Plasma-derived exosomal miRNA profiling in dengue patients with and without warning signs
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ABSTRACT:
PROVIDER: PRJNA1322508 | ENA |
REPOSITORIES: ENA
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Project description:Dengue virus infection is recognized as one of the most important mosquitos borne human diseases of the 21st century. It can manifest clinically as a moderate febrile illness, or a severe life-threatening disease called dengue haemorrhagic fever. Notably, there are currently no predictive diagnostic values for individuals prone to bleeding manifestations associated with this infection. This study explores the potential solution by focusing on exosomes, lipid vesicles enriched in specific microRNA. These exosomal microRNAs have the potential to form a disease-specific diagnostic signature, paving the way for an analysis of exosomal plasma microRNA expression to predict bleeding tendency in dengue infection. In total, 6 blood plasma exosome samples, dengue without warning sign (n = 3) and dengue with warning sign (n = 3) were used to isolate total RNA. Small RNA analysis and microarray-based expression profiling was used to detect the miRNA profile of plasma exosomes to identify predictive biomarker for bleeding manifestations in patients with warning sign as compared to patients without warning signs. Microarray profiling revealed that 24 miRNAs were upregulated in the plasma derived exosome miRNA in the dengue patients with warning signs. Functional analysis of target genes of these miRNAs in silico indicated their involvement in bleeding manifestation in dengue infection.
2025-09-12 | GSE307678 | GEO
Project description:According to the WHO 2009 classification, dengue with warning signs (D+W) is at the risk of developing severe form of dengue disease. One of the most important warning signs is plasma leakage, which is a serious complication associated with higher morbidity and mortality. We report that the frequency of CD4+CD8+ double-positive (DP) T cells is significantly increased in patients at risk of developing plasma leakage. Transcriptomic analysis demonstrated that CD4+CD8+ DP cells were distinct from CD4+ Single Positive (SP) T cells, but co-clustered with CD8+ SP cells indicating a largely similar transcriptional profile. 20 significant differentially expressed (DE) genes were identified between CD4+CD8+ DP and CD8+ SP cells. These genes encode OX40 and CCR4 (TNFRSF4 and CCR4), as well as other molecules associated with cell signaling on the cell surface (NT5E, MXRA8, PTPRK). While 5 significant DE genes were identified, the profile of gene expression in CD4+CD8+ DP cells was mostly similar between patients with and without warning signs of plasma leakage, implying a role of CD4+CD8+ DP cells in plasma leakage through a quantitative increase rather than functional alteration. The differentially expressed genes identified could have diagnostic utility, perhaps as PCR-based diagnostic markers.
2021-06-16 | GSE178240 | GEO
Project description:This pilot study, aimed to profile the host transcriptome as a potential strategy for identifying specific biomarkers for dengue prediction and detection. High-throughput RNA-sequencing (RNA-seq) was employed to generate host transcriptome profiles in 16 dengue patients and 10 healthy controls. Differentially expressed genes (DEGs) were identified in patients with severe dengue and those with dengue with warning signs compared to healthy individuals. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to elucidate the functions of upregulated and downregulated genes. Compared to healthy controls, 6466 genes were significantly differentially expressed (P < 0.05) in the dengue with warning signs group and 3082 genes in the severe dengue group, with over half being upregulated. The major KEGG pathways implicated included transport and catabolism (14.4%-16.3%), signal transduction (6.6%-7.3%), global and overview maps (6.7%-7.1%), viral diseases (4.6%-4.8%), and the immune system (4.4%-4.6%). Several genes exhibited consistent and significant upregulation across all dengue patients, regardless of severity: Interferon alpha inducible protein 27 (IFI27), Potassium Channel Tetramerisation Domain Containing 14 (KCTD14), Syndecan 1 (SDC1), DCC netrin 1 receptor (DCC), Ubiquitin C-terminal hydrolase L1 (UCHL1), Marginal zone B and B1 cell specific protein (MZB1), Nestin (NES), C-C motif chemokine ligand 2 (CCL2), TNF receptor superfamily member 17 (TNFSF17), and TNF receptor superfamily member 13B (TNFRSF13B). Further analysis revealed potential biomarkers for severe dengue prediction, including TNF superfamily member 15 (TNFSF15), Plasminogen Activator Inhibitor-2 (SERPINB2), motif chemokine ligand 7 (CCL7), aconitate decarboxylase 1 (ACOD1), Metallothionein 1G (MT1G) and Myosin Light Chain Kinase (MYLK2), which were expressed 3.5 times, 2.9 times, 2.3 times, 2.1 times, 1.7 times, and 1.4 times greater, respectively, than dengue patients exhibiting warning signs. The identification of these host biomarkers through RNA-sequencing holds promising implications and potential to augment existing dengue detection algorithms, contributing significantly to improved diagnostic and prognostic capabilities.
