Epigenetic mechanism and survival prognosis analysis of serum exosomes from ovarian cancer patients based on sequencing technology and Bioinformatics
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PROVIDER: PRJNA799786 | ENA |
REPOSITORIES: ENA
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Project description:Background: This study aimed to screen the signaling axis of epigenetic modification in serum exosomes of ovarian cancer patients based on sequencing technology and raw signal analysis, perform an in-depth study of the potential mechanism of action of ovarian cancer, predict potential therapeutic targets and perform a survival prognosis analysis of potential targets Methods: Serum exosomes from three ovarian cancer patients were selected as the experimental group, and serum exosomes from three uterine fibroid patients were selected as the control group. The whole transcriptomes of serum exosomes were used to obtain differentially expressed lncRNAs and mRNAs in ovarian cancer. The miRcode database and miRNA target gene prediction website were used to predict the target genes. Cytoscape software was used to draw a ceRNA network model of epigenetic modification of ovarian cancer serum exosomes, and R language was used for GO and KEGG enrichment analyses of the target genes. Finally, the TCGA website was used to download clinical and expression data related to ovarian cancer, and the common potential target genes obtained in the previous period were analyzed for survival. Results: A total of 117 differentially expressed lncRNAs and 513 differentially expressed mRNAs (P < 0.05, |log2 FC|≥ 1.0) were obtained by combining sequencing data and raw signal analysis, and 841 predicted target genes were reciprocally mapped by combining the miRcode database and the miRNA target gene prediction website, resulting in 11 potential target genes related to ovarian cancer (FGFR3, BMPR1B, TRIM29, FBN2, PAPPA, CCDC58, IGSF3, FBXO10, GPAM, HOXA10, LHFPL4). Survival prognosis analysis of the above 11 target genes revealed that the survival curve was statistically significant (P < 0.05) for HOXA10-only genes but not for the other genes. Through enrichment analysis, we found that the above target genes were mainly involved in biological processes such as regulation of transmembrane receptor protein kinase activity, structural molecule activity with elasticity, transforming growth factor-activated receptor activity, and GABA receptor binding, and were mainly enriched in metabolism pathways regulating stem cell pluripotency, bladder cancer, glycerolipid metabolism, central carbon metabolism of cancer, and resistance to EGFR tyrosine kinase inhibitors. Conclusions: The serum exosomal DIO3OS-hsa-miR-27a-3p-HOXA10 epigenetic modification signaling axis affects ovarian cancer development and disease survival prognosis by targeting transcriptional dysregulation pathways in cancer.
2022-06-20 | GSE194238 | GEO
Project description:microRNA profiles of Exosomes from Pooled NPC Patients serum comparing Control Exosomes from Healthy donors serum Two-condition experiment, Exosomes from Pooled Healthy donors serum vs. Exosomes from Pooled NPC Patients serum. Biological replicates: 1 Exosomes from Pooled Healthy donors serum, 1 Exosomes from Pooled NPC Patients serum,
2014-05-06 | E-GEOD-57319 | biostudies-arrayexpress
Project description:The dysregulation of exosomal microRNAs (miRNAs) play a crucial role in the development and progression of cancer. Differentially expressed miRNAs were identified in serum exosomes of GC patients and healthy individuals using next-generation sequencing and bioinformatics.
2023-11-01 | E-MTAB-12763 | biostudies-arrayexpress
Project description:Purpose: The purpose of this study is to apply RNA-Seq to identify diffeerentially expressed RNA in hepatocellular-derived serum exosomes compared with non hepatocellular carcinoma derived serum exosomes to evaluate prognosis-related and tumorigenesis-related potential biomarkers. Methods: Genome profiles of serum exosomes isolated from liver cirrohosis subjects, early-stage HCC subjects amd advanced stage HCC subjects respectively were generated by deep sequencing, using Illumina. The sequence reads that passed quality filters were aligned and analyzed using HISAT2 and STRINGTIE. The constructed transcriptome profiles were conveyed to further analysis. Results: With the help of RNA-Seq technology, 58,243 genes and 200,478 transcripts were aligned, and genome and transcriptome RNA-Seq archives were constructed, showcasing the abundance and depth of our sequencing. Then we systematically screened the RNA type, and selected long non-coding RNA (lncRNA) expression profiles. We used DESeq2 algorithm and set |log2 (fold-change)|>1 and P-value <0.05 as criteria. Finally we discovered 2,070 genes, 6,543 transcripts, 942 lncRNAs were differentially expressed in group advanced stage HCC compared with group liver cirrohosis. 1,600 genes, 6,904 transcripts, 1,067 lncRNAs were differentially expressed in group early stage HCC compared with group liver cirrohosis. Conclusions: Our study creatively represented the detailed analysis of serum exosomes genomes and transcriptomes, which were generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that compared with liver cirrohosis serum exosome samples, the early-stage and advanced stage hepatocellular carcinoma groups detected some unique differential mRNAs and miRNAs, which can be potential biomarkers.
