Analysis of microRNA-target interactions across diverse cancer types

Jacobsen, Anders; Silber, Joachim; Harinath, Girish; Huse, Jason T.; Schultz, Nikolaus; Sander, Chris

doi:10.1038/nsmb.2678

Cited by 188 publications

(207 citation statements)

References 47 publications

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“…This result is consistent with recent observations that although individual genetic alterations appear to affect the gene expression and methylation levels, these are rare (Gibbs et al 2010). These observations demonstrated that ncRNA expression can be controlled not only by genetic but also epigenetic determinants, which is consistent with recent observations (Aure et al 2013;Jacobsen et al 2013). Next, we identified a panel of ncRNA biomarkers that can effectively discriminate cancer and normal samples.…”

Section: Cc-by-nc-nd 40 International License Peer-reviewed) Is the supporting

confidence: 80%

Genome-wide DNA methylome analysis reveals novel epigenetically dysregulated non-coding RNAs in human breast cancer

Zhang

et al. 2014

Preprint

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The development of human breast cancer is driven by changes in the genetic and epigenetic landscape of the cell. Despite growing appreciation of the importance of epigenetics in breast cancers, our knowledge of epigenetic alterations of non-coding RNAs (ncRNAs) in breast cancers remains limited. Here, we explored the epigenetic patterns of ncRNAs in breast cancers via a sequencing-based comparative methylome analysis, mainly focusing on two most popular ncRNA biotypes, long non-coding RNAs (lncRNAs) and miRNAs. Besides global hypomethylation and extensive CpG islands (CGIs) hypermethylation, we observed widely aberrant methylation in the promoters of ncRNAs, which was higher than that of protein-coding genes. Specifically, intergenic ncRNAs were observed to contribute a large slice of the aberrantly methylated ncRNA promoters. Moreover, we summarized five patterns of ncRNA promoter aberrant methylation in the context of genomic CGIs, where aberrant methylation occurred not only on the CGIs, but also flanking regions and CGI sparse promoters. Integration with transcriptional datasets, we found that the ncRNA promoter methylation events were associated with transcriptional changes. Furthermore, a panel of ncRNAs were identified as biomarkers that were able to discriminate between disease phenotypes (AUCs>0.90). Finally, the potential functions for aberrantly methylated ncRNAs were predicted based on similar patterns, adjacency and/or target genes, highlighting that ncRNAs and coding genes coordinately mediated pathways dysregulation in the development and progression of breast cancers. This study presents the aberrant methylation patterns of ncRNAs, which will be a highly valuable resource for investigations at understanding epigenetic regulation of breast cancers.

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Section: Cc-by-nc-nd 40 International License Peer-reviewed) Is the supporting

confidence: 80%

Genome-wide DNA methylome analysis reveals novel epigenetically dysregulated non-coding RNAs in human breast cancer

Zhang

et al. 2014

Preprint

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“…The extent to which individual miRNAs regulate common processes of tumor biology across diverse cancer types is beginning to be known and new examples of miRNAs that coordinately regulate cancer pathways (i.e., DNA demethylation pathway members) are emerging (35). Genomic analysis of PTC tumors in TCGA clearly suggests that miRNA expression patterns (36).…”

Section: From Cancer Genes To Signaling and Differentiation: Toward Amentioning

confidence: 99%

ENDOCRINE TUMOURS: Advances in the molecular pathogenesis of thyroid cancer: lessons from the cancer genome

Riesco‐Eizaguirre

Santisteban

2016

European Journal of Endocrinology

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Thyroid cancer is the most common endocrine malignancy giving rise to one of the most indolent solid cancers, but also one of the most lethal. In recent years, systematic studies of the cancer genome, most importantly those derived from The Cancer Genome Altas (TCGA), have catalogued aberrations in the DNA, chromatin, and RNA of the genomes of thousands of tumors relative to matched normal cellular genomes and have analyzed their epigenetic and protein consequences. Cancer genomics is therefore providing new information on cancer development and behavior, as well as new insights into genetic alterations and molecular pathways. From this genomic perspective, we will review the main advances concerning some essential aspects of the molecular pathogenesis of thyroid cancer such as mutational mechanisms, new cancer genes implicated in tumor initiation and progression, the role of non-coding RNA, and the advent of new susceptibility genes in thyroid cancer predisposition. This look across these genomic and cellular alterations results in the reshaping of the multistep development of thyroid tumors and offers new tools and opportunities for further research and clinical development of novel treatment strategies.

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“…Each is predicted to individually regulate hundreds to thousands of mRNAs, depending on cell type, context, and binding of cofactors 11, 12. Further, specific mRNAs can also be modulated by numerous different miRNAs, thus allowing for widespread regulation of gene expression.…”

Section: Introductionmentioning

confidence: 99%

MicroRNAs in glioblastoma multiforme pathogenesis and therapeutics

Harish²,

et al. 2016

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Glioblastoma multiforme (GBM) is the most common and lethal cancer of the adult brain, remaining incurable with a median survival time of only 15 months. In an effort to identify new targets for GBM diagnostics and therapeutics, recent studies have focused on molecular phenotyping of GBM subtypes. This has resulted in mounting interest in microRNAs (miRNAs) due to their regulatory capacities in both normal development and in pathological conditions such as cancer. miRNAs have a wide range of targets, allowing them to modulate many pathways critical to cancer progression, including proliferation, cell death, metastasis, angiogenesis, and drug resistance. This review explores our current understