Study on long noncoding RNA in enterovirus 71-induced severe hand-foot-mouth disease

2020 ◽  
Author(s):  
Fang Fang ◽  
He yi ◽  
Xu feng
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Target Gene ◽  
Target Genes ◽  
Enterovirus 71 ◽  
Mouth Disease ◽  
Differentially Expressed ◽  
Kegg Analysis ◽  
Hand Foot Mouth Disease ◽  
Critical Type

Abstract Background: To identify the critical type of severe hand-foot-mouth disease (HFMD) in early stage, long noncoding ribonucleic acid (LncRNA) microarray was used to screen specific LncRNA and to predictpossible pathogenesis and target genes of HFMD. Methods: Twenty cases of EV71-induced severe HFMD were collected in Children’s Hospital of Chongqing Medical University from September 2015 to September 2016. LncRNA microarray was used to analyze the expression of LncRNA and mRNA in peripheral blood of children between severe type and critical type, and then verify the validity by real-time polymerase chain reaction. Bioinformatic methods were used to investigate differentially expressed mRNA by gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Results: We obtained differentially expressed profiles of LncRNA and mRNA from peripheral blood of children with EV71-induced severe HFMD, and the number of LncRNA was 1949, the total mRNA profiles were 1422. GO analysis found that differentially expressed mRNAs were involved in the processes of immune response, immune defense, nucleic acid metabolism, and protein and molecule binding. KEGG analysis revealed that the differentially expressed mRNAs were involved in the p53 signaling pathway, NOD-like receptor signaling pathway, osteoblast differentiation, and so on. The target gene SLPI was closely related to the critical type of severe HFMD by cis/trans target gene prediction, and the pathogenic processes was regulated by LncRNA NR_038337. Conclusion: Since differentially expressed LncRNAs and mRNAs are present in severe HFMD, our findings provide a new method to explore the pathogenesis of the critical type of severe HFMD, andfurther study on specific LncRNA and target genes in critical type has great significance for diagnosis and treatment of severe HFMD. Keywords: Long noncoding RNA; Enterovirus 71; Severe hand-foot-mouth disease; Target gene Trial registration:ChiCTR-DCD-15007192.Registered 8 October,2015, http://www.chictr.org.cn/ ChiCTR-DCD-15007192

scholarly journals Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep

2020 ◽  
Author(s):  
Xige He ◽  
Rihan Wu ◽  
Yueying Yun ◽  
Xia Qin ◽  
Lu Chen ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Messenger Rna ◽  
Noncoding Rna ◽  
Target Genes ◽  
Early Stage ◽  
Expression Profiles ◽  
Theoretical Data ◽  
Differentially Expressed ◽  
Growth Stages ◽  
Complex Biological Process

Abstract Background: Sunite sheep are a fat-tailed sheep species with a low percentage of intramuscular fat and good quality lean meat, and their tail fat can be used as a source of dietary fat by humans. To understand the potential regulatory mechanism of different growth stages of tail fat in Sunite sheep, we performed high-throughput RNA sequencing to characterize the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of the sheep tail fat at the age of 6 months, 18 months, and 30 months.Results: A total of 223 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs were found in the tail fat of 6-, 18-, and 30-month-old sheep (false discovery rate < 0.05, |Fold Change| ≥ 2). Based on the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, we found that fat-related DEGs were mainly expressed at 6 months of age, and gradually decreased at 18 and 30 months of age. The target gene prediction analysis shows that most of the lncRNAs target more than 20 mRNAs as their trans-regulators (53 mRNAs at most). Further, we obtained several fat-related differentially-expressed target genes; these target genes interact with different differentially expressed lncRNAs at various ages and play an important role in the development of tail fat. Based on the DEGs and differentially expressed lncRNAs, we established three co-expression networks for each comparison group. Conclusions: Finally, we conclude that the development of the sheep tail fat is more active during the early stage of growth and gradually decreases with the increase in age. The mutual regulation of lncRNAs and mRNAs may play a key role in this complex biological process, and our findings will provide some basic theoretical data for future studies on tail fat development of fat-tailed sheep.

