scholarly journals Comprehensive analysis of differentially expressed microRNAs and mRNAs in MDBK cells expressing bovine papillomavirus E5 oncogene

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8098 ◽  
Author(s):  
Feng Pang ◽  
Zhen Chen ◽  
Chengqiang Wang ◽  
Mengmeng Zhang ◽  
Zhenxing Zhang ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Cancer Progression ◽  
Expression Profiles ◽  
Mirna Gene ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Bovine Papillomavirus ◽  
Mdbk Cells ◽  
Gene Regulatory ◽  
First Time

Delta bovine papillomaviruses (δBPVs) causes fibropapillomas or bladder cancer in cattle. E5 is the major oncogene of δBPVs; however, the influence that E5 oncogene has on host microRNA (miRNA) and mRNA expression profiles remains little elucidated. In the present study, small RNA sequencing and RNA sequencing were used to explore alterations in miRNAs and mRNAs in E5 over-expressing Madin-Darby bovine kidney (MDBK) cells compared with controls. In total, 77 miRNAs (including 30 bovine-derived miRNAs) and 223 genes were differentially expressed (DE) following E5 overexpression. The dysregulated genes were mainly involved in metabolic and biosynthetic processes. We constructed a potential miRNA-gene regulatory network from the differentially expressed genes (DEGs) and DE miRNAs. Finally, 22 DEGs and nine DE miRNAs were selected for RT-qPCR validation. Of these, downregulation of six miRNAs, bta-miR-34c, bta-miR-122, bta-miR-195, bta-miR-449b, bta-miR-2425-5p, and bta-miR-2428-3p were confirmed; In addition, upregulation of 16 genes, ACSS2, DDIT4, INHBE, INSIG1, PNRC1, PSAT1, PSPH, PYCR1, SC4MOL, SLC34A2, SCD, SPARC, IDI1, PCK2, HMGCS1, and SMIM14 and downregulation of two genes, BATF3 and WFDC2 were confirmed. Specially, bta-miR-34c and bta-miR-449b potentially regulated PYCR1 and DDIT4, which were involved in cancer progression and angiogenesis. Our study presented for the first time the comprehensive miRNA and mRNA alterations in MDBK cells expressing the BPV E5 oncogene, providing new insights into the tumorigenesis induced by BPV E5.

scholarly journals Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7442 ◽  
Author(s):  
Feng Pang ◽  
Mengmeng Zhang ◽  
Guohua Li ◽  
Zhenxing Zhang ◽  
Haifeng Huang ◽  
...  
Keyword(s):  
Immune Response ◽  
Rna Sequencing ◽  
Expression Profiles ◽  
Mirna Gene ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Bovine Papillomavirus ◽  
3T3 Cells ◽  
Nih 3T3 ◽  
Nih 3T3 Cells

Delta bovine papillomaviruses (δBPVs) mainly infect cattle and cause fibropapillomas. δBPVs encode three oncogenes, E5, E6 and E7. The effect of E6 on microRNA (miRNA) and mRNA expression profiles is not well characterized. In this study, RNA sequencing and small RNA sequencing were used to explore alterations in mRNAs and miRNAs in E6 over-expressing NIH/3T3 cells (NH-E6) compared with control cells (NH-GFP). We found that 350 genes (181 upregulated and 169 downregulated) and 54 miRNAs (26 upregulated and 28 downregulated) were differentially expressed (DE) following E6 expression. The top 20 significantly enriched GO terms in “biological process” included inflammatory response, innate immune response, immune response, immune system process, positive regulation of apoptotic process, cell adhesion, and angiogenesis. We constructed a potential miRNA-gene regulatory network from the differentially expressed genes (DEGs) and DE miRNAs. Finally, we selected 19 immune-response related DEGs and 11 DE miRNAs for qPCR validation. Of these, upregulation of 12 genes, Ccl2, Ccl7, Cxcl1, Cxcl5, Tlr2, Nfkbia, Fas, Il1rl1, Ltbp1, Rab32, and Zc3h12a, Dclk1 and downregulation of four genes, Agtr2, Ptx3, Sfrp1, and Thbs1 were confirmed. Ccl2, Ccl7, Cxcl1 and Cxcl5 were upregulated more than ten-fold in NH-E6 compared with NH-GFP. Also, upregulation of three miRNAs, mmu-miR-129-2-3p, mmu-miR-149-5p-R-2 and mmu-miR-222-3p, and downregulation of five miRNAs, mmu-miR-582-3p-R+1, mmu-miR-582-5p, mmu-miR-708-3p, mmu-miR-708-5p and mmu-miR-1197-3p, were confirmed. Our study describes changes in both mRNA and miRNA profiles in response to BPV E6 expression, providing new insights into BPV E6 oncogene functions.

