Anaplastic Thyroid Carcinoma: A ceRNA Analysis Pointed to a Crosstalk between<i>SOX2</i>,<i>TP53</i>, and microRNA Biogenesis

Arancio, Walter; Carina, Valeria; Pizzolanti, Giuseppe; Tomasello, Laura; Pitrone, Maria; Baiamonte, Concetta; Amato, Marco; Giordano, Carla

doi:10.1155/2015/439370

Cited by 13 publications

(8 citation statements)

References 36 publications

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“…Moreover, they show the ability to combine the same miRNA varies with each other, thus constructing multiplex RNA regulatory networks centered on miRNA. This network regulates RNA expression level, allow them to influence each other, and eventually affect the function of cells, which is called competitive endogenous RNA (ceRNA) mechanism 9,10 . Long noncoding RNA (lncRNA) is a noncoding protein‐nucleic acid sequence with a length of more than 200 bp, which is critical for the incidence and progression of cancers including BC 11,12 .…”

Section: Introductionmentioning

confidence: 99%

lncRNA CERS6‐AS1 as ceRNA promote cell proliferation of breast cancer by sponging miR‐125a‐5p to upregulate BAP1 expression

Yan

Feng

et al. 2020

Molecular Carcinogenesis

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Long noncoding RNAs (lncRNAs) can act as oncogene and tumor suppressor genes in many types of cancers including breast cancer (BC). Our previous study has indicated microRNA (miR)‐125a‐5p was downregulated and function as a tumor suppressor in BC. However, its upstream regulation mechanism is still unclear. In this study, we used bioinformatics algorithms, RNA pulldown assay, and dual‐luciferase reports assay to predict and confirm lncRNA CERS6‐AS1 interacted with miR‐125a‐5p. Then we found CERS6‐AS1 was upregulated in BC tissues. Experimental results of tumor growth in nude mice show that CERS6‐AS1 promotes tumor growth. Furthermore, CERS6‐AS1 regulated BC susceptibility gene 1‐associated protein 1 (BAP1) expression via sponging miR‐125a‐5p via Western blot analysis and quantitative polymerase chain reaction arrays. Finally, we showed that miR‐125a‐5p had opposing effects to those of CERS6‐AS1 on BC cells, demonstrating that CERS6‐AS1 may promote cell proliferation and inhibit cell apoptosis via sponging miR‐125a‐5p. Our results indicated CERS6‐AS1 promote BC cell proliferation and inhibit cell apoptosis via sponging miR‐125a‐5p to upregulate BAP1 expression.

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Section: Introductionmentioning

confidence: 99%

lncRNA CERS6‐AS1 as ceRNA promote cell proliferation of breast cancer by sponging miR‐125a‐5p to upregulate BAP1 expression

Yan

Feng

et al. 2020

Molecular Carcinogenesis

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“…ceRNAs are RNAs that share miRNA recognition elements (MREs) thereby competing for miRNA binding and regulating each other. Numerous recent studies of mammalian cells and tissues have demonstrated the competition between the protein-coding targets of miRNAs, which supportis a regulatory role for mRNAs independent of their protein coding function (13,14). Large-scale analyses of human gliomas have led to the conclusion that thousands of transcripts may act as target decoys, and the combined effects of multiple ceRNAs can have a major impact on gene expression and cellular phenotypes (15,16).…”

Section: Introductionmentioning

confidence: 94%

Extensive ceRNA–ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues

Han

et al. 2016

Nucleic Acids Res

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Crosstalk between RNAs mediated by shared microRNAs (miRNAs) represents a novel layer of gene regulation, which plays important roles in development. In this study, we analyzed time series expression data for coding genes and long non-coding RNAs (lncRNAs) to identify thousands of interactions among competitive endogenous RNAs (ceRNAs) in four rhesus tissues. The ceRNAs exhibited dynamic expression and regulatory patterns during each tissue development process, which suggests that ceRNAs might work synergistically during different developmental stages or tissues to control specific functions. In addition, lncRNAs exhibit higher specificity as ceRNAs than coding-genes and their functions were predicted based on their competitive coding-gene partners to discover their important developmental roles. In addition to the specificity of tissue development, functional analyses demonstrated that the combined effects of multiple ceRNAs can have major impacts on general developmental and metabolic processes in multiple tissues, especially transcription-related functions where competitive interactions. Moreover, ceRNA interactions could sequentially and/or synergistically mediate the crosstalk among different signaling pathways during brain development. Analyzing ceRNA interactions during the development of multiple tissues will provideinsights in the regulation of normal development and the dysregulation of key mechanisms during pathogenesis.

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“…PGG family 1149 is of interest because it contains the proto-oncogene RELA which has been implicated in pseudogene regulatory activity 34,35 . Another family of interest is 1235 that contains SOX2, which has been identified as a member of ceRNA networks 36,37 .…”

Section: Resultsmentioning

confidence: 99%

Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials

Johnson¹,

Kho

et al. 2017

Biocomputing 2018

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Pseudogenes are fossil relatives of genes. Pseudogenes have long been thought of as "junk DNAs", since they do not code proteins in normal tissues. Although most of the human pseudogenes do not have noticeable functions, ~20% of them exhibit transcriptional activity. There has been evidence showing that some pseudogenes adopted functions as lncRNAs and work as regulators of gene expression. Furthermore, pseudogenes can even be "reactivated" in some conditions, such as cancer initiation. Some pseudogenes are transcribed in specific cancer types, and some are even translated into proteins as observed in several cancer cell lines. All the above have shown that pseudogenes could have functional roles or potentials in the genome. Evaluating the relationships between pseudogenes and their gene counterparts could help us reveal the evolutionary path of pseudogenes and associate pseudogenes with functional potentials. It also provides an insight into the regulatory networks involving pseudogenes with transcriptional and even translational activities.In this study, we develop a novel approach integrating graph analysis, sequence alignment and functional analysis to evaluate pseudogene-gene relationships, and apply it to human gene homologs and pseudogenes. We generated a comprehensive set of 445 pseudogene-gene (PGG) families from the original 3,281 gene families (13.56%). Of these 438 (98.4% PGG, 13.3% total) were non-trivial (containing more than one pseudogene). Each PGG family contains multiple genes and pseudogenes with high sequence similarity. For each family, we generate a sequence alignment network and phylogenetic trees recapitulating the evolutionary paths. We find evidence supporting the evolution history of olfactory family (both genes and pseudogenes) in human, which also supports the validity of our analysis method. Next, we evaluate these networks in respect to the gene ontology from which we identify functions enriched in these pseudogene-gene families and infer functional impact of pseudogenes involved in the networks. This demonstrates the application of our PGG network database in the study of pseudogene function in disease context.

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Anaplastic Thyroid Carcinoma: A ceRNA Analysis Pointed to a Crosstalk betweenSOX2,TP53, and microRNA Biogenesis

Cited by 13 publications

References 36 publications

lncRNA CERS6‐AS1 as ceRNA promote cell proliferation of breast cancer by sponging miR‐125a‐5p to upregulate BAP1 expression

lncRNA CERS6‐AS1 as ceRNA promote cell proliferation of breast cancer by sponging miR‐125a‐5p to upregulate BAP1 expression

Extensive ceRNA–ceRNA interaction networks mediated by miRNAs regulate development in multiple rhesus tissues

Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials

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