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In silico characterization of miRNA and long non-coding RNA interplay in multiple myeloma (30 PCL lncRNA data sets)

ABSTRACT: 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 RNAs (ceRNAs) 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 significant correlation between lncRNA and miRNA expression levels, we identified 10 lncRNA-miRNA relationships suggestive of novel ceRNA network with relevance in MM.

ORGANISM(S): Homo sapiens

PROVIDER: GSE106745 | GEO | 2017/11/09

SECONDARY ACCESSION(S): PRJNA417826

REPOSITORIES: GEO

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In silico characterization of miRNA and long non-coding RNA interplay in multiple myeloma (30 PCL miRNA data sets)

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 RNAs (ceRNAs) 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 significant correlation between lncRNA and miRNA expression levels, we identified 10 lncRNA-miRNA relationships suggestive of novel ceRNA network with relevance in MM.

2017-11-09 | GSE106744 | GEO

In silico characterization of miRNA and long non-coding RNA interplay in multiple myeloma (95 MM lncRNA data sets)

2017-02-10 | GSE87829 | GEO

In silico characterization of miRNA and long non-coding RNA interplay in multiple myeloma (95 MM miRNA data sets)

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Identification of lncRNA UCA1-associated microRNAs in breast cancer cell line MDA231 using miRNA-Seq

Project description:LncRNA urothelial carcinoma-associated 1 (UCA1) is an oncogene in breast cancer. Previous reports indicates that lncRNAs may function as competing endogenous RNAs (ceRNAs) to sponge miRNAs, thereby modulating the derepression of miRNA targets. To characterize microRNAs that associated with UCA1, the microRNAs associated with UCA1 were extracted from the UCA1-MS2 RNP complexes and analyzed by miRNA-seq.

2016-12-14 | GSE92319 | GEO

Transcriptome analyses of cerebral ischemia reveal functional lncRNAs in ischemia stroke

Project description:Background and Purpose: Long noncoding RNAs (lncRNAs) are an emerging class of genomic regulatory molecules reported in neurodevelopment and many diseases. Despite extensive studies have identified lncRNAs and discovered their functions in CNS diseases, the function of lncRNAs in ischemia stroke remains poorly understood. Method: Ischemia was induced by transient middle cerebral artery occlusion. Expression profiles of lncRNAs, miRNAs and mRNAs after ischemia stroke were obtained using high throughput sequencing technology. A correlation network was constructed to predict lncRNA functions. LncRNA-miRNA-mRNA network was constructed to discover ceRNAs. Results: 1924 novel lncRNAs were identified, indicating that the ischemia stroke has a complex effect on lncRNAs. The top 10 regulated lncRNAs was validated by qRT-PCR. We have also predicted function of lncRNAs, and subjected them to gene co-expression network analysis, revealing the involvement of lncRNAs in many important biological process including injury and repair that are implicated in the regulation of ischemia stroke. Furthermore, lncRNAs mediated SMD (Staufen1-mediated mRNA decay) was analyzed and ceRNA (competitive endogenous RNAs) network was constructed in ischemia stroke. Conclusions: This study reports the genome-wide lncRNA profiles in ischemia stroke using high throughput sequencing and constructs a systematic lncRNA-miRNA-mRNA network which reveals a complex functional noncoding RNA regulatory network in ischemia stroke.

2017-02-23 | GSE78200 | GEO

A Competing Endogenous RNA Network in Circulating Extracellular Vesicles Reveals Differentially-expressed Functional lncRNA in Human Subjects with Metabolic Syndrome

Project description:The metabolic syndrome (MetS), a collective cluster of disease risk factors that includes dyslipidemia, obesity, inflammation, hypertension, and insulin resistance, affects numerous people worldwide. Accumulating studies have shown that long-noncoding RNAs (lncRNA) serve as competing endogenous RNA (ceRNA) to play essential roles in regulating gene expression in various diseases. To explore the role of lncRNAs as ceRNAs in MetS, we examined a MetS-associated network in circulating extracellular vesicles (EVs) collected from systemic blood of MetS and control patients (n=5 each). MetS patients showed elevated body-weight, glucose, blood pressure, insulin, liver injury and inflammatory markers levels. In total, 191 differentially-expressed (DE) lncRNAs, 1389 mRNAs, and 138 miRNAs were selected for further analysis. Biological processes and pathway functional enrichment analysis were performed based on the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database. LncRNA/mRNA/miRNA ceRNA network was constructed by Cytoscape v3.8 based on the DE-RNAs, and included 13 lncRNAs, 8 miRNAs, and 64 mRNAs. We found that the lncRNA-associated ceRNA network members potentially serve as regulators of central cellular processes and complications of MetS, including cancer. These findings suggest that MetS alters the interactions among the ceRNA network components in circulating EV-specific ceRNA network, and implicate the cargo of circulating EVs in ramifications of MetS.

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Molecular mechanisms in lung tissue of yak provide insights into high-altitude adaptation by transcriptome-wide analysis [miRNA-seq]

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2020-07-08 | GSE153962 | GEO

Molecular mechanisms in lung tissue of yak provide insights into high-altitude adaptation by transcriptome-wide analysis [RNA-seq]

2020-07-08 | GSE153956 | GEO

miRNA-seq in human lung cancer tissues

Project description:we conducted transcriptome and small RNA sequencing to identify differentially expressed genes (DEGs), miRNAs (DEMs), and lncRNAs (DELs). Function analysis on DEM-target genes can explain the regulatory roles of miRNAs in LC. The lncRNA-miRNA pairs, miRNA-mRNA pairs, and lncRNA-mRNA pairs were identified, which were then combined to construct the interplay of lncRNAs/miRNAs/mRNAs. And we used the online databases to verify the selected DEMs, DELs, and DEGs. Our study identified 2509 DEGs, 34 DEMs, and 432 DELs in LC patients. miRNA-mRNA pairs, including 1 miRNA (hsa-miR-21-5p) and 5 targeted genes (RECK, TIMP3, EHD1, RASGRP1 and ERG), were figured out. We finally found the hub subnetwork (LINC00632/has-miR-21-5p/TIMP3) by combining lncRNA-miRNA pairs, miRNA-mRNA pairs and lncRNA-mRNA pairs.

2022-01-27 | GSE194300 | GEO

lncRNA-seq in human lung cancer tissues

Project description:We conducted transcriptome and small RNA sequencing to identify differentially expressed genes (DEGs), miRNAs (DEMs), and lncRNAs (DELs). Function analysis on DEM-target genes can explain the regulatory roles of miRNAs in LC. The lncRNA-miRNA pairs, miRNA-mRNA pairs, and lncRNA-mRNA pairs were identified, which were then combined to construct the interplay of lncRNAs/miRNAs/mRNAs. And we used the online databases to verify the selected DEMs, DELs, and DEGs. Our study identified 2509 DEGs, 34 DEMs, and 432 DELs in LC patients. miRNA-mRNA pairs, including 1 miRNA (hsa-miR-21-5p) and 5 targeted genes (RECK, TIMP3, EHD1, RASGRP1 and ERG), were figured out. We finally found the hub subnetwork (LINC00632/has-miR-21-5p/TIMP3) by combining lncRNA-miRNA pairs, miRNA-mRNA pairs and lncRNA-mRNA pairs.

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