scholarly journals Analysis of conserved miRNAs in cynomolgus macaque genome using small RNA sequencing and homology searching

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9347
Author(s):  
Xia Huang ◽  
Shijia Li ◽  
Xiaoming Liu ◽  
Shuting Huang ◽  
Shuang Li ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Mirna Gene ◽  
Cynomolgus Macaque ◽  
Future Research ◽  
Small Rna Sequencing ◽  
Homology Searching ◽  
Macaque Genome ◽  
Cynomolgus Macaques ◽  
Mirna Clusters

MicroRNAs (miRNAs) are important regulators that fine-tune diverse cellular activities. Cynomolgus macaques (Macaca fascicularis) are used extensively in biomedical and pharmaceutical research; however, substantially fewer miRNAs have been identified in this species than in humans. Consequently, we investigated conserved miRNA profiles in cynomolgus macaques by homology searching and small RNA sequencing. In total, 1,455 high-confidence miRNA gene loci were identified, 408 of which were also confirmed by RNA sequencing, including 73 new miRNA loci reported in cynomolgus macaques for the first time. Comparing miRNA expression with age, we found a positive correlation between sequence conservation and expression levels during miRNA evolution. Additionally, we found that the miRNA gene locations in cynomolgus macaque genome were very flexible. Most were embedded in intergenic spaces or introns and clustered together. Several miRNAs were found in certain gene locations, including 64 exon-resident miRNAs, six splice-site-overlapping miRNAs (SO-miRNAs), and two pairs of distinct mirror miRNAs. We also identified 78 miRNA clusters, 68 of which were conserved in the human genome, including 10 large miRNA clusters predicted to regulate diverse developmental and cellular processes in cynomolgus macaque. Thus, this study not only expands the number of identified miRNAs in cynomolgus macaques but also provides clues for future research on the differences in miRNA repertoire between macaques and humans.

2181The prothrombotic transcriptome of reticulated platelets

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
D Bongiovanni ◽  
G Santamaria ◽  
M Klug ◽  
D Santovito ◽  
A Felicetta ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Platelet Activation ◽  
Small Rna ◽  
Peripheral Blood ◽  
Cardiovascular Events ◽  
Platelet Reactivity ◽  
Gene Set Enrichment Analysis ◽  
Small Rna Sequencing ◽  
Reticulated Platelets ◽  
First Time

Abstract Introduction Reticulated platelets (RPs) are young, hyper-reactive platelets that are larger and contain significantly more RNA compared to older mature platelets. High levels of RPs in peripheral blood are predictors of an insufficient response to dual antiplatelet therapy in cardiovascular patients and of adverse cardiovascular events also in non-cardiac patients. However, the mechanisms underlying these correlations remains widely unknown and the biology of RPs has not been investigated yet. Purpose We aimed to compare for the first time the transcriptomic profiles of RPs and mature platelets (MPs). Methods RPs and MPs from peripheral blood of healthy donors were identified and isolated using FACS/Sorting based on their RNA-content. Immediately after sorting, RNA was extracted and quality, concentration and integrity was assessed with the Tapestation 4200 platform (Agilent). Total- and small-RNA libraries were prepared, multiplexed and sequenced on a NextSeq 500 Illumina platform Results Total-RNA-sequencing revealed 1744 differentially expressed genes (670 downregulated 1074 upregulated) in RPs compared to MPs (Figure 1A, B). In particular, transcripts for the collagen receptor GP6, thromboxane receptor A2 (TBXA2R), thrombin receptor PAR4 (F2RL3) and ATP receptor P2RX1 were significantly enriched in RPs, whereas several RNA regulators as the ribonuclease PARN, the RISC-component TNRC6A and the splicing factor LUC7L3 were downregulated in RPs. Gene ontology analysis revealed an enrichment of relevant biological categories in RPs including platelet activation and blood coagulation (Figure 1C). Gene Set Enrichment Analysis showed an enrichment of several activation pathways like thrombin, thromboxane and GPIIb/IIIa signaling in RPs. Small-RNA-sequencing reported 9 miRNAs significantly downregulated in RPs with targets involved in platelet reactivity. Figure 1 Conclusions This study represents the first comparative transcriptome analysis of RPs and MPs and reports for the first time a differential enrichment of transcripts involved in platelet activation. The clear upregulation of prothrombotic signaling in RPs could explain, at least in part, their hyper-activity and their correlation with cardiovascular events in different pathological settings (trancripts enriched in RPs: Figure 1D). Acknowledgement/Funding German Society of Cardiology (DGK Nr.102018) ESC First conctact initiative grant 2018

