scholarly journals Integrated Analysis of Differentially Expressed miRNAs and mRNAs in Goat Skin Fibroblast Cells in Response to Orf Virus Infection Reveals That cfa-let-7a Regulates Thrombospondin 1 Expression

Viruses ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 118
Author(s):  
Feng Pang ◽  
Xinying Wang ◽  
Zhen Chen ◽  
Zhenxing Zhang ◽  
Mengmeng Zhang ◽  
...  
Keyword(s):  
Gene Networks ◽  
Skin Fibroblast ◽  
Mirna Gene ◽  
Differentially Expressed ◽  
Orf Virus ◽  
Economic Losses ◽  
Integrated Analysis ◽  
Goat Skin ◽  
Micro Rnas ◽  
Thrombospondin 1

Orf is a zoonotic disease that has caused huge economic losses globally. Systematical analysis of dysregulated cellular micro RNAs (miRNAs) in response to Orf virus (ORFV) infection has not been reported. In the current study, miRNA sequencing and RNA sequencing (RNA-seq) were performed in goat skin fibroblast (GSF) cells at 0, 18, and 30 h post infection (h.p.i). We identified 140 and 221 differentially expressed (DE) miRNAs at 18 and 30 h.p.i, respectively. We also identified 729 and 3961 DE genes (DEGs) at 18 and 30 h.p.i, respectively. GO enrichment analysis indicates enrichment of apoptotic regulation, defense response to virus, immune response, and inflammatory response at both time points. DE miRNAs and DEGs with reverse expression were used to construct miRNA-gene networks. Seven DE miRNAs and seven DEGs related to “negative regulation of viral genome replication” were identified. These were validated by RT-qPCR. Cfa-let-7a, a significantly upregulated miRNA, was found to repress Thrombospondin 1 (THBS1) mRNA and protein expression by directly targeting the THBS1 3′ untranslated region. THBS1 has been reported to induce apoptosis; therefore, the cfa-let-7a-THBS1 axis may play an important role in cellular apoptosis during ORFV infection. This study provides new insights into ORFV and host cell interaction mechanisms.

scholarly journals Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6267 ◽  
Author(s):  
Feng Pang ◽  
Mengmeng Zhang ◽  
Xiaojian Yang ◽  
Guohua Li ◽  
Shu Zhu ◽  
...  
Keyword(s):  
Skin Fibroblast ◽  
Agricultural Sector ◽  
Orf Virus ◽  
Economic Losses ◽  
Circular Rnas ◽  
Small Rna Sequencing ◽  
Transferase Activity ◽  
Fibroblast Cells ◽  
Positive Regulation ◽  
Goat Skin

Orf, caused by Orf virus (ORFV), is a globally distributed zoonotic disease responsible for serious economic losses in the agricultural sector. However, the mechanism underlying ORFV infection remains largely unknown. Circular RNAs (circRNAs), a novel type of endogenous non-coding RNAs, play important roles in various pathological processes but their involvement in ORFV infection and host response is unclear. In the current study, whole transcriptome sequencing and small RNA sequencing were performed in ORFV-infected goat skin fibroblast cells and uninfected cells. A total of 151 circRNAs, 341 messenger RNAs (mRNAs), and 56 microRNAs (miRNAs) were differently expressed following ORFV infection. Four circRNAs: circRNA1001, circRNA1684, circRNA3127 and circRNA7880 were validated by qRT-PCR and Sanger sequencing. Gene ontology (GO) analysis indicated that host genes of differently expressed circRNAs were significantly enriched in regulation of inflammatory response, epithelial structure maintenance, positive regulation of cell migration, positive regulation of ubiquitin-protein transferase activity, regulation of ion transmembrane transport, etc. The constructed circRNA-miRNA-mRNA network suggested that circRNAs may function as miRNA sponges indirectly regulating gene expression following ORFV infection. Our study presented the first comprehensive profiles of circRNAs in response to ORFV infection, thus providing new clues for the mechanisms of interactions between ORFV and the host.

scholarly journals Pulmonary microRNA profiling in a mouse model of ventilator-induced lung injury