scholarly journals Comprehensive analysis of long noncoding RNA and mRNA in five colorectal cancer tissues and five normal tissues

2020 ◽  
Vol 40 (2) ◽  
Author(s):  
Zhen-Xu Zhou ◽  
Xiao-Ming Chen ◽  
Yu-Qi Zhang ◽  
Liu Peng ◽  
Xiang-Yang Xue ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Target Genes ◽  
R Package ◽  
Structural Features ◽  
Differentially Expressed ◽  
Normal Tissues ◽  
Regulatory Effects ◽  
Differentially Expressed Mrna

Abstract The present study investigated the role of abnormally expressed mRNA and long noncoding RNA (lncRNA) in the development of colorectal cancer (CRC). We used lncRNA sequencing to analyze the transcriptome (mRNA and lncRNA) of five pairs of CRC tissues and adjacent normal tissues. The total expression of mRNAs and lncRNAs in each sample was determined using the R package and the gene expression was calculated using normalized FPKM. The structural features and expression of all detected lncRNAs were compared with those of mRNAs. Differentially expressed mRNAs were selected to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. The functional analysis of differentially expressed lncRNAs was performed by analyzing the GO and KEGG enrichment of predicted cis-regulated target genes. A total of 18.2 × 108 reads were obtained by sequencing, in which the clean reads reached ≥ 94.67%, with a total of 245.2 G bases. The number of mRNAs and lncRNAs differentially expressed in CRC tissues and normal tissues were 113 and 6, respectively. Further predictive analysis of target genes of lncRNAs revealed that six lncRNA genes had potential cis-regulatory effects on 13 differentially expressed mRNA genes and co-expressed with 53 mRNAs. Up-regulated CTD-2256P15.4 and RP11-229P13.23 were the most important lncRNAs in these CRC tissues and involved in cell proliferation and pathway in cancer. In conclusion, our study provides evidence regarding the mRNA and lncRNA transcription in CRC tissues, as well as new insights into the lncRNAs and mRNAs involved in the development of CRC.

scholarly journals Genomewide analysis of circular RNA in pituitaries of normal and heat-stressed sows

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Haojie Zhang ◽  
Baoyu Hu ◽  
Jiali Xiong ◽  
Ting Chen ◽  
Qianyun Xi ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Noncoding Rna ◽  
Target Genes ◽  
Hormone Secretion ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Pituitary Hormone

Abstract Background As a newly characterized type of noncoding RNA, circular RNA (circRNA) has been shown to have functions in diverse biological processes of animals. It has been reported that several noncoding RNAs may regulate animals’ response to heat stress which can be easily induced by hyperthermia in summer. However, the expression and functions of circRNAs in the pituitary of sows and whether they participate in heat stress adaption are still unclear. Results In this study, we found that high temperature over the thermoneutral zone of sows during the summer increased the serum heat shock protein 70 (HSP70) level, decreased the superoxide dismutase (SOD) vitality and prolactin (PRL) concentration, and induced heat stress in sows. Then, we explored circRNA in the pituitary of heat-stressed and normal sows using RNA sequencing and bioinformatics analysis. In total, 12,035 circRNAs were detected, with 59 circRNAs differentially expressed, including 42 up-regulated and 17 down-regulated circRNAs in pituitaries of the heat-stressed sows. Six randomly selected circRNAs were identified through reverse transcription PCR followed by DNA sequencing and other 7 randomly selected differentially expressed circRNAs were verified by quantitative real-time PCR analysis. The predicted target genes regulated by circRNAs through sponging microRNAs (miRNAs) were enriched in metabolic pathway. Furthermore, the predicted circRNA–miRNA–mRNA interactions showed that some circRNAs might sponge miRNAs to regulate pituitary-specific genes and heat shock protein family members, indicating circRNA’s roles in pituitary hormone secretion and heat stress response. Conclusions Our results provided a meaningful reference to understand the functions of circRNA in the porcine pituitary and the mechanisms by which circRNA may participate in animals’ response to heat stress.