2022-03-30 | GSE199509 | GEO
Project description:microRNA profiles of Exosomes from Pooled NPC Patients serum comparing Control Exosomes from Healthy donors serum
2014-05-06 | GSE57319 | GEO
Project description:Breast milk is a complex liquid that enriched in immunological components and affect the development of the infant immune system. Exosomes, the membranous vesicles of endocytic origin, are ubiquitously in various body fluids which can mediate intercellular communication. MicroRNAs (miRNAs), a well-defined group of non-coding small RNAs, in human breast milk are packaged inside exosomes. Here, we present the identification of miRNAs in human breast milk exosomes using deep sequencing technology. We found that the immune-related miRNAs are enriched in breast milk exosomes, and are resistant to the general harsh conditions. Four small RNA libraries in human breast milk exosomes from four healthy women (30 +/- 0.9 years old, primiparity) when the infant were aged at 60 days were sequenced.
2011-12-21 | E-GEOD-32253 | biostudies-arrayexpress
Project description:Mouse serum exosomes were harvested from OCExoInhib-treated mice or vehicle-treated mice at 2w after anterior cruciate ligament transection (ACLT). The exosomes were lysated and processed by Exosome RNA Column Purification Kit (System Biosciences). The miRNA were profiled using the Exosomal microRNA Amplification and Profiling Kit (System Biosciences)
2021-03-01 | GSE167160 | GEO
Project description:Mouse serum exosomes were harvested from osteoclast-exosome blockage (OCExo-BLK) mice or osteoclast-exosome intact (OCExo-Intact) mice at 2w after anterior cruciate ligament transection (ACLT). The exosomes were lysated and processed by Exosome RNA Column Purification Kit (System Biosciences). The miRNA were profiled using the Exosomal microRNA Amplification and Profiling Kit (System Biosciences)
2021-03-01 | GSE167162 | GEO
Project description:Extracellular vesicles (EVs) are on the edge of innovation aimed at regenerative and therapeutic applications, including wound healing, by containing therapeutic agents originating from secreting cells. Moreover, silver nanoparticles (AgNPs) play a role in wound healing because they have antiseptic activities. Therefore, in this study, we used sequencing technology to investigate the mRNA profile in UCMSC-derived exosomes (EXs). We also attempted to determine the role of the transcriptome, particularly in cutaneous wound healing, using bioinformatics analysis. Additionally, we investigated the efficacy of utilising a combination of UCMSC-derived EXs and AgNPs on burned animal models. Results showed that a large number of protein-coding genes (4578 genes) have been detected in UCMSC-derived EXs, among which 2004 genes are upregulated in exosomes while 2574 genes are downregulated compared to secreting cells. Interestingly, many genes enriched in exosomes were associated with the biology of the wound healing process. Gene ontology (GO) term and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated the upregulated exosomal genes belonging to GO terms and KEGG pathways related to signaling pathways such as DNA replication, ribosome, cell cycle, and pyrimidine metabolism. Further investigations that aimed to test exosomes and AgNPs in wound healing stimulation confirmed the faster healing capacity belongs to all exosomes, AgNPs, and a combination of EXs and AgNPs in the early healing process. The exosomes also expressed their capacity to enhance the dermal fibroblast proliferation. Our findings indicated the selective sorting of mRNAs into EXs, the potential of EXs, and the combination of EXs with AgNPs in cutaneous wound healing. Extracellular vesicles (EVs) are on the edge of innovation aimed at regenerative and therapeutic applications, including wound healing, by containing therapeutic agents originating from secreting cells. Moreover, silver nanoparticles (AgNPs) play a role in wound healing because they have antiseptic activities. Therefore, in this study, we used sequencing technology to investigate the mRNA profile in UCMSC-derived exosomes (EXs). We also attempted to determine the role of the transcriptome, particularly in cutaneous wound healing, using bioinformatics analysis. Additionally, we investigated the efficacy of utilising a combination of UCMSC-derived EXs and AgNPs on burned animal models. Results showed that a large number of protein-coding genes (4578 genes) have been detected in UCMSC-derived EXs, among which 2004 genes are upregulated in exosomes while 2574 genes are