2012 ◽  
Vol 303 (3) ◽  
pp. L199-L207 ◽  
Author(s):  
Katerina Vaporidi ◽  
Eleni Vergadi ◽  
Evangelos Kaniaris ◽  
Maria Hatziapostolou ◽  
Eleni Lagoudaki ◽  
...  
Keyword(s):  
Lung Injury ◽  
Mirna Expression ◽  
Gene Networks ◽  
Target Genes ◽  
Statistical Significance ◽  
Mirna Gene ◽  
Lung Compliance ◽  
Negative Control ◽  
Arterial Oxygen ◽  
Micro Rnas

The aim of this study was to investigate the changes induced by high tidal volume ventilation (HVTV) in pulmonary expression of micro-RNAs (miRNAs) and identify potential target genes and corresponding miRNA-gene networks. Using a real-time RT-PCR-based array in RNA samples from lungs of mice subjected to HVTV for 1 or 4 h and control mice, we identified 65 miRNAs whose expression changed more than twofold upon HVTV. An inflammatory and a TGF-β-signaling miRNA-gene network were identified by in silico pathway analysis being at highest statistical significance ( P = 10−43 and P = 10−28, respectively). In the inflammatory network, IL-6 and SOCS-1, regulated by miRNAs let-7 and miR-155, respectively, appeared as central nodes. In TGF-β-signaling network, SMAD-4, regulated by miR-146, appeared as a central node. The contribution of miRNAs to the development of lung injury was evaluated in mice subjected to HVTV treated with a precursor or antagonist of miR-21, a miRNA highly upregulated by HVTV. Lung compliance was preserved only in mice treated with anti-miR-21 but not in mice treated with pre-miR-21 or negative-control miRNA. Both alveolar-arterial oxygen difference and protein levels in bronchoalveolar lavage were lower in mice treated with anti-miR-21 than in mice treated with pre-miR-21 or negative-control miRNA (DA-a: 66 ± 27 vs. 131 ± 22, 144 ± 10 mmHg, respectively, P < 0.001; protein concentration: 1.1 ± 0.2 vs. 2.3 ± 1, 2.1 ± 0.4 mg/ml, respectively, P < 0.01). Our results show that HVTV induces changes in miRNA expression in mouse lungs. Modulation of miRNA expression can affect the development of HVTV-induced lung injury.

scholarly journals Integrated Analysis of lncRNA, miRNA and mRNA Reveals Novel Insights into the Fertility Regulation of Large White Sows

2019 ◽  
Author(s):  
Huiyan Hu ◽  
Qing Jia ◽  
Jianzhong Xi ◽  
Bo Zhou ◽  
Zhiqiang Li
Keyword(s):  
Molecular Mechanisms ◽  
Ovarian Tissue ◽  
Length Distribution ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Large White ◽  
Reproductive Process ◽  
Mrna Targets ◽  
Micro Rnas

Abstract Background: Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular phases (F) of the estrous cycle in Large White pigs with high (H) and low fecundity (L), and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics. Results: In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P < 0.05 and |log2 (fold change)| ≥ 1to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P < 0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data.Conclusions: These results provide further insights into the fertility of pigs and can contribute to further experimental investigation of the functions of these genes.

scholarly journals Integrated Analysis of lncRNA, miRNA and mRNA Reveals Novel Insights into the Fertility Regulation of Large White Sows

2020 ◽  
Author(s):  
Huiyan Hu ◽  
Qing Jia ◽  
Jianzhong Xi ◽  
Bo Zhou ◽  
Zhiqiang Li
Keyword(s):  
Molecular Mechanisms ◽  
Ovarian Tissue ◽  
Length Distribution ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Large White ◽  
Reproductive Process ◽  
Mrna Targets ◽  
Micro Rnas

Abstract Background: Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular (F) phases of the estrous cycle in Large White pigs with high (H) and low (L) fecundity, and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics.Results: In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P <0.05 and |log2 (fold change)| ≥ 1 to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P <0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data.Conclusions: These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.

scholarly journals Integrated Analysis of lncRNA, miRNA and mRNA Reveals Novel Insights into the Fertility Regulation of Large White Sows

2020 ◽  
Author(s):  
Huiyan Hu ◽  
Qing Jia ◽  
Jianzhong Xi ◽  
Bo Zhou ◽  
Zhiqiang Li
Keyword(s):  
Molecular Mechanisms ◽  
Ovarian Tissue ◽  
Length Distribution ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Large White ◽  
Reproductive Process ◽  
Mrna Targets ◽  
Micro Rnas

