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New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma

ABSTRACT: New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma

PROVIDER: PRJNA481894 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7541170.fastq.gz	Fastqsanger.gz
	SRR7541180.fastq.gz	Fastqsanger.gz
	SRR7541190.fastq.gz	Fastqsanger.gz
	SRR7541171.fastq.gz	Fastqsanger.gz
	SRR7541181.fastq.gz	Fastqsanger.gz

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New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma [array]

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New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma [miRNA-Seq]

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New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma [array]

Project description:Microarray analysis of the miRNome in multiple myeloma (MM) has unraveled the differential expression of miRNAs in cytogenetic subgroups, their involvement in the tumor biology and their effectiveness in prognostic models. Herein, we provide a view of small RNA transcriptional landscape in MM at a higher definition, exploiting the possibilities offered by small RNA-sequencing (sRNA-seq), including improved detection of known/new mature species and accurate investigation of isomiRs and miRNA-offset RNAs (moRNAs). Matched sRNA-seq data and miRNA microarray profiles in a panel of 30 primary MM tumors were obtained and compared. A good concordance was observed in the detection of the expression level of known species and in the differential analysis between subgroups. The superior discovery power of RNA-seq allowed characterizing 655 known and 17 new mature miRNAs, and describing 74 moRNAs, most of which highly expressed and group-specific. Ectopic expression of miR-135 in t(4;14) patients, undetected by arrays was detected by RNA-seq and validated by qPCR.

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New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma

Project description:This SuperSeries is composed of the SubSeries listed below.

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MicroRNA-offset RNA regulates gene expression and cell proliferation

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Expanding the repertoire of miRNAs and miRNA-offset RNAs expressed in multiple myeloma by small RNA deep sequencing.

Project description:Microarray analysis of the multiple myeloma (MM) miRNome has unraveled the differential expression of miRNAs in cytogenetic subgroups, their involvement in the tumor biology and their effectiveness in prognostic models. Herein, the small RNA transcriptional landscape in MM has been investigated exploiting the possibilities offered by small RNA-seq, including accurate quantification of known mature species, discovery and characterization of isomiRs, and miRNA-offset RNAs (moRNAs). Matched small RNA-seq and miRNA GeneChip® microarray expression profiles were obtained in a representative panel of 30 primary MM tumors, fully characterized for genomic aberrations and mutations. RNA-seq and microarray gave concordant estimations of known species. Enhanced analysis of RNA-seq data with the miR&moRe pipeline led to the characterization of 655 known and 17 new mature miRNAs and of 74 moRNAs expressed in the considered cohort, 5 of which (moR-150-3p, moR-24-2-5p, moR-421-5p, moR-21-5p, and moR-6724-5p) at high level. Ectopic expression of miR-135a-3p in t(4;14) patients, upregulation of moR-150-3p and moR-21-5p in t(14;16)/t(14;20) samples, and of moR-6724-1-5p in patients overexpressing CCND1 were uncovered and validated by qRT-PCR. Overall, RNA-seq offered a more complete overview of small non-coding RNA in MM tumors, indicating specific moRNAs that demand further investigations to explore their role in MM biology.

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MicroRNA-offset RNA regulates gene expression and cell proliferation (BeadChip)

2016-06-01 | GSE75112 | GEO

MicroRNA-offset RNA regulates gene expression and cell proliferation (Small RNA-Seq)

2016-06-01 | GSE75113 | GEO

MicroRNA-offset RNA regulates gene expression and cell proliferation (BeadChip)

Project description:MicroRNA-offset RNAs (moRs) were first identified in simple chordates and subsequently in mouse and human cells by deep sequencing of short RNAs. MoRs are derived from sequences located immediately adjacent to microRNAs (miRs) in the primary miR (pri-miR). Currently moRs are considered to be simply a by-product of miR biosynthesis that lack biological activity. Here we show for the first time that a moR is biologically active. We now demonstrate that endogenous and over-expressed moR-21 significantly alters gene expression and inhibits the proliferation of vascular smooth muscle cells (VSMC). We report that the seed region of moR-21 as well as the seed match region in the target gene 3'UTR are indispensable for moR-21-mediated gene down-regulation. We further demonstrated that moR-21-mediated gene repression is Argonaute 2 (Ago2) dependent. In addition, we find that miR-21 and moR-21 may regulate different genes in a given pathway and can oppose each other in regulating certain genes. Taken together, these findings provide the first evidence that microRNA offset RNA regulates gene expression and is biologically active. Primary mouse aortic smooth muscle cells (AoSMCs) were transfected with scrambled control or moR-21 mimetics at 5nM final concentration. Triplicate samples were prepared for each treatment. Total RNA was isolated at 48hr post-transfection. Labeling and hybridization to MouseRef-8 v2.0 Expression BeadChip (llumina) were performed according to the Yale Center for Genome Analysis protocol (YCGA, http://ycga.yale.edu/). Beadstudio suite of programs were used to calculate the quantile normalized expression values for probe sets. Bioconductor packages Lumi and Limma Linear models and empirical Bayes methods for assessing differential expression in microarray experiments were use to process and annotate the expression values and calculate the fold changes and P-values.

2016-06-01 | E-GEOD-75112 | biostudies-arrayexpress

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