Exploration of small RNA biomarkers for testicular injury in the serum exosomes of rats
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ABSTRACT:
PROVIDER: PRJNA601481 | ENA |
REPOSITORIES: ENA
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Project description:Testicular injury is often observed in drug development. Serum hormones are usually used as non-invasive biomarkers for testicular injury; however, their sensitivity is low. Therefore, it is difficult to monitor testicular injury in pre-clinical and clinical drug developments. In recent years, molecules in body fluid exosomes are attracting attention as disease biomarkers such as cancer. In this study, small RNAs in serum exosomes were analyzed for identifying non-invasive biomarkers of testicular injury in rats, which are mainly used in a pre-clinical drug development. Testicular injury models in rats were prepared by a single oral administration of 2000 mg/kg ethylene glycol monomethyl ether in which spermatocytes degeneration and sertoli cells vacuolation were observed, or 400 mg/kg carbendazim in which sertoli cells vacuolation and seminiferous tubules dilation were observed. Serum exosome small RNA-seq was performed in these models. The analysis identified 3 small RNAs that fluctuated in common between the models, and miR-423-5p and miR-128-3p were selected as candidate markers. For qPCR validation of the candidates, testicular injury models were further prepared by a single oral administration of 60 mg/kg 1,3-dinitrobenzene or 500 mg/kg nitrofurazone in which spermatocytes degeneration and sertoli cells vacuolation were observed. In qPCR analysis, the selected two miRNAs in exosomes were upregulated in the all models except for 1,3-dinitrobenzene model in which severe hemolysis was observed. On the other hand, the miRNAs in serum did not significantly change in the any models. In conclusion, we identified miR-423-5p and miR-128-3p in serum exosome as non-invasive biomarkers for testicular injury in rats.
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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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2019-11-25 | PXD012283 | Pride
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
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 11 healthy controls and 88 colorectal cancer patients with various TNM stages (I; n=20, stage II; n=20, stage IIIa; n=20, stage IIIb: n=16, stage IV; n=12) (age; 35-65) .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.
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