial ischemia, as compared with injury caused by vascular occlusion. The spinal cord, as the primary afferent and efferent center of cardiac sensory and sympathetic nerve fibres, has received increased attention in recent years with regards to the regulation of MIRIs. Previous studies have revealed that MIRI has a strong correlation with the abnormal expression of long non-coding (lnc)RNAs in the myocardium; however, there are limited reports on the effects of the altered expression of lncRNAs in the spinal cord following MIRI. To investigate the expression patterns of lncRNAs in the spinal cord after MIRI and their potential role in the early stage of reperfusion, a MIRI model was established in rats. After 30 min of myocardial ischemia and 2 h of reperfusion, the upper thoracic spinal cord tissues were immediately dissected and isolated. lncRNAs and mRNAs in spinal cord tissues were screened using transcriptome sequencing technology, and the expression of several highly deregulated mRNAs, including Frs3, Zfp52, Dnajc6, Nedd4l, Tep1, Myef2, Tgfbr1, Fgf12, Mef2c, Tfdp1 and lncRNA, including ENSRNOT00000080713, ENSRNOT00000090564, ENSRNOT00000082588, ENSRNOT00000091080, ENSRNOT00000091570, ENSRNOT00000087777, ENSRNOT00000082061, ENSRNOT00000091108, ENSRNOT00000087028, ENSRNOT00000086475, were further validated via reverse transcription-quantitative PCR. The number of altered expressed lncRNAs was 126, among which there were 41 upregulated probe sets and 85 downregulated sets. A total of 470 mRNAs were differentially expressed, in which 231 probe sets were upregulated and 239 were downregulated. Gene Ontology analysis indicated that dysregulated transcripts related to biological processes were mainly associated with ‘cell-cell signaling’. Moreover, pathway analysis demonstrated significant changes in the ‘PI3K/Akt signaling pathway’ and the ‘p53 signaling pathway’. Thus, the altered expression of lncRNAs in the spinal cord may be of considerable importance in the process of MIRI. The present results could provide an insight into the potential roles and mechanism of lncRNAs during the early stage of reperfusion.

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Section: Methodsmentioning

confidence: 99%

Characterization of novel lncRNAs in upper thoracic spinal cords of rats with myocardial ischemia‑reperfusion injuries

Wang

et al. 2021

Exp Ther Med

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“…The data on exosomal miRNAs obtained from the three groups were compared, and the expression levels of isolated miRNAs were normalized to the default 90th percentile. According to relevant criteria, miRNAs with their |log2 (Flod change)| ≥ 1 and Q value ≤ 0.001 are considered as differential genes, and a Log2 (Flod change) value greater than 0 indicates upregulated miRNA expression, while a Log 2 value less than 0 means signifies downregulated miRNA expression, the Q value refers to FDR adjusted P ‐value, and Flod change is the ratio between two gene expression levels, 17,18 a heat map for cluster analysis was created based on the relevant |log2| values, featuring miRNAs with remarkable differences, for further observation of differences in miRNAs among the three groups, meanwhile, prediction of target genes of the selected differential miRNAs was conducted based on RNAhybrid (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/), miRand (http://www.microrna.org/Microrna/home.do) and TargetScan (http://www.the http://targetscan.org/) databases, and the gene ontology (GO) and KEGG enrichment analyses of the obtained target genes were also performed.…”

Section: Methodsmentioning

confidence: 99%

Section: Prediction and Enrichment Analysis Of Mirna Target Genesmentioning

confidence: 99%

Expression of miRNAs in plasma exosomes derived from patients with atrial fibrillation

