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Deep Sequencing Analysis of the MicroRNAs in the Serum of Chronic Hepatitis B with Persistently Normal Alanine Aminotransferase

ABSTRACT: Background: Circulating miRNAs, a new family of miRNAs presentin plasma and serum, have shown great potential as novel body fluid biomarkers for non-invasive diagnosis and prognosis of several diseases. Methods: In the present study, we employed next-generation sequencing technology to analyze the expression profiles of circulating miRNAs in the serum of chronic hepatitis B (CHB) patients presenting persistently normal alanine aminotransferase with significant histological features (SPNALT),PNALT patients with no significant histological features (NSPNALT),and healthy control patients. Results: MiRNAs were found to be the major constituents of small RNA-annotated reads by comparing the annotate draw sequence reads with miRNA databases and genome and other small RNA libraries. Our results point to a total of 2767 unique reads that can be mapped to human miRNAs or pre-miRNAs in miRbase, and the pre-miRNAs can be further mapped to the human genome. Thirty novel miRNA genes were identified in three groups. The differential expression levels of 143 miRNAs showed significant variation when the SPNALT and control group were compared. Among these, 22 miRNAs were >4-fold up-regulated (P<0.01) in SPNALT group and 4 were >2-fold down-regulated (P<0.01).When the SPNALT and NSPNALT group were compared, the differential expression levels of 84 miRNAs showed significant variation. Among these, 13 miRNAs showed a >4-fold up-regulation (P<0.01) in the SPNALT group and 21 showed a >2-fold down-regulation (P<0.01). Conclusions: Our results show that circulating miRNAs in the serum of SPNALT patients could be more comprehensively detected by the next-generation sequencing technology. Newly identified miRNAs might be used as biomarkers for diagnosis of chronic hepatitis B patients presenting persistently normal alanine aminotransferase with significant histological features.

ORGANISM(S): Homo sapiens

PROVIDER: GSE62290 | GEO | 2016/12/31

SECONDARY ACCESSION(S): PRJNA263767

REPOSITORIES: GEO

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Project description:Low fertility remains a leading cause of poor productivity in dairy cattle. In this context, there is significant interest in developing novel tools for accurate early diagnosis of pregnancy. MicroRNAs (miRNAs) are short RNA molecules which are critically involved in regulating gene expression during both health and disease. MiRNAs have been shown to regulate ovarian function, uterine receptivity, embryonic development and placental function. Circulating miRNAs can provide useful biomarkers of tissue function and disease; importantly, differential miRNA profiles have been linked to pregnancy and preeclampsia in humans. This study sought to establish the potential of circulating miRNAs as biomarkers of early pregnancy in cattle. We applied Illumina small-RNA sequencing to profile miRNAs in plasma samples collected from eight non-pregnant heifers on Days 0, 8 and 16 of the oestrous cycle and 11 heifers on Days 16 and 24 of pregnancy. We sequenced a total of 46 samples and generated 9.2 million miRNA reads per sample. There were no differences in miRNA read abundance between any of the pregnant and non-pregnant time-points (FDR > 0.1). As a complementary approach, we analysed sample pools (3-4 samples/pool) corresponding to Days 0, 8 and 16 of the oestrous cycle and Day 24 of pregnancy (n = 3 pools/group) using Qiagen PCR arrays. A total of 16 miRNAs were differentially expressed (FDR < 0.1) in plasma between pregnant and non-pregnant animals. RT-qPCR validation using the same plasma samples confirmed that miR-26a was differentially upregulated on Day 16 pregnant relative to non-pregnant heifers (1.7-fold; P = 0.043), whereas miR-1249 tended to be upregulated in Day 16 pregnant heifers (1.6-fold; P = 0.081). Further validation in an independent group of heifers confirmed an increase in plasma miR-26a levels during early pregnancy, which was significant only on Day 24 (2.0-fold; P = 0.027). Through genome-wide analyses we have successfully profiled plasma miRNA populations associated with early pregnancy in cattle. We have identified miR-26a as a potential circulating biomarker of early pregnancy.

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Deep Sequencing Analysis of the MicroRNAs in the Serum of Chronic Hepatitis B with Persistently Normal Alanine Aminotransferase

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