MiRNA profiling in DVT patients and control subjects
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE173461 | GEO | 2022/04/27
REPOSITORIES: GEO
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Project description:Circulating microRNAs (miRNAs) in serum may serve as promising diagnostic biomarkers for patients with gastric cancer (GC). Using quantitative reverse transcription polymerase chain reaction (qRT-PCR) based Exiqon panel, we identified 58 differentially expressed miRNAs from 3 GC pool samples and 1 normal control (NC) pool in the initial screening phase. Identified miRNAs were further validated in the training (49 GC VS. 47 NCs) and validation phases (154 GC VS. 120 NCs) using qRT-PCR. Consequently, six serum miRNAs (miR-10b-5p, miR-132-3p, miR-185-5p, miR-195-5p, miR-20a-3p and miR-296-5p) were significantly overexpressed in GC compared with NCs. The areas under the receiver operating characteristic (ROC) curve of the six-miRNA panel were 0.764 and 0.702 for the training and validation phases, respectively. In conclusion, we identified a six-miRNA panel in serum for the detection of GC.
2016-08-31 | GSE86226 | GEO
Project description:Objective:This study aims to discover circulating exosomal miRNAs as potential noninvasive biomarkers early detection of fetus with ventricular septal defect (VSD). Method:A total of 182 pregnant women including 91 VSD cases and 91 matched controls were included in this study. Exosomes were isolated and next-generation sequencing was used to obtain a profile of dysregulated exosomal miRNA. The differential abundance was verified by quantitative real-time PCR (q RT-PCR). . Receiver operating characteristic (ROC) curves were conducted to evaluate the diagnostic accucary Results: 77 serum exosomal miRNA were uncovered to be differentially expressed in the VSD group as compared to the control group. Among these, five down-regulated exosomal miRNA were validated by qRT-PCR. hsa-miR-146a-5p was identified to be capable of distinguishing VSDs from controls (area under the ROC (AUC): 0.997; p < 2.2e-16). Conclusion: circulating exosomal miRNA, in particular, hsa-miR-146a-5pmay be a predictive biomarker for non-invasive prenatal diagnosis of fetal VSDs.
2021-06-05 | GSE176134 | GEO
Project description:Objective: The expression pattern of exosomal miRNAs derived from parathyroid tumor is still unknown. In the present work, we aimed to examine the differences on microRNA (miRNA) expression, present in serum exosomes, by comparing parathyroid carcinoma (PC) and parathyroid adenoma (PA). Methods: MiRNA expression profile of serum exosomes, derived from 4 PC patients and 4 PA patients, were analyzed by next-generation sequencing technology. The differential expressions of target miRNAs were further verified in both serum exosomes and tissues of PC/PA patients by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Lastly, receiver operating characteristic (ROC) curves were plotted to investigate the efficiency of target exosomal miRNAs in distinguishing PC patients from PA controls. Results: Multiple differentially expressed miRNAs of serum exosomes were screened out by sequencing. Based on this screening, hsa-miR-146b-5p (p=0.0846), hsa-miR-27a-5p (p=0.0412), hsa-miR-93-5p (p=0.73), hsa-miR-381-3p (p=0.1239) and hsa-miR-134-5p (p=0.0694) were up-regulated in the serum exosomes of PC patients. These results were validated by qPCR, where the trend on differential miRNA expression was consistent with the sequencing results. Specifically, the expression of exosomal hsa-miR-27a-5p was able to clearly distinguish PC patients from PA controls, and related analysis indicated that the area under the ROC curve was 0.8594 (p=0.0157). Conclusion: Here we present, for the first time, the miRNA expression profile of serum exosomes derived from PC patients. Based on this result, we presently suggest that the exosomal hsa-miR-27a-5p may serve as a putative tumor marker for preoperative identification of PC and PA subjects.
2020-11-13 | GSE161339 | GEO
Project description:The aim of this study was to conduct a comparison of tissue miRNA in thyroid cancer (papillary (PTC), follicular (FTC), and microcancer (PTMC)) and healthy thyroid tissue (Control). The expression level of 798 miRNAs using NanoString technology was examined. ROC curve analysis, and logistic regression modeling were performed. Gene ontology (GO), canonical pathways analysis were used to explore the biological functions of the miRNA target genes. The study revealed that 10 miRNAs were deregulated in samples of patients with PTC. Pathway analysis showed that miRNA target genes were mainly significantly enriched in endocrine resistance, EGFR tyrosine kinase inhibitor resistance, and pathways in cancer. ROC analysis demonstrated that miR-146-5p, miR-551b-3p, and miR-222-3p can be introduced as a diagnostic tool for PTC (AUC=0.770; 0.740; 0.720; respectively). Validation by qRT-PCR confirmed our findings. The results suggest that tissue miRNAs can potentially be used as predictive biomarkers of PTC in patients.
2022-05-26 | GSE191117 | GEO
Project description:Introduction: MicroRNAs (miRNAs) in circulation have emerged as promising biomarkers. In this study we aimed to identify a circulating miRNA signature for osteoarthritis (OA) patients. Methods: Serum samples were collected from 12 primary OA patients and 12 healthy individuals and were screened using the Agilent Human miRNA Microarray. Receiver Operating Characteristic (ROC) curves were constructed to evaluate the diagnostic performance of the deregulated miRNAs. Expression levels of selected miRNAs were validated by quantitative Real-time PCR (qRT-PCR) in all serum samples and in articular cartilage samples from OA patients (n=12) and healthy individuals (n=7). Bioinformatics analysis was used to investigate the involved pathways and target genes of the above miRNAs. Results: We identified 279 differentially expressed miRNAs in the serum of OA patients compared to healthy controls. 205 (73.5%) were up-regulated and 74 (26.5%) down-regulated. ROC analysis revealed that 77 miRNAs had area under the curve (AUC)> 0.8 and p<0.05. Bioinformatics analysis in 7 out of the 77 selected miRNAs (hsa-miR-33b-3p, hsa-miR-4284, hsa-miR-671-3p, hsa-miR-663a, hsa-miR-140-3p, hsa-miR-150-5p and hsa-miR-1233-3p) revealed that their target genes were involved in multiple signaling pathways, among which FOXO, mTOR, pI3K/akt, lipid metabolism and TGF-β. A serum miRNA signature including three down-regulated miRNAs (hsa-miR-33b-3p, hsa-miR-671-3p and hsa-miR-140-3p) were also verified by qRT-PCR in OA patients. Furthermore, we found that hsa-miR-140-3p, hsa-miR-671-3p and potentially hsa-miR-33b-3p expression levels were consistently down-regulated in articular cartilage of OA patients compared to healthy individuals. Conclusions: A global miRNA serum signature was revealed in OA patients. We identified a three- miRNA signature in peripheral serum which could be potential osteoarthritis biomarkers.
2017-10-17 | GSE105027 | GEO
Project description:The aim of this study was to conduct a baseline comparison of serum-circulating miRNA in prediabetic individuals with the distinction between those who later progressed to type 2 diabetes (T2DM) and those who did not. The expression level of 798 miRNAs using NanoString technology was examined. Spearman correlation, ROC curve analysis, and logistic regression modeling were performed. Gene ontology (GO), canonical pathways analysis were used to explore the biological functions of the miRNA target genes. The study revealed that 18 miRNAs were upregulated in serum samples of patients who later progressed to T2DM. Pathway analysis showed that miRNA target genes were mainly significantly enriched in neuroinflammation signaling, Myc mediated apoptosis signaling and tumoricidal function of hepatic natural killer (NK) cells. ROC analysis demonstrated that miR-491-5p, miR-1307-3p, and miR-298 can be introduced as a diagnostic tool for the prediction of T2DM (AUC=97.1%; 90.2%; 88.7%; respectively). Validation by qRT-PCR confirmed our findings. The results suggest that circulating miRNAs can potentially be used as predictive biomarkers of T2DM in prediabetic patients.
2020-07-21 | GSE148961 | GEO
Project description:Cervical cancer is a malignant disease that causes around 350 000 deaths annually. One of the essential things in enhancing the survival rates of cervical cancer is the availability of high-quality, sensitive, and specific diagnostic tests capturing the early stages of the disease. In this study, we analyzed the differential expression of microRNA in cervical cancer FFPE tissue samples. The comprehensive miRNA expression profile was detected using modern small-RNA sequencing technology, and the results were validated by real-time PCR. The relative expression of selected miRNAs was determined using the 2-ΔΔCt method. Moreover, two strategies for endogenous control selection were compared. miRNA profiling by small-RNA sequencing and a commercially supplied microfluidic card with 30recommended endogenous controls predesigned by the manufacturer. The RefFinder algorithm and coefficient of variation were used for endogenous control selection. A combination of miR-181a-5p and miR-423-3p was chosen as the most optimal normalizer. Statistically significant upregulation ofmiR-320a-3p, miR-7704, and downregulation of miR-26a-5p was detected, so we propose the combination as a new potential miRNA cervical cancer diagnostic panel. Using ROC curve analysis, the proposed panel showed 93.33% specificity and 96.97% sensitivity with AUC = 0.985. Inconclusion, our study suggests an optimal combination of two endogenous miRNAs for data normalization of miRNA expression studies in the cervical tissue (miR-181a-5p and miR-423-3p) and a novel diagnostic marker panel of three miRNAs (miR-320a-3p, miR-7704, miR-26a-5p) for cervical cancer.
2023-03-25 | GSE227693 | GEO
Project description:MiRNAs regulate posttranscriptional gene expression and are widely implicated in the pathogenesis of complex diseases. We aim to elucidate miRNA regulation of the atrial mRNA signatures that associate with AF. This may provide novel mechanistical insights and candidate targets for therapies using miRNA mimics or antimiRs.
We present combined miRNAs-mRNAs sequencing in atrial tissues of patient without AF (n=22), with paroxysmal AF (n=22) and with persistent AF (n=20). MiRNA and mRNA signatures followed an ordinal scale from nonAF to paroxysmal to persistent AF patients. The previously reported mRNA sequencing identified 5228 differentially expressed genes involved in epithelial to mesenchymal transition, endothelial cell proliferation and extracellular matrix remodelling involving collagens, glycoproteins and proteoglycans. We discovered 103 differentially expressed miRNAs. Key downregulated miRNAs included miR-135b-5p, miR-138-5p, miR-200a-3p, miR-200b-3p and miR-31-5p and key upregulated miRNAs were miR-144-3p, miR-15b-3p, miR-182-5p miR-18b-5p, miR-4306 and miR-206. The expression levels of differentially expressed miRNAs were negatively correlated with the expression levels of their predicted target mRNAs. The downregulated miRNAs demonstrated a more profound transcriptome effect than the upregulated miRNAs. Upregulated biological processes enriched in miRNAs targets related to epithelial and endothelial cell migration and glycosaminoglycan biosynthesis, in line with the processes discovered by the mRNA sequencing analysis.
Combined analysis of miRNA and mRNA sequencing uncovered miRNAs with a broad transcriptional effect in human AF. Epithelial to mesenchymal transition and endothelial cell proliferation were processes controlled by downregulated miR-135b-5p, miR-138-5p, miR-200a-3p, miR-200b-3p and miR-31-5p, which in turn may contribute to (myo)fibroblast activation and structural remodeling.\
| EGAS00001005296 | EGA
Project description:MicroRNAs (miRNAs) are important regulators of many biological functions, including embryo implantation and development. Recently, it is reported that miRNAs in biofluids are predictive for physiological and pathological processes. In this study, we aim to investigate whether the miRNAs secreted by human embryos in culture medium can be used as embryonic biomarkers. The culture media were prospectively collected from embryos of patients who underwent routine in vitro fertilization (IVF) or intracytoplasmic sperm injection (ICSI) at reproductive medicine center with informed consent. A high-throughput miRNA sequencing method was applied to detect the miRNAs profiles in culture media of embryos with different reproductive outcomes. Compared with embryos with failed pregnancy, the embryos with successful pregnancy secreted different miRNA profiles into the culture media. These differentially expressed miRNAs were predicted to be involved in multiple biological processes, cellular components and molecular functions. After bioinformatics analysis, 18 miRNAs were selected for validation by quantitative real-time polymerase chain reaction (qRT-PCR) and droplet digital PCR (ddPCR). We found that the cleavage embryos with successful pregnancy presented decreased expression of hsa-miR-26b-5p and hsa-miR-21-5p in the culture media. Moreover, the Receiver Operating Characteristic (ROC) curve analysis indicated that hsa-miR-26b-5p and hsa-miR-21-5p could serve as potential biomarkers for reproductive outcomes. Together, our findings highlight the important predictive potential of miRNAs secreted by human embryos in culture media, which is meaningful for noninvasive embryo selection during IVF cycles.
2020-02-28 | GSE142824 | GEO
Project description:The contribution of microRNA-mediated posttranscriptional regulation on the final proteome in differentiating cells remains elusive. Here, we evaluated the impact of microRNAs (miRNAs) on the proteome of human umbilical cord blood-derived unrestricted somatic stem cells (USSC) during retinoic acid (RA) differentiation by a systemic approach using next generation sequencing analysing mRNA and miRNA expression and quantitative mass spectrometry-based proteome analyses. Interestingly, regulation of mRNAs and their dedicated proteins highly correlated during RA-incubation. Additionally, RA-induced USSC demonstrated a clear separation from native USSC thereby shifting from a proliferating to a metabolic phenotype. Bioinformatic integration of up- and downregulated miRNAs and proteins initially implied a strong impact of the miRNome on the XXL-USSC proteome. However, quantitative proteome analysis of the miRNA contribution on the final proteome after ectopic overexpression of downregulated miR-27a-5p and miR-221-5p or inhibition of upregulated miR-34a-5p, respectively, followed by RA-induction revealed only minor proportions of differentially abundant proteins. In addition, only small overlaps of these regulated proteins with inversely abundant proteins in non-transfected RA-treated USSC were observed. Hence, mRNA transcription rather than miRNA-mediated regulation is the driving force for protein regulation upon RA-incubation, strongly suggesting that miRNAs are fine-tuning regulators rather than active primary switches during RA-induction of USSC.
2020-01-31 | PXD016915 | Pride