A comprehensive survey of maternal plasma miRNAs expression profiles using high-throughput sequencing

2012 ◽  
Vol 413 (5-6) ◽  
pp. 568-576 ◽  
Author(s):  
Hailing Li ◽  
Li Guo ◽  
Qian Wu ◽  
JiaFeng Lu ◽  
Qinyu Ge ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Maternal Plasma ◽  
Comprehensive Survey ◽  
Mirnas Expression ◽  
Plasma Mirnas

scholarly journals Maternal Plasma miRNAs Expression in Preeclamptic Pregnancies

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Hailing Li ◽  
Qinyu Ge ◽  
Li Guo ◽  
Zuhong Lu
Keyword(s):  
Large Scale ◽  
Expression Profiles ◽  
Maternal Plasma ◽  
Differentially Expressed ◽  
Control Group ◽  
Specific Syndrome ◽  
Noninvasive Biomarkers ◽  
Mirnas Expression ◽  
And Control ◽  
Plasma Mirnas

Objective. Preeclampsia (PE) is a pregnancy-specific syndrome and one of the leading causes of maternal and fetal morbidity and mortality. The pathophysiological mechanisms of PE remain poorly known. Recently, circulating miRNAs are considered as potential useful noninvasive biomarkers. The aim of this study was to identify differentially expressed plasma miRNAs in preeclamptic pregnancies compared with normal pregnancies.Methods. Maternal plasma miRNA expression profiles were detected by SOLiD sequencing. Differential expressions between mPE/sPE and control group were found. Next, four differentially expressed plasma miRNAs were chosen to validate their expression in other large scale samples by real-time PCR.Results. In terms of sequencing results, we identified that 51 miRNAs were differentially expressed. Four differentially expressed plasma miRNAs (miR-141, miR-144, miR-221, and miR-29a) were selected to validate the sequencing results. RT-PCR data confirmed the reliability of sequencing results. The further statistical analysis showed that maternal plasma miR-141 and miR-29a are significantly overexpressed in mPE (P<0.05). Maternal plasma miR-144 is significantly underexpressed in mPE and sPE (P<0.05).Conclusions. Results showed that there were differentially expressed maternal plasma miRNAs in patients with preeclampsia. These plasma miRNAs might be used as notable biomarkers for diagnosis of preeclampsia.

scholarly journals Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Rachelle Bester ◽  
Glynnis Cook ◽  
Johannes H. J. Breytenbach ◽  
Chanel Steyn ◽  
Rochelle De Bruyn ◽  
...  
Keyword(s):  
High Throughput ◽  
Extraction Method ◽  
Pathogen Detection ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Rna Extraction ◽  
Healthy Plant ◽  
Ion Torrent ◽  
Extraction Protocol ◽  
Zymo Research

Abstract Background High-throughput sequencing (HTS) has been applied successfully for virus and viroid discovery in many agricultural crops leading to the current drive to apply this technology in routine pathogen detection. The validation of HTS-based pathogen detection is therefore paramount. Methods Plant infections were established by graft inoculating a suite of viruses and viroids from established sources for further study. Four plants (one healthy plant and three infected) were sampled in triplicate and total RNA was extracted using two different methods (CTAB extraction protocol and the Zymo Research Quick-RNA Plant Miniprep Kit) and sent for Illumina HTS. One replicate sample of each plant for each RNA extraction method was also sent for HTS on an Ion Torrent platform. The data were evaluated for biological and technical variation focussing on RNA extraction method, platform used and bioinformatic analysis. Results The study evaluated the influence of different HTS protocols on the sensitivity, specificity and repeatability of HTS as a detection tool. Both extraction methods and sequencing platforms resulted in significant differences between the data sets. Using a de novo assembly approach, complemented with read mapping, the Illumina data allowed a greater proportion of the expected pathogen scaffolds to be inferred, and an accurate virome profile was constructed. The complete virome profile was also constructed using the Ion Torrent data but analyses showed that more sequencing depth is required to be comparative to the Illumina protocol and produce consistent results. The CTAB extraction protocol lowered the proportion of viroid sequences recovered with HTS, and the Zymo Research kit resulted in more variation in the read counts obtained per pathogen sequence. The expression profiles of reference genes were also investigated to assess the suitability of these genes as internal controls to allow for the comparison between samples across different protocols. Conclusions This study highlights the need to measure the level of variation that can arise from the different variables of an HTS protocol, from sample preparation to data analysis. HTS is more comprehensive than any assay previously used, but with the necessary validations and standard operating procedures, the implementation of HTS as part of routine pathogen screening practices is possible.

scholarly journals A Randomized Controlled Trial of Chuanhutongfeng Mixture for the Treatment of Chronic Gouty Arthritis by Regulating miRNAs