scholarly journals Global Long Noncoding RNA and mRNA Expression Changes between Prenatal and Neonatal Lung Tissue in Pigs

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 443 ◽  
Author(s):  
Long Jin ◽  
Silu Hu ◽  
Teng Tu ◽  
Zhiqing Huang ◽  
Qianzi Tang ◽  
...  
Keyword(s):  
Immune Response ◽  
Cell Proliferation ◽  
Lung Tissue ◽  
Long Noncoding Rna ◽  
Lung Development ◽  
Noncoding Rna ◽  
Differentially Expressed ◽  
P Value ◽  
Distal Lung ◽  
Neonatal Lungs

Lung tissue plays an important role in the respiratory system of mammals after birth. Early lung development includes six key stages, of which the saccular stage spans the pre- and neonatal periods and prepares the distal lung for alveolarization and gas-exchange. However, little is known about the changes in gene expression between fetal and neonatal lungs. In this study, we performed transcriptomic analysis of messenger RNA (mRNA) and long noncoding RNA (lncRNA) expressed in the lung tissue of fetal and neonatal piglets. A total of 19,310 lncRNAs and 14,579 mRNAs were identified and substantially expressed. Furthermore, 3248 mRNAs were significantly (FDR-adjusted p value ≤ 0.05, FDR: False Discovery Rate) differentially expressed and were mainly enriched in categories related to cell proliferation, immune response, hypoxia response, and mitochondrial activation. For example, CCNA2, an important gene involved in the cell cycle and DNA replication, was upregulated in neonatal lungs. We also identified 452 significantly (FDR-adjusted p value ≤ 0.05) differentially expressed lncRNAs, which might function in cell proliferation, mitochondrial activation, and immune response, similar to the differentially expressed mRNAs. These results suggest that differentially expressed mRNAs and lncRNAs might co-regulate lung development in early postnatal pigs. Notably, the TU64359 lncRNA might promote distal lung development by up-regulating the heparin-binding epidermal growth factor-like (HB-EGF) expression. Our research provides basic lung development datasets and will accelerate clinical researches of newborn lung diseases with pig models.

scholarly journals Effect of miR-27b-5p on apoptosis of human vascular endothelial cells induced by simulated microgravity

APOPTOSIS ◽  
2019 ◽  
Vol 25 (1-2) ◽  
pp. 73-91 ◽  
Author(s):  
Yi-Kai Pan ◽  
Cheng-Fei Li ◽  
Yuan Gao ◽  
Yong-Chun Wang ◽  
Xi-Qing Sun
Keyword(s):  
Endothelial Cells ◽  
Western Blot ◽  
Target Gene ◽  
Simulated Microgravity ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Luciferase Assay ◽  
Qrt Pcr ◽  
Differentially Expressed Mirnas

AbstractWeightlessness-induced cardiovascular dysfunction can lead to physiological and pathological consequences. It has been shown that spaceflight or simulated microgravity can alter expression profiles of some microRNAs (miRNAs). Here, we attempt to identify the role of miRNAs in human umbilical vein endothelial cells (HUVECs) apoptosis under simulated microgravity. RNA-sequencing and quantitative real-time PCR (qRT-PCR) assays were used to identify differentially expressed miRNAs in HUVECs under simulated microgravity. Then we obtained the target genes of these miRNAs through target analysis software. Moreover, GO and KEGG enrichment analysis were performed. The effects of these miRNAs on HUVECs apoptosis were evaluated by flow cytometry, Western blot and Hoechst staining. Furthermore, we obtained the target gene of miR-27b-5p by luciferase assay, qRT-PCR and Western blot. Finally, we investigated the relationship between this target gene and miR-27b-5p in HUVECs apoptosis under normal gravity or simulated microgravity. We found 29 differentially expressed miRNAs in HUVECs under simulated microgravity. Of them, the expressions of 3 miRNAs were validated by qRT-PCR. We demonstrated that miR-27b-5p affected HUVECs apoptosis by inhibiting zinc fingers and homeoboxes 1 (ZHX1). Our results reported here demonstrate for the first time that simulated microgravity can alter the expression of some miRNAs in HUVECs and miR-27b-5p may protect HUVECs from apoptosis under simulated microgravity by targeting ZHX1.