scholarly journals Small RNA Sequencing Uncovers New miRNAs and moRNAs Differentially Expressed in Normal and Primary Myelofibrosis CD34+ Cells

PLoS ONE ◽  
2015 ◽  
Vol 10 (10) ◽  
pp. e0140445 ◽  
Author(s):  
Paola Guglielmelli ◽  
Andrea Bisognin ◽  
Claudia Saccoman ◽  
Carmela Mannarelli ◽  
Alessandro Coppe ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Primary Myelofibrosis ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Cd34 Cells

scholarly journals Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus

Pathogens ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 183 ◽  
Author(s):  
Oh ◽  
Lim ◽  
Song ◽  
Ahn ◽  
Lee ◽  
...  
Keyword(s):  
Varicella Zoster Virus ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Dermal Fibroblasts ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Human Dermal Fibroblasts ◽  
Varicella Zoster ◽  
Low Passage

Licensed live attenuated vaccines have been developed to prevent varicella zoster virus (VZV) infection, which causes chickenpox and shingles. The genomic sequences of both clinical- and vaccine-derived VZV strains have been analyzed previously. To further characterize the molecular signatures and complexity of wildtype (clinical) versus attenuated (vaccine-derived) VZV-mediated host cellular responses, we performed high-throughput next generation sequencing to quantify and compare the expression patterns of mRNAs and microRNAs (miRNAs) in primary human dermal fibroblasts (HDFs) infected with wildtype (YC01 low passage) and attenuated (YC01 high passage, SuduVax, and VarilRix) VZV strains. 3D-multidimensional scaling of the differentially expressed genes demonstrated the distinct grouping of wildtype and attenuated strains. In particular, we observed that HDFs infected with attenuated strains had more differentially expressed genes (DEGs) involved in the retinoic-acid inducible gene–I-like receptor and interferon-mediated signaling pathways compared with wildtype strains. Additionally, miRNA expression patterns were profiled following the infection of HDFs with VZV. Small RNA sequencing identified that several miRNAs were upregulated, including miR-146a-5p, which has been associated with other herpesvirus infections, whereas let-7a-3p was downregulated in both wildtype and attenuated VZV-infected cells. This study identified genes and miRNAs that may be essential in VZV pathogenesis.

scholarly journals Identification of Hub Prognosis-Associated Oxidative Stress Genes in Pancreatic Cancer Using Integrated Bioinformatics Analysis

2020 ◽  
Vol 11 ◽  
Author(s):  
Xin Qiu ◽  
Qin-Han Hou ◽  
Qiu-Yue Shi ◽  
Hai-Xing Jiang ◽  
Shan-Yu Qin
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Pancreatic Cancer ◽  
Cancer Progression ◽  
Risk Model ◽  
Cox Regression ◽  
Expression Profiles ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Cox Regression Analysis

