A Catalogue of Glioblastoma and Brain MicroRNAs Identified by Deep Sequencing

Hua, Dasong; Mo, Fan; Ding, Dong; Li, Lisa; Han, Xu; Zhao, Na; Foltz, Gregory; Lin, Biaoyang; Lan, Qing; Huang, Qiang

doi:10.1089/omi.2012.0069

Cited by 51 publications

(45 citation statements)

References 30 publications

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“…To our knowledge, this is the first time the small RNA fraction of CSF has been sequenced. We surveyed our sequencing results from five subjects' CSF alongside the miRNA counts from normal human brain tissue sequenced by Hua et al (2012) FIGURE 5. Repeated extraction of the organic phase results in higher RNA yield.…”

Section: Discussionmentioning

confidence: 99%

Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing

Burgos

Javaherian

Bomprezzi

et al. 2013

RNA

178

174

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There has been a growing interest in using next-generation sequencing (NGS) to profile extracellular small RNAs from the blood and cerebrospinal fluid (CSF) of patients with neurological diseases, CNS tumors, or traumatic brain injury for biomarker discovery. Small sample volumes and samples with low RNA abundance create challenges for downstream small RNA sequencing assays. Plasma, serum, and CSF contain low amounts of total RNA, of which small RNAs make up a fraction. The purpose of this study was to maximize RNA isolation from RNA-limited samples and apply these methods to profile the miRNA in human CSF by small RNA deep sequencing. We systematically tested RNA isolation efficiency using ten commercially available kits and compared their performance on human plasma samples. We used RiboGreen to quantify total RNA yield and custom TaqMan assays to determine the efficiency of small RNA isolation for each of the kits. We significantly increased the recovery of small RNA by repeating the aqueous extraction during the phenol-chloroform purification in the top performing kits. We subsequently used the methods with the highest small RNA yield to purify RNA from CSF and serum samples from the same individual. We then prepared small RNA sequencing libraries using Illumina's TruSeq sample preparation kit and sequenced the samples on the HiSeq 2000. Not surprisingly, we found that the miRNA expression profile of CSF is substantially different from that of serum. To our knowledge, this is the first time that the small RNA fraction from CSF has been profiled using next-generation sequencing.

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Section: Discussionmentioning

confidence: 99%

Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing

Burgos

Javaherian

Bomprezzi

et al. 2013

RNA

178

174

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“…The construction of a small RNA sequencing library and Illumina sequencing were performed as described in our previous report (Hua et al, 2012). After sequencing, we aligned each sequence to the human miRNA precursor (Sanger miRBase 17.0) using BLAST (version 2.2.11).…”

Section: Small Rna Sequencing and Data Analysismentioning

confidence: 99%

Next Generation Sequencing Analysis of miRNAs: MiR-127-3p Inhibits Glioblastoma Proliferation and Activates TGF-β Signaling by Targeting SKI

Jiang

Jin

Liu

et al. 2014

OMICS: A Journal of Integrative Biology

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Glioblastoma (GBM) proliferation is a multistep process during which the expression levels of many genes that control cell proliferation, cell death, and genetic stability are altered. MicroRNAs (miRNAs) are emerging as important modulators of cellular signaling, including cell proliferation in cancer. In this study, using next generation sequencing analysis of miRNAs, we found that miR-127-3p was downregulated in GBM tissues compared with normal brain tissues; we validated this result by RT-PCR. We further showed that DNA demethylation and histone deacetylase inhibition resulted in downregulation of miR-127-3p. We demonstrated that miR-127-3p overexpression inhibited GBM cell growth by inducing G1-phase arrest both in vitro and in vivo. We showed that miR-127-3p targeted SKI (v-ski sarcoma viral oncogene homolog [avian]), RGMA (RGM domain family, member A), ZWINT (ZW10 interactor, kinetochore protein), SERPINB9 (serpin peptidase inhibitor, clade B [ovalbumin], member 9), and SFRP1 (secreted frizzled-related protein 1). Finally, we found that miR-127-3p suppressed GBM cell growth by inhibiting tumor-promoting SKI and activating the tumor suppression effect of transforming growth factor-b (TGF-b) signaling. This study showed, for the first time, that miR-127-3p and its targeted gene SKI, play important roles in GBM and may serve as potential targets for GBM therapy.

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“…The site#1 MRE-free DNMT3B3 transcript may escape translational suppression by hsa-miR-148a, which is expressed in many tissues, such as human embryonic stem cell [30], brain [31], cervix [32] and other tissues [33]. Therefore, the different isoforms transcribed from the DNMT3B gene might be a good starting point to explore the effect of alternative splicing on microRNA-mediated suppression of protein expression.…”

Section: Resultsmentioning

confidence: 99%

Fine-tuning of microRNA-mediated repression of mRNA by splicing-regulated and highly repressive microRNA recognition element

Chiou²,

Chiu³

et al. 2013

BMC Genomics

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BackgroundMicroRNAs are very small non-coding RNAs that interact with microRNA recognition elements (MREs) on their target messenger RNAs. Varying the concentration of a given microRNA may influence the expression of many target proteins. Yet, the expression of a specific target protein can be fine-tuned by alternative cleavage and polyadenylation to the corresponding mRNA.ResultsThis study showed that alternative splicing of mRNA is a fine-tuning mechanism in the cellular regulatory network. The splicing-regulated MREs are often highly repressive MREs. This phenomenon was observed not only in the hsa-miR-148a-regulated DNMT3B gene, but also in many target genes regulated by hsa-miR-124, hsa-miR-1, and hsa-miR-181a. When a gene contains multiple MREs in transcripts, such as the VEGF gene, the splicing-regulated MREs are again the highly repressive MREs. Approximately one-third of the analysable human MREs in MiRTarBase and TarBase can potentially perform the splicing-regulated fine-tuning. Interestingly, the high (+30%) repression ratios observed in most of these splicing-regulated MREs indicate associations with functions. For example, the MRE-free transcripts of many oncogenes, such as N-RAS and others may escape microRNA-mediated suppression in cancer tissues.ConclusionsThis fine-tuning mechanism revealed associations with highly repressive MRE. Since high-repression MREs are involved in many important biological phenomena, the described association implies that splicing-regulated MREs are functional. A possible application of this observed association is in distinguishing functionally relevant MREs from predicted MREs.

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A Catalogue of Glioblastoma and Brain MicroRNAs Identified by Deep Sequencing

Cited by 51 publications

References 30 publications

Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing

Identification of extracellular miRNA in human cerebrospinal fluid by next-generation sequencing

Next Generation Sequencing Analysis of miRNAs: MiR-127-3p Inhibits Glioblastoma Proliferation and Activates TGF-β Signaling by Targeting SKI

Fine-tuning of microRNA-mediated repression of mRNA by splicing-regulated and highly repressive microRNA recognition element

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