2024-10-10 | GSE279208 | GEO
Project description:Exosomes, endosome-derived membrane microvesicles, contain a specific set of RNA transcripts that are involved in cell-cell communication and hold a great potential as disease biomarkers. To systemically characterize exosomal RNA profiles, we performed RNA sequencing analysis using three human plasma samples and evaluated efficacies of small RNA library preparation protocols from 3 manufacturers. We tested the six samples (A1 and A2, B1 and B2, C1 and C2) using two small RNA library preparation kits: NEBNext Multiplex Small RNA library Prep Set from New England Biolab (NEB) and NEXTflex Small RNA Sequencing Kit from Bioo Scientific (BS). We also tested IlluminaM-bM-^@M-^Ys TrueSeq Small RNA Sample Preparation Kit (ILMN) in sample A1 and A2. Together, we tested these plasma samples by sequencing 14 indexed libraries. This study allowed direct comparison of current small RNA library preparation protocols and identified the most suitable strategy for future exosomal RNA sequencing analysis.
2013-05-15 | E-GEOD-45722 | biostudies-arrayexpress
Project description:Purpose: To identify a panel of plasma exosomal miRNAs as potential biomarkers for lung cancer from the genome-wide set of currently known human miRNAs. Methods: Plasma samples from 4 lung cancer patients and 4 patients with benign lung disease were collected, and plasma exosomes were extracted by ultracentrifugation. Exosomal miRNA profiles were generated by deep sequencing based on Illumina NextSeq 500 platform. And differentially expressed exosomal miRNAs between lung cancer and benign lung disease were identified by edgeR with the default threshold of |log2 (fold change) | ≥ 1.5 and P-value < 0.05. Results: A total of 983 detectable exosomal miRNAs were analyzed to identify differentially expressed miRNAs between two groups. There were 6 significantly up-regulated miRNAs and 63 significantly down-regulated miRNAs in lung cancer cases when compared with benign lung disease. Conclusion: The comparative analysis of plasma exosomal miRNAs between lung cancer and benign lung diseases provided a reference for exploring potential biomarkers of lung cancer. And the clinical value of candidate exosomal miRNAs needs to be further verified in lung cancer clinical trials.
2025-02-04 | GSE196159 | GEO
Project description:Exosomal RNA isolated from plasma was successfully profiled with a total of 65 immunology-related miNRAs in 13 mouse samples
2018-07-10 | GSE116829 | GEO
Project description:We have isolated extracellular vesicles from healthy donors' plasma, other febrile illness plasma, mild dengue patients (Platelet counts= >100,000 per mm3 of blood) , and severe dengue patients' plasma (Platelet counts= <30,000 per mm3 of blood) by ultracentrifugation. For understanding, the differences in protein cargo among the EVs isolated from these groups were subjected to SWATH analysis. We have used three biological replicates of each group of EVs. A- EVS DERIVED FROM SEVERE DENGUE PLASMA B- EVS DERIVED FROM MILD DENGUE PLASMA C- EVS DERIVED FROM OTHER FEBRILE ILLNESS PLASMA D- EVS DERIVED FROM HEALTHY DONORS PLASMA
2024-12-25 | PXD058037 | Pride
Project description:Exosomes were isolated from plasma and saliva of healthy individuals and head and neck cancer (HNSCC) patients. miRNA profiling of plasma- and saliva-derived exosomes was performed using nCounter SPRINT system. Diagnostic panels were selected from the exosomal miRNA profile.
2022-08-31 | GSE209670 | GEO
Project description:Exosomal miRNAs play important roles in cancer progression and therapeutic resistance and have shown great potential as liquid biopsy biomarkers for cancer diagnosis/prognosis. We investigated for the first time plasma exosomal miRNAs for their association with and early detection potential of castration-resistant prostate cancer (CRPC). RNA-sequencing was performed to identify candidate exosomal miRNAs associated with development of CRPC in 24 treatment-naive prostate cancer (PCa) and 24 CRPC patients.
2021-01-07 | GSE136321 | GEO
Project description:Plasma exosomal miRNA may differ between adolescent idiopathic scoliosis patients and healthy individuals. Sequencing analysis was used to find these differential miRNAs.
2024-05-15 | GSE235203 | GEO