downregulated compared to secreting cells. Interestingly, many genes enriched in exosomes were associated with the biology of the wound healing process. Gene ontology (GO) term and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated the upregulated exosomal genes belonging to GO terms and KEGG pathways related to signaling pathways such as DNA replication, ribosome, cell cycle, and pyrimidine metabolism. Further investigations that aimed to test exosomes and AgNPs in wound healing stimulation confirmed the faster healing capacity belongs to all exosomes, AgNPs, and a combination of EXs and AgNPs in the early healing process. The exosomes also expressed their capacity to enhance the dermal fibroblast proliferation. Our findings indicated the selective sorting of mRNAs into EXs, the potential of EXs, and the combination of EXs with AgNPs in cutaneous wound healing. Extracellular vesicles (EVs) are on the edge of innovation aimed at regenerative and therapeutic applications, including wound healing, by containing therapeutic agents originating from secreting cells. Moreover, silver nanoparticles (AgNPs) play a role in wound healing because they have antiseptic activities. Therefore, in this study, we used sequencing technology to investigate the mRNA profile in UCMSC-derived exosomes (EXs). We also attempted to determine the role of the transcriptome, particularly in cutaneous wound healing, using bioinformatics analysis. Additionally, we investigated the efficacy of utilising a combination of UCMSC-derived EXs and AgNPs on burned animal models. Results showed that a large number of protein-coding genes (4578 genes) have been detected in UCMSC-derived EXs, among which 2004 genes are upregulated in exosomes while 2574 genes are downregulated compared to secreting cells. Interestingly, many genes enriched in exosomes were associated with the biology of the wound healing process. Gene ontology (GO) term and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated the upregulated exosomal genes belonging to GO terms and KEGG pathways related to signaling pathways such as DNA replication, ribosome, cell cycle, and pyrimidine metabolism. Further investigations that aimed to test exosomes and AgNPs in wound healing stimulation confirmed the faster healing capacity belongs to all exosomes, AgNPs, and a combination of EXs and AgNPs in the early healing process. The exosomes also expressed their capacity to enhance the dermal fibroblast proliferation. Our findings indicated the selective sorting of mRNAs into EXs, the potential of EXs, and the combination of EXs with AgNPs in cutaneous wound healing.
2024-01-01 | GSE252017 | GEO
Project description:MicroRNAs (miRNAs) are intrinsic regulators in the various cellular processes, and their abnormalities are considered to be involved in the onset of human disorders, including cancer. Circulating miRNA is focused as new cancer biomarker however it is regarded that circulating RNA are released not only from tumor but also by various pathways. Recently, exosomes, small membrane vesicles, have been a major interest in cancer research field, because of their unique biological properties. Exosomes are secreted from various cells and the components (Lipids, mRNAs, miRNAs and proteins) reflect origin of the cells secreting them. Identification of exosomal miRNAs from cancer cells is expected to provide useful biomarkers of cancer. To identify specific exosomal miRNAs as candidate biomarkers for colorectal cancer, we profiled exosomal miRNAs in sera of colon cancer patients (n=88) at various TNM stages (I to IV) and healthy controls (n=11) and selected significantly higher microRNAs in serum exosomes of colorectal cancer patients than that of healthy controls. Moreover, we tried to detect their serum exosome levels of using samples from patients after surgical resection of primary tumors (n=24). Serum exosomes were prepared by step-wise ultra-centrifugation methods in 24 colorectal cancer patients (age; 35-65) after surgical resection of primary tumor (TNM stage I; n=6, stage II; n=5, stage IIIa; n=5, stage IIIb; n=5, stage IV; n=3) .Exosome fraction was mixed with Trizol-LS reagent (Invitrogen), and aqueous phase was collected by adding chloroform. After addition of ethanol to the aqueous phase, it was placed on to an RNeasy mini spin column (Qiagen) for the purification of total RNAs. The total RNAs were analyzed by Agilent Human miRNA V3 Microarray (G4470C) according to the manufacturer's instructions.
2014-04-01 | E-GEOD-40246 | biostudies-arrayexpress