2019 ◽  
Vol 2019 ◽  
pp. 1-11
Author(s):  
Yao Wang ◽  
Liping Dong ◽  
Peng Liu ◽  
Ying Chen ◽  
Shaodan Jia ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Controlled Trial ◽  
Gouty Arthritis ◽  
Positive Control ◽  
Mirna Expression Profiles ◽  
Before And After ◽  
And Cluster Analysis ◽  
Mirnas Expression ◽  
And Control ◽  
Plasma Mirnas

Background. We investigated whether Chuanhutongfeng mixture has actions on chronic gouty arthritis (CGA) by regulating miRNAs. Methods. A total of 255 patients with CGA and 30 controls were enrolled. miRNA expression profiles and cluster analysis were preformed; RT-qPCR was used to detect miRNAs associated with CGA. Patients were allocated into Chuanhutongfeng mixture, allopurinol (positive control), and control (etoricoxib) groups. Expression of plasma miRNAs was measured before and after treatments; expression of chemokine 2 (CCL2) and interleukin 8 (CXCL8) was determined by ELISA. Results. 48 miRNAs were differentially expressed and compared to controls. 36 miRNAs expression levels were > 1.5 times and 12 miRNAs < 1.5 times compared to the controls. miR-339-5p, miR-486-5p, and miR-361-5p levels in patients with CGA were lower than in controls (P < 0.05). This trial showed that the Chuanhutongfeng mixture and allopurinol groups had upregulated the expressions of miR-486-5, miR-339-5p, and miR-361-5p and decreased levels of CCL2 and CXCL8 proteins. After 8 weeks of treatment, Chuanhutongfeng mixture decreased serum uric acid levels more than allopurinol (P < 0.05) and reduced levels of CCL2 and CXCL8 protein significantly more than in the allopurinol and control groups. Conclusions. The therapeutic actions of Chuanhutongfeng mixture inhibit the expression of proteins CCL2 and CXCL8 in plasma and upregulated the expressions of three miRNAs (miR-486-5p, miR-339-5p, and miR-361-5p).

scholarly journals Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 30
Author(s):  
Yaodong Zhao ◽  
Wenjing Ma ◽  
Xiaohong Wei ◽  
Yu Long ◽  
Ying Zhao ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Drought Stress ◽  
Medicago Sativa ◽  
High Throughput ◽  
Drought Resistance ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Medicago Sativa L

Alfalfa (Medicago sativa L.) is a high quality leguminous forage. Drought stress is one of the main factors that restrict the development of the alfalfa industry. High-throughput sequencing was used to analyze the microRNA (miRNA) profiles of alfalfa plants treated with CK (normal water), PEG (polyethylene glycol-6000; drought stress), and PEG + SNP (sodium nitroprusside; nitric oxide (NO) sprayed externally under drought stress). We identified 90 known miRNAs belonging to 46 families and predicted 177 new miRNAs. Real-time quantitative fluorescent PCR (qRT-PCR) was used to validate high-throughput expression analysis data. A total of 32 (14 known miRNAs and 18 new miRNAs) and 55 (24 known miRNAs and 31 new miRNAs) differentially expressed miRNAs were identified in PEG and PEG + SNP samples. This suggested that exogenous NO can induce more new miRNAs. The differentially expressed miRNA maturation sequences in the two treatment groups were targeted by 86 and 157 potential target genes, separately. The function of target genes was annotated by gene ontology (GO) enrichment and kyoto encyclopedia of genes and genomes (KEGG) analysis. The expression profiles of nine selected miRNAs and their target genes verified that their expression patterns were opposite. This study has documented that analysis of miRNA under PEG and PEG + SNP conditions provides important insights into the improvement of drought resistance of alfalfa by exogenous NO at the molecular level. This has important scientific value and practical significance for the improvement of plant drought resistance by exogenous NO.

143 TRANSCRIPTIONAL PROFILING BY HIGH-THROUGHPUT SEQUENCING OF PORCINE PRE- AND PERI-IMPLANTATION EMBRYOS

2012 ◽  
Vol 24 (1) ◽  
pp. 184 ◽  
Author(s):  
S. C. Isom ◽  
J. R. Stevens ◽  
R. Li ◽  
L. D. Spate ◽  
W. G. Spollen ◽  
...  
Keyword(s):  
Somatic Cell ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Assisted Reproductive Technologies ◽  
Inner Cell Mass ◽  
Expression Profiles ◽  
Cell Mass ◽  
Reproductive Technologies ◽  
Regulation Of Transcription

Significant embryo mortality occurs at or around the time of implantation or attachment in virtually all mammalian species studied to date, even in naturally conceived embryos. Embryos resulting from assisted reproductive technologies (ART) are even more susceptible to peri-implantation failure. Herein we describe our effort to characterise the transcriptomes of embryonic disc (ED) and trophoblast (TE) cells from porcine embryos derived from AI, IVF, parthenogenetic oocyte activation (PA) and somatic cell nuclear transfer (NT) on Days 10, 12 and 14 of gestation. The IVF, PA and somatic cell NT embryos were generated using in vitro–matured oocytes, cultured overnight in vitro and then transferred at the 1- to 2-cell stage into appropriately synchronized recipient gilts. On the appropriate collection day, embryos were flushed from the uterus and ED was separated from TE by mechanical dissection. Double-stranded cDNA from the collected samples was sequenced using the GAII platform from Illumina (San Diego, CA, USA). The resulting sequencing reads were aligned to a custom swine transcriptome database (see Isom et al. 2010). A generalized linear model was fit for each of 41 693 genomic regions, for ED and TE samples separately, accounting for embryo type, gestation day and their interaction and using total lane read count as a normalizing offset. Genes with significant embryo type differences (controlling the false discovery rate at 0.10) were subsequently tested for differences between IVF and each of AI, PA and NT. Those genes with significant post hoc differences (either up- or down-regulated compared with IVF) were characterised in terms of gene ontologies and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways using a gene set enrichment test. Bone morphogenetic protein signalling was down-regulated (KEGG; P = 0.0099; adjusted to control for FDR at 0.05) in the ED of IVF embryos when compared with AI embryos. In TE cells from IVF embryos, ubiquitin-mediated proteolysis and ErbB signalling (adj P = 0.031 for both pathways) were aberrantly regulated when compared with AI embryos. Of particular interest is the observation that expression of genes involved in chromatin modification (GO:BiologicalProcess; q-value = 0.00005) and epigenetic regulation of transcription (q = 0.00007) was very significantly disrupted in inner cell mass cells from NT embryos compared with IVF embryos. Surprisingly, no such disruption of the epigenetic machinery was observed in the TE cells from NT embryos. In summary, we have used high-throughput sequencing technologies to compare gene expression profiles of various ART embryo types during peri-implantation development. We expect that these data will provide important insight into the root causes of (and possible opportunities for mitigation of) suboptimal development of embryos derived from ART. Funding was received from NIH R01 RR013438 and Food for the 21st Century (RSP) and the Utah Agricultural Experiment Station (UTA00151 and UTA00560 for S. C. Isom and J. R. Stevens, respectively).

scholarly journals Identification of Stress Associated microRNAs in Solanum lycopersicum by High-Throughput Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 475 ◽  
Author(s):  
López-Galiano ◽  
Sentandreu ◽  
Martínez-Ramírez ◽  
Rausell ◽  
Real ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Solanum Lycopersicum ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Plant Defence ◽  
Stress Conditions ◽  
Differentially Expressed ◽  
Physiological Adaptation ◽  
Biotic And Abiotic Stress

Tomato (Solanum lycopersicum) is one of the most important crops around the world and also a model plant to study response to stress. High-throughput sequencing was used to analyse the microRNA (miRNA) profile of tomato plants undergoing five biotic and abiotic stress conditions (drought, heat, P. syringae infection, B. cinerea infection, and herbivore insect attack with Leptinotarsa decemlineata larvae) and one chemical treatment with a plant defence inducer, hexanoic acid. We identified 104 conserved miRNAs belonging to 37 families and we predicted 61 novel tomato miRNAs. Among those 165 miRNAs, 41 were stress-responsive. Reverse transcription quantitative PCR (RT-qPCR) was used to validate high-throughput expression analysis data, confirming the expression profiles of 10 out of 11 randomly selected miRNAs. Most of the differentially expressed miRNAs were stress-specific, except for sly-miR167c-3p upregulated in B. cinerea and P. syringae infection, sly-newmiR26-3p upregulated in drought and Hx treatment samples, and sly-newmiR33-3p, sly-newmiR6-3p and sly-newmiR8-3p differentially expressed both in biotic and abiotic stresses. From mature miRNAs sequences of the 41 stress-responsive miRNAs 279 targets were predicted. An inverse correlation between the expression profiles of 4 selected miRNAs (sly-miR171a, sly-miR172c, sly-newmiR22-3p and sly-miR167c-3p) and their target genes (Kinesin, PPR, GRAS40, ABC transporter, GDP and RLP1) was confirmed by RT-qPCR. Altogether, our analysis of miRNAs in different biotic and abiotic stress conditions highlight the interest to understand the functional role of miRNAs in tomato stress response as well as their putative targets which could help to elucidate plants molecular and physiological adaptation to stress.

scholarly journals Circular RNA EPB41 Expression Predicts Unfavorable Prognoses in NSCLC by Regulating miR-486-3p/eIF5A Axis-Mediated Stemness

2021 ◽  
Author(s):  
Xiyu Liu ◽  
Yue Wu ◽  
Yuqing Lou ◽  
Mingming Jin ◽  
Xue Li ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Luciferase Reporter ◽  
Circular Rnas ◽  
Reporter System ◽  
Bioinformatics Analyses

Abstract Dysregulation of circular RNAs (circRNAs) has recently been found to play an important role in the progression and development of cancers such as non-small cell lung cancer (NSCLC). Yet the functions of many circRNAs in NSCLC remain unclear. In this study, the circRNA expression profiles in NSCLC tumor tissues and adjacent non-tumorous tissues were detected by high-throughput sequencing. Bioinformatics analyses, the dual-luciferase reporter system, fluorescence in situ hybridization (FISH) and miRNA/mRNA high-throughput sequencing were used to identify circ-EPB41 and its downstream target. The subcutaneous tumor/caudal vein transfer mouse model was used for tumor growth and invasion analysis. The results show that the circ-EPB41 was upregulated in NSCLC tissues and cell lines. Increased circ-EPB41 expression in NSCLC was significantly correlated with malignant characteristics, and positive to post-surgical overall survival of NSCLC patients. Reduced circ-EPB41 expression in NSCLC decreased cell proliferation and invasion in both in vitro and in vivo experiments. The miRNA/mRNA high-throughput sequencing suggested that downregulation of circ-EPB41 promoted microRNA (miR)-486-3p and suppressed eukaryotic translation initiation factor 5A (eIF5A) expression. Luciferase reporter experiments confirmed that miR-486-3p/eIF5A were downstream targets of circ-EPB41. In addition, we also found that downregulation of circ-EPB41 suppressed self-renewal and decreased expression of stemness markers SOX2, OCT-4, Nanog and CD133 by sponging miR-486-3p to enhance eIF5A expression. Taken togeter, these data revealed the important role of circ-EPB41 in regulating NSCLC cell invasion and proliferation by modifying miR-486-3p/eIF5A axis-mediated stemness. We believe our study provides a novel perspective regarding the role of circRNAs in NSCLC progression.

scholarly journals High-Throughput Data of Circular RNA Profiles in Human Temporal Cortex Tissue Reveals Novel Insights into Temporal Lobe Epilepsy

2018 ◽  
Vol 45 (2) ◽  
pp. 677-691 ◽  
Author(s):  
Jiaxin Li ◽  
Haijun Lin ◽  
Zhenrong Sun ◽  
Guanyi Kong ◽  
Xu Yan ◽  
...  
Keyword(s):  
Temporal Lobe Epilepsy ◽  
Temporal Lobe ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Expression Profiles ◽  
Temporal Cortex ◽  
Bioinformatic Analysis ◽  
Circular Rna ◽  
Expression Level ◽  
Circular Rnas

Background/Aims: Circular RNAs (circRNAs) are a class of long noncoding RNAs with a closed loop structure that regulate gene expression as microRNA sponges. CircRNAs are more enriched in brain tissue, but knowledge of the role of circRNAs in temporal lobe epilepsy (TLE) has remained limited. This study is the first to identify the global expression profiles and characteristics of circRNAs in human temporal cortex tissue from TLE patients. Methods: Temporal cortices were collected from 17 TLE patients and 17 non-TLE patients. Total RNA was isolated, and high-throughput sequencing was used to profile the transcriptome of dysregulated circRNAs. Quantitative PCR was performed for the validation of changed circRNAs. Results: In total, 78983 circRNAs, including 15.29% known and 84.71% novel circRNAs, were detected in this study. Intriguingly, 442 circRNAs were differentially expressed between the TLE and non-TLE groups (fold change≥2.0 and FDR≤0.05). Of these circRNAs, 188 were up-regulated, and 254 were down-regulated in the TLE patient group. Eight circRNAs were validated by real-time PCR. Remarkably, circ-EFCAB2 was intensely up-regulated, while circ-DROSHA expression was significantly lower in the TLE group than in the non-TLE group (P<0.05). Bioinformatic analysis revealed that circ-EFCAB2 binds to miR-485-5p to increase the expression level of the ion channel CLCN6, while circ-DROSHA interacts with miR-1252-5p to decrease the expression level of ATP1A2. Conclusions: The dysregulations of circRNAs may reflect the pathogenesis of TLE and circ-EFCAB2 and circ-DROSHA might be potential therapeutic targets and biomarkers in TLE patients.

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