Zhang

Shaohuan

et al. 2020

Clinical Cardiology

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Background: Studies have revealed the association between exosomes and cardiovascular diseases. However, the typical changes of plasma miRNAs in patients with atrial fibrillation (AF) are still controversial, the use of exosomal miRNAs to diagnose and predict the prognosis of AF has not been described. Hypothesis: We hypothesized that there were differences in the exosomal miRNAs between AF and normal sinus rhythm (SR) patients, which might be used as the novel biomarkers to reflect the progression of AF. Methods: miRNAs were isolated from the plasma of patients, and the target genes of differential miRNAs via enrichment analysis to discover potential pathogenesis related to AF. Combined with high-throughput sequencing results, real-time PCR was used to verify the relative expression of target miRNAs in patients. Results: This study confirmed that the expression of plasma-derived exosomal miRNAs between patients with AF and SR were different. Target gene enrichment analysis suggested that the target genes of 20 miRNAs, which were significantly upregulated were mainly enriched in biological processes such as gene expression process, inflammation response, enzyme modification, etc. Meanwhile, mitogenactivated protein kinase (MAPK), mammalian target of rapamycin (mTOR), and other pathways were highly enriched. The expressions of miR-92b-3p, miR-1306-5p, and miR-let-7b-3p had differences between patients with AF and SR. Conclusion: These miRNAs and target genes were involved in the process of AF through affecting biological processes such as energy metabolism, lipid metabolism, inflammation, and enzyme activity. It suggested that the exosomal miRNAs might be used as the novel biomarkers to reflect the progression of AF.

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“…However, to date, a holistic approach to identify differences in gene signatures between short- and long-term SARS-CoV-2 infections is lacking. Meanwhile, there are numerous studies working on potential messenger (m)RNA candidates associated with CoV infection and their downstream target genes ( Nilsson et al, 2019 ; Abele et al, 2020 ; Lopez et al, 2020 ; Pan et al, 2020 ). Predictive markers and therapeutic strategies for CoVs have not been identified and systematically investigated.…”

Section: Introductionmentioning

confidence: 99%

Gene signatures of SARS-CoV/SARS-CoV-2-infected ferret lungs in short- and long-term models

Liu

Yeh

Phan

et al. 2020

Infection, Genetics and Evolution

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Coronaviruses (CoVs) consist of six strains, and the severe acute respiratory syndrome coronavirus (SARS-CoV), newly found coronavirus (SARS-CoV-2) has rapidly spread leading to a global outbreak. The ferret ( Mustela putorius furo) serves as a useful animal model for studying SARS-CoV/SARS-CoV-2 infection and developing therapeutic strategies. A holistic approach for distinguishing differences in gene signatures during disease progression is lacking. The present study discovered gene expression profiles of short-term (3 days) and long-term (14 days) ferret models after SARS-CoV/SARS-CoV-2 infection using a bioinformatics approach. Through Gene Ontology (GO) and MetaCore analyses, we found that the development of stemness signaling was related to short-term SARS-CoV/SARS-CoV-2 infection. In contrast, pathways involving extracellular matrix and immune responses were associated with long-term SARS-CoV/SARS-CoV-2 infection. Some highly expressed genes in both short- and long-term models played a crucial role in the progression of SARS-CoV/SARS-CoV-2 infection, including DPP4, BMP2, NFIA, AXIN2, DAAM1, ZNF608, ME1, MGLL, LGR4, ABHD6 , and ACADM. Meanwhile, we revealed that metabolic, glucocorticoid, and reactive oxygen species-associated networks were enriched in both short- and long-term infection models. The present study showed alterations in gene expressions from short-term to long-term SARS-CoV/SARS-CoV-2 infection. The current result provides an explanation of the pathophysiology for post-infectious sequelae and potential targets for treatment.

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The Encystment-Related MicroRNAs and Its Regulation Molecular Mechanism in Pseudourostyla cristata Revealed by High Throughput Small RNA Sequencing

Cited by 5 publications

References 51 publications

Characterization of novel lncRNAs in upper thoracic spinal cords of rats with myocardial ischemia‑reperfusion injuries

Characterization of novel lncRNAs in upper thoracic spinal cords of rats with myocardial ischemia‑reperfusion injuries

Expression of miRNAs in plasma exosomes derived from patients with atrial fibrillation

Gene signatures of SARS-CoV/SARS-CoV-2-infected ferret lungs in short- and long-term models

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