Similar Datasets
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.
2019-02-27 | GSE117365 | GEO
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.
2019-02-27 | GSE117113 | GEO
Project description:New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma
| PRJNA481894 | ENA
Project description:New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma [miRNA-Seq]
| PRJNA481916 | ENA
Project description:New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma [array]
| PRJNA481063 | ENA
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.
| S-EPMC6381125 | biostudies-literature
Project description:The identification of deregulated microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in multiple myeloma (MM) has progressively added a further level of complexity to MM biology. In addition, the cross-regulation between lncRNAs and miRNAs has begun to emerge, and theoretical and experimental studies have demonstrated the competing endogenous RNA (ceRNA) activity of lncRNAs as natural miRNA decoys in pathophysiological conditions, including cancer. Currently, information concerning lncRNA and miRNA interplay in MM is virtually absent. Herein, we investigated in silico the lncRNA and miRNA relationship in a representative datasets encompassing 95 MM and 30 plasma cell leukemia patients at diagnosis and in four normal controls, whose expression profiles were generated by a custom annotation pipeline to detect specific lncRNAs. We applied target prediction analysis based on miRanda and RNA22 algorithms to 235 lncRNAs and 459 miRNAs selected with a potential pivotal role in the pathology of MM. Among pairs that showed a significant correlation between lncRNA and miRNA expression levels, we identified 11 lncRNA-miRNA relationships suggestive of a novel ceRNA network with relevance in MM.
| S-EPMC5192483 | biostudies-literature
Project description:We perform a thorough analysis of RNA velocity methods, with a view towards understanding the suitability of the various assumptions underlying popular implementations. In addition to providing a self-contained exposition of the underlying mathematics, we undertake simulations and perform controlled experiments on biological datasets to assess workflow sensitivity to parameter choices and underlying biology. Finally, we argue for a more rigorous approach to RNA velocity, and present a framework for Markovian analysis that points to directions for improvement and mitigation of current problems.
| S-EPMC9499228 | biostudies-literature
Project description:Exosomes, secreted by several cell types, including cancer cells, can be isolated from the peripheral blood and have been shown to be powerful markers of disease progression in cancer. In this study, we examined the prognostic significance of circulating exosomal microRNAs (miRNAs) in multiple myeloma (MM). A cohort of 156 patients with newly diagnosed MM, uniformly treated and followed, was studied. Circulating exosomal miRNAs were isolated and used to perform a small RNA sequencing analysis on 10 samples and a quantitative reverse transcription polymerase chain reaction (qRT-PCR) array on 156 samples. We studied the relationship between miRNA levels and patient outcomes, including progression-free survival (PFS) and overall survival (OS). We identified miRNAs as the most predominant small RNAs present in exosomes isolated from the serum of patients with MM and healthy controls by small RNA sequencing of circulating exosomes. We then analyzed exosomes isolated from serum samples of 156 patients using a qRT-PCR array for 22 miRNAs. Two of these miRNAs, let-7b and miR-18a, were significantly associated with both PFS and OS in the univariate analysis and were still statistically significant after adjusting for the International Staging System and adverse cytogenetics in the multivariate analysis. Our findings support the use of circulating exosomal miRNAs to improve the identification of patients with newly diagnosed MM with poor outcomes. The results require further validation in other independent prospective MM cohorts.
| S-EPMC5409448 | biostudies-literature
Project description:More and more evidences suggested that the flow of genetic information can be spatially and temporally regulated by non-coding RNAs (ncRNAs), such as microRNAs (miRNAs). Although biogenesis and function of miRNAs have been well detailed, elucidation of the dynamic interplays between miRNAs and mRNAs have just begun. Here, we highlighted that the miRNA-mRNA interactions which could take place in different cellular locations. During dynamic interactions, miRNA binding sites included not only 3'UTRs, but also 5'UTRs and CDSs. Under different physiological or pathological conditions, miRNAs could switch from translational inhibition to activation. Dynamic miRNA-mRNA paradigms which suggested a novel tip of the iceberg beneath the gene regulation network will provide clues for function studies of other ncRNAs.
| S-EPMC5669400 | biostudies-literature