BackgroundIntratumoral oxidative stress (OS) has been associated with the progression of various tumors. However, OS has not been considered a candidate therapeutic target for pancreatic cancer (PC) owing to the lack of validated biomarkers.MethodsWe compared gene expression profiles of PC samples and the transcriptome data of normal pancreas tissues from The Cancer Genome Atlas (TCGA) and Genome Tissue Expression (GTEx) databases to identify differentially expressed OS genes in PC. PC patients’ gene profile from the Gene Expression Omnibus (GEO) database was used as a validation cohort.ResultsA total of 148 differentially expressed OS-related genes in PC were used to construct a protein-protein interaction network. Univariate Cox regression analysis, least absolute shrinkage, selection operator analysis revealed seven hub prognosis-associated OS genes that served to construct a prognostic risk model. Based on integrated bioinformatics analyses, our prognostic model, whose diagnostic accuracy was validated in both cohorts, reliably predicted the overall survival of patients with PC and cancer progression. Further analysis revealed significant associations between seven hub gene expression levels and patient outcomes, which were validated at the protein level using the Human Protein Atlas database. A nomogram based on the expression of these seven hub genes exhibited prognostic value in PC.ConclusionOur study provides novel insights into PC pathogenesis and provides new genetic markers for prognosis prediction and clinical treatment personalization for PC patients.

Analysis of the miRNA transcriptome during testicular development and spermatogenesis of the Mongolian horse

2020 ◽  
Vol 32 (6) ◽  
pp. 582
Author(s):  
Bei Li ◽  
Xiaolong He ◽  
Yiping Zhao ◽  
Dongyi Bai ◽  
Dandan Li ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Mammalian Species ◽  
Mature Mirnas ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
P Value ◽  
Testicular Development ◽  
Interaction Sites ◽  
Mongolian Horse

Numerous studies have shown that microRNAs (miRNAs) are essential for testicular development and spermatogenesis. In order to further characterise these physiological processes, three immature and three mature testes of the Mongolian horse were collected and six libraries were established. Using small RNA sequencing technology, 531 mature miRNAs were identified, including 46 novel miRNAs without previously ascribed functions. Among the 531 miRNAs, 421 were expressed in both immature and mature libraries, 65 miRNAs were found solely in immature testis libraries and 45 miRNAs were found solely in mature testis libraries. Furthermore, among the miRNAs that were identified in both immature and mature libraries, 107 were significantly differentially expressed (corrected P value (padj)<0.05). Among the miRNAs that were only expressed in immature testes, two miRNAs were differentially expressed, whereas among the miRNAs that were only expressed in mature testes, nine miRNAs were differentially expressed. Comprehensive analysis of miRNA and mRNA expression profiles predicted 107 miRNA–mRNA interaction sites. Gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis of the predicted target genes suggested roles of the differentially expressed miRNAs in testicular development and spermatogenesis. These findings identify miRNAs as key factors in the development of the testes and spermatogenesis in the Mongolian horse, which may also help us to understand the mechanisms of fertility in related mammalian species.

scholarly journals Small RNA Sequencing Reveals Differentially Expressed miRNAs in Necrotizing Enterocolitis in Rats

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Ren-qiang Yu ◽  
Min Wang ◽  
Shan-yu Jiang ◽  
Ying-hui Zhang ◽  
Xiao-yu Zhou ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Signaling Pathway ◽  
Rna Sequencing ◽  
Necrotizing Enterocolitis ◽  
Small Rna ◽  
Mirna Expression ◽  
Expression Patterns ◽  
Wnt Signaling Pathway ◽  
Differentially Expressed ◽  
Small Rna Sequencing

Necrotizing enterocolitis (NEC) is the leading cause of death due to gastrointestinal disease in preterm infants. The role of miRNAs in NEC is still unknown. The objective of this study was to identify differentially expressed (DE) miRNAs in rats with NEC and analyze their possible roles. In this study, a NEC rat model was established using Sprague-Dawley rat pups. Small RNA sequencing was used to analyze the miRNA expression profiles in the NEC and control rats. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out to identify target mRNAs for the DE miRNAs and to explore their potential roles. The DE miRNAs were verified by real-time quantitative PCR (RT-qPCR). The status of intestinal injury and the elevated levels of inflammatory cytokines in the NEC group confirmed that the NEC model was successfully established. The 16 miRNAs were found to be differentially expressed between the NEC group and the control group of rats. Bioinformatics analysis indicated that the parental genes of the DE miRNAs were predominantly implicated in the phosphorylation, cell migration, and protein phosphorylation processes. Moreover, the DE miRNAs were mainly found to be involved in the pathways of axon guidance, endocytosis, and focal adhesion, as well as in the Wnt signaling pathway, which is related to colitis. The expression patterns of the candidate miRNAs (rno-miR-27a-5p and rno-miR-187-3p), as assessed by RT-qPCR, were in accordance with the expression patterns obtained by miRNA-sequencing. The miRNA/mRNA/pathway network revealed that rno-miR-27a-5p and rno-miR-187-3p might be involved in NEC via the Wnt signaling pathway. We found an altered miRNA expression pattern in rats with NEC. We hypothesize that rno-miR-27a-5p and rno-miR-187-3p might mediate the NEC pathophysiological processes via the Wnt signaling pathway.

scholarly journals Role of miRNAs in Sigmoid Colon Cancer: A Search for Potential Biomarkers

Cancers ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 3311
Author(s):  
Diego Marques ◽  
Layse Raynara Ferreira-Costa ◽  
Lorenna Larissa Ferreira-Costa ◽  
Ana Beatriz Bezerra-Oliveira ◽  
Romualdo da Silva Correa ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Sigmoid Colon ◽  
Cancer Progression ◽  
Target Genes ◽  
Mirna Gene ◽  
Differentially Expressed ◽  
Sigmoid Colon Cancer ◽  
Colon Tissue ◽  
Aberrant Expression ◽  
Differentially Expressed Mirnas

The aberrant expression of microRNAs in known to play a crucial role in carcinogenesis. Here, we evaluated the miRNA expression profile of sigmoid colon cancer (SCC) compared to adjacent-to-tumor (ADJ) and sigmoid colon healthy (SCH) tissues obtained from colon biopsy extracted from Brazilian patients. Comparisons were performed between each group separately, considering as significant p-values < 0.05 and |Log2(Fold-Change)| > 2. We found 20 differentially expressed miRNAs (DEmiRNAs) in all comparisons, two of which were shared between SCC vs. ADJ and SCC vs. SCH. We used miRTarBase, and miRTargetLink to identify target-genes of the differentially expressed miRNAs, and DAVID and REACTOME databases for gene enrichment analysis. We also used TCGA and GTEx databases to build miRNA-gene regulatory networks and check for the reproducibility in our results. As findings, in addition to previously known miRNAs associated with colorectal cancer, we identified three potential novel biomarkers. We showed that the three types of colon tissue could be clearly distinguished using a panel composed by the 20 DEmiRNAs. Additionally, we found enriched pathways related to the carcinogenic process in which miRNA could be involved, indicating that adjacent-to-tumor tissues may be already altered and cannot be considered as healthy tissues. Overall, we expect that these findings may help in the search for biomarkers to prevent cancer progression or, at least, allow its early detection, however, more studies are needed to confirm our results.

scholarly journals The origin, fate and function of macrophages in the peripheral nervous system—an update

2020 ◽  
Vol 32 (11) ◽  
pp. 709-717 ◽  
Author(s):  
Lukas Amann ◽  
Marco Prinz
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
Rna Sequencing ◽  
Peripheral Nervous System ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
New Techniques ◽  
Macrophage Populations ◽  
And Function ◽  
First Time

Abstract The field of macrophage biology has made enormous progress over recent years. This was triggered by the advent of several new techniques such as the establishment of Cre/loxP-based transgenic mouse models that allowed for the first time delineation of the ontogeny and function of specific macrophage populations across many tissues. In addition, the introduction of new high-throughput technologies like bulk RNA sequencing and later single-cell RNA sequencing as well as advances in epigenetic analysis have helped to establish gene expression profiles, enhancer landscapes and local signaling cues that define and shape the identity of diverse macrophage populations. Nonetheless, some macrophage populations, like the ones residing in the peripheral nervous system (PNS), have not been studied in such detail yet. Here, we discuss recent studies that shed new light on the ontogeny, heterogeneity and gene expression profiles of resident macrophages in peripheral nerves and described differential activation of macrophage subsets during and after acute sciatic nerve injury.

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