Abstract Background: Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular (F) phases of the estrous cycle in Large White pigs with high (H) and low (L) fecundity, and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics.Results: In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P <0.05 and |log2 (fold change)| ≥ 1 to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P <0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data.Conclusions: These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.

scholarly journals Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Huiyan Hu ◽  
Qing Jia ◽  
Jianzhong Xi ◽  
Bo Zhou ◽  
Zhiqiang Li
Keyword(s):  
Molecular Mechanisms ◽  
Ovarian Tissue ◽  
Length Distribution ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Large White ◽  
Reproductive Process ◽  
Mrna Targets ◽  
Micro Rnas

Abstract Background Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular (F) phases of the estrous cycle in Large White pigs with high (H) and low (L) fecundity, and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics. Results In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P < 0.05 and |log2 (fold change)| ≥ 1 to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P < 0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data. Conclusions These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.

scholarly journals Genome-wide profiling of miRNA expression patterns in tubal endometriosis

Reproduction ◽  
2019 ◽  
Vol 157 (6) ◽  
pp. 525-534 ◽  
Author(s):  
Hang Qi ◽  
Guiling Liang ◽  
Jin Yu ◽  
Xiaofeng Wang ◽  
Yan Liang ◽  
...  
Keyword(s):  
Pathway Analysis ◽  
Mirna Expression ◽  
Gene Networks ◽  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Mirna Gene ◽  
Differentially Expressed ◽  
Signal Pathways ◽  
Differentially Expressed Mirnas

MicroRNA (miRNA) expression profiles in tubal endometriosis (EM) are still poorly understood. In this study, we analyzed the differential expression of miRNAs and the related gene networks and signaling pathways in tubal EM. Four tubal epithelium samples from tubal EM patients and five normal tubal epithelium samples from uterine leiomyoma patients were collected for miRNA microarray. Bioinformatics analyses, including Ingenuity Pathway Analysis (IPA), Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, were performed. Quantitative real-time polymerase chain reaction (qRT-PCR) validation of five miRNAs was performed in six tubal epithelium samples from tubal EM and six from control. A total of 17 significantly differentially expressed miRNAs and 4343 potential miRNA-target genes involved in tubal EM were identified (fold change >1.5 and FDR-adjustedPvalue <0.05). IPA indicated connections between miRNAs, target genes and other gynecological diseases like endometrial carcinoma. GO and KEGG analysis revealed that most of the identified genes were involved in the mTOR signaling pathway, SNARE interactions in vesicular transport and endocytosis. We constructed an miRNA-gene-disease network using target gene prediction. Functional analysis showed that the mTOR pathway was connected closely to tubal EM. Our results demonstrate for the first time the differentially expressed miRNAs and the related signal pathways involved in the pathogenesis of tubal EM which contribute to elucidating the pathogenic mechanism of tubal EM-related infertility.

scholarly journals Parapoxvirus orf virus infection induces an increase in interleukin-8, tumour necrosis factor-α, and decorin in goat skin fibroblast cells

2016 ◽  
Vol 60 (3) ◽  
pp. 239-243 ◽  
Author(s):  
Lingling Wang ◽  
Bingzhou Lu ◽  
Haixue Zheng ◽  
Keshan Zhang ◽  
Xiangtao Liu
Keyword(s):  
Immune Response ◽  
Tumour Necrosis Factor ◽  
Tumour Necrosis ◽  
Skin Fibroblast ◽  
Interleukin 8 ◽  
Orf Virus ◽  
Enzyme Linked Immunosorbent Assay ◽  
Goat Skin ◽  
Tnf Α ◽  
Necrosis Factor

AbstractIntroduction: Orf virus (ORFV) is a prototype Parapoxvirus species in the Poxviridae family that causes serious zoonotic infectious disease. Goat skin fibroblast (GSF) cells are the major host targets of ORFV. Interleukin 8 (IL-8) and tumour necrosis factor (TNF)-α are known to play a vital role in immune response during viral infections. However, the manner of variation over time of their level of expression in GSF cells remains unclear.Material and Methods: In this study, quantitative enzyme-linked immunosorbent assay chips were used to detect changes in the levels of these cytokines expressed and secreted in GSF cells after ORFV infection.Results: Results showed that the expression of IL-8, TNF-α, and decorin was upregulated in the cell lysates, and that secreted decorin and IL-8 were significantly increased in cell supernatant.Conclusion: The results provided possible approaches to elucidation of how ORFV infection initiates host cell immune response.

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