scholarly journals Study the current scenario of hand foot mouth disease an Indian prospective

2020 ◽  
Vol 7 (7) ◽  
pp. 1558
Author(s):  
Ravi Sahota ◽  
Navpreet Kaur ◽  
Gurpal Singh ◽  
Nisha Upadhyay
Keyword(s):  
Communicable Disease ◽  
Enterovirus 71 ◽  
Foot And Mouth Disease ◽  
Neurological Complications ◽  
Mouth Disease ◽  
Human Enterovirus ◽  
Cross Sectional ◽  
Timely Initiation ◽  
Human Enterovirus 71 ◽  
Hand Foot Mouth Disease

Background: The hand-foot-mouth disease (HFMD) is an acute communicable disease, mostly affecting children under 5 years of age and caused by human enterovirus 71 (EV-A71) and coxsackievirus A16 (CV-A16). The usual incubation period is 3 to 7 days. Early symptoms are likely to be fever often followed by a sore throat followed by loss of appetite and general malaise. Aim and objectives was to study the trend of hand foot and mouth disease in a private hospital in Uttarakhand over 5 successive years.Methods: This cross-sectional study was carried among 297 cases of HFMD newborn screened at pediatrics department of Sahota Super-specialty hospital, Kashipur, Uttarakhand during year 2015 to 2019 after ethical clearance of institutional ethical committee. Diagnosis is coded with ICD-10. SPSS version 20 was used to calculate frequencies and percentiles.Results: Almost 29 cases of HMFD were picked in 2015, 32 cases in 2016, 43 cases in 2017, 81 cases in 2018, 112 in 2019. Fever observed in 86% cases. Neurological complications were observed in 9 (3%) cases, pneumonitis in 14 (4.7%) cases, cardiomyopathy observed in 3 (<1%) case. One death was reported.Conclusions: It is vital to screen patients with HFMD for these abnormal clinical presentations, allowing timely initiation of appropriate interventions to reduce the mortality. Increased awareness about vaccination in a developing nation like India and vaccination program at the grass root levels have eradicated certain lethal diseases.

scholarly journals Identification of miRNA and Their Regulatory Effects Induced by Total Flavonoids From Dracocephalum moldavica in the Treatment of Vascular Dementia

2021 ◽  
Vol 12 ◽  
Author(s):  
Mimin Liu ◽  
Guangzhi Shan ◽  
Hailun Jiang ◽  
Li Zeng ◽  
Kaiyue Zhao ◽  
...  
Keyword(s):  
Vascular Dementia ◽  
Target Gene ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Bioinformatics Analysis ◽  
Gene Profiling ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Total Flavonoids ◽  
Compound Target

Vascular dementia (VaD) is a general term used to describe difficulties in memory, reasoning, judgment, and planning caused by a reduced blood flow to the brain and consequent brain damage, in which microRNAs (miRNAs) are involved. Dracocephalum moldavica L. (D. moldavica) is traditionally used in the treatment of cardiovascular diseases as well as VaD, but the biomolecular mechanisms underlying its therapeutic effect are obscure. In the present study, the molecular mechanisms involved in the treatment of VaD by the total flavonoids from Dracocephalum moldavica L. (TFDM) were explored by the identification of miRNA profiling using bioinformatics analysis and experimental verification. A total of 2,562 differentially expressed miRNAs (DEMs) and 3,522 differentially expressed genes (DEGs) were obtained from the GSE120584 and GSE122063 datasets, in which the gene functional enrichment and protein-protein interaction network of 93 core targets, originated from the intersection of the top DEM target genes and DEGs, were established for VaD gene profiling. One hundred and eighty-five targets interacting with 42 flavonoids in the TFDM were included in a compound-target network, subsequently found that they overlapped with potential targets for VaD. These 43 targets could be considered in the treatment of VaD by TFDM, and included CaMKII, MAPK, MAPT, PI3K, and KDR, closely associated with the vascular protective effect of TFDM, as well as anti-oxidative, anti-inflammatory, and anti-apoptotic properties. The subsequent analysis of the compound-target gene-miRNA network indicated that eight miRNAs that mediated 43 targets had a close interaction with TFDM, suggesting that the neuroprotective effects were principally due to kaempferol, apigenin, luteolin, and quercetin, which were mostly associated with the miR-3184-3p/ESR1, miR-6762-3p/CDK1, miR-6777-3p/ESRRA, and other related axes. Furthermore, the in vitro oxygen-glucose deprivation (OGD) model demonstrated that the dysregulation of miR-3184-3p and miR-6875-5p found by qRT-PCR was consistent with the changes in the bioinformatics analysis. TFDM and its active compounds involving tilianin, luteolin, and apigenin showed significant effects on the upregulation of miR-3184-3p and downregulation of miR-6875-5p in OGD-injured cells, in line with the improved cell viability. In conclusion, our findings revealed the underlying miRNA-target gene network and potential targets of TFDM in the treatment of VaD.

scholarly journals Transcriptome Profile of Key CircRNAs and MiRNAs in Oviduct that Affect Sheep Reproduction

2020 ◽  
Author(s):  
Zhifeng Li ◽  
Xiaoyun He ◽  
Xiaosheng Zhang ◽  
Jinlong Zhang ◽  
Xiaofei Guo ◽  
...  
Keyword(s):  
Insulin Secretion ◽  
Signaling Pathway ◽  
Luteal Phase ◽  
Target Genes ◽  
Follicular Phase ◽  
Differentially Expressed ◽  
Kegg Analysis ◽  
Non Coding Rna ◽  
Comparison Groups ◽  
Host Genes

Abstract Background: CircRNA and miRNA, as classes of non-coding RNA, have been found to play pivotal roles in sheep reproduction. There are many reports of circRNA and miRNA in ovary and uterus, but few in oviduct. In this study, RNA-Seq was performed to analyze the expression profile of circRNA and miRNA in oviduct between follicular phase and luteal phase in FecBBB (MM) and FecB++ (WW) sheep.Results: The result showed that 15 circRNAs were found differentially expressed between the follicular phase and luteal phase of FecBBB genotype (MF VS. ML), no circRNAs were found differentially expressed between the follicular phase and luteal phase of FecB++ genotype (WF VS. WL). 9 and 1 differentially expressed miRNAs were identified in MF VS. ML, and WF VS. WL, respectively. GO and KEGG analysis showed that the host genes of circRNAs in MF VS. ML were mainly involved in the Rap1 signaling pathway and PI3K-Akt signaling pathway. GO and KEGG analysis of miRNAs showed that the predicted target genes were mainly involved in the Insulin secretion and Rap1 signaling pathway in MF VS. ML. In WF VS. WL, the result showed that the predicted target genes were mainly involved in the TGF-β signaling pathway, Insulin secretion and Rap1 signaling pathway. In 3 comparison groups, GO and KEGG analysis indicated that a number of host genes and target genes (XPR1, LPAR3, SLC7A11, RAB3A, PLCB3, CREB3L4, LPAR1, LPAR2, FGF18, TACR3, BMP6, SMAD4, SKP1) were found to influence sheep reproduction. Conclusion: The results of the study will help to elucidate the regulatory mechanisms of circRNAs and miRNAs in sheep reproduction. And, this study will enrich the sheep circRNA and miRNA databases, which provide a basis for further research on sheep reproduction.

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