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Next Generation Sequencing Quantitative Analysis of exosomes of hepatocellular carcinoma patients and healthy people

ABSTRACT: Next Generation Sequencing Quantitative Analysis of exosomes of hepatocellular carcinoma patients and healthy people

PROVIDER: PRJNA1000608 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25469284.fastq.gz	Fastqsanger.gz
	SRR25469285.fastq.gz	Fastqsanger.gz
	SRR25469286.fastq.gz	Fastqsanger.gz
	SRR25469287.fastq.gz	Fastqsanger.gz
	SRR25469288.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Quantitative Analysis of exosomes of hepatocellular carcinoma patients and healthy people

Project description:We report the application of miRNAs analysis in exosomes based on second-generation high-throughput sequencing. Plasma samples from 3 hepatocellular carcinoma patients and 3 healthy controls were collected, and exosomes were isolated by ultra-centrifugation. MiRNAs in exosomes were then extracted and high-throughput sequencing was performed.By comparing the sequencing data, we screened out differentially expressed miRNAs and validated them with qRT-PCR in exosome samples, establishing and verifying the diagnostic panel of hepatocellular carcinoma composed of miR-212-5p, miR-519b-3p, miR-1248 and miR-1250-5p.

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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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