Next Generation Sequencing Quantitative Analysis of exosomes of hepatocellular carcinoma patients and healthy people
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ABSTRACT:
PROVIDER: PRJNA1000608 | ENA |
REPOSITORIES: ENA
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Project description:Circular RNAs (circRNAs) are recently found to be promising kind of biomarkers for tumors. However, plasma exosomal circRNAs in the diagnosis of hepatocellular carcinoma (HCC) is largely unknown. In this study, we report the application of next-generation sequencing technology for high-throughput profiling of plasma exosome general transcriptome between 3 cases of hepatocellular carcinoma patients and 3 cases of healthy control. We obtained exosomes through ultrahigh-speed centrifugation techniques and verified exosomes through immunoblotting, NanoSight NS300(Malvern Panalytical, Malvern, UK) and JEM-1230 transmission electron microscope (TEM) (JEOL, Tokyo, Japan). And then, we find that there are 41 circRNAs that have differential expression. This study discovered the differences between hepatocellular carcinoma and healthy people preliminarily.
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Project description:Background and Aims: Insulin resistance is a key factor in the pathogenesis of NAFLD. We evaluated the importance of subcutaneous abdominal adipose tissue (SAAT) inflammation and both plasma and SAAT-derived exosomes in regulating insulin sensitivity in people with obesity and NAFLD. Methods: Adipose tissue inflammation (macrophage and T cell content and gene expression of proinflammatory cytokines), liver and whole-body insulin sensitivity (assessed by a hyperinsulinemic-euglycemic clamp and glucose tracer infusion), and 24-hour serial plasma cytokine concentrations were evaluated in three groups stratified by adiposity, insulin sensitivity and intrahepatic triglyceride (IHTG) content: 1) metabolically-healthy lean (LEAN; n=14); 2) metabolically-healthy obese with normal IHTG content (OB-NL; n=28); and 3) metabolically-unhealthy obese with NAFLD (OB-NAFLD; n=28). The effect of plasma and SAAT-derived exosomes on insulin action (insulin-stimulated Akt phosphorylation) in human skeletal muscle myotubes was assessed in a subset of participants. Results: Proinflammatory macrophages, proinflammatory CD4 and CD8 T cell populations, and gene expression of several cytokines in SAAT were greater in the OB-NAFLD than the OB-NL and LEAN groups. However, with the exception of PAI-1, which was greater in the OB-NAFLD than the LEAN and OB-NL groups, 24-hour plasma cytokine concentration areas-under-the-curve (AUC) were not different between groups. The percentage of proinflammatory macrophages and plasma PAI-1 concentration AUC were inversely correlated with both hepatic and whole-body insulin sensitivity. Compared with exosomes from OB-NL participants, plasma and SAAT-derived exosomes obtained from the OB-NAFLD group impaired insulin action in myotubes. Conclusion: These results suggest SAAT-derived exosomes and PAI-1 are involved in the pathogenesis of systemic insulin resistance in people with obesity and NAFLD. ClinicalTrials.gov number: NCT02706262.
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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.
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Project description:Background:
There are about 100 trillion microbial cells in a person s gut. This is called the human gut microbiota. When this is disrupted, it can lead to many diseases. Studies show that the gut microbiota in people with cancer is different than that found in healthy people. Researchers want to study links between the gut microbiota and the immune system in people with a liver disease called hepatocellular carcinoma (HCC).
Objective:
To study links between gut microbiota and the immune system in people with HCC.
Eligibility:
People at least 18 years old with HCC. They must be scheduled to have tumors removed by surgery.
Design:
* People having surgery for primary liver tumors at the Mount Sinai Medical Center will be screened for this study.
* At the initial visit, blood, rectal swabs, urine, and stool will be collected. Participants will answer questions about their medical condition.
* Before surgery, blood, rectal swabs, urine, and stool will be collected. This will be done at a routine visit.
* When they have surgery, a piece of liver tissue with the tumor will be collected. This will be sent to the National Cancer Institute for tests.
* After surgery, blood, rectal swabs, urine, and stool will be collected 3 times. This will be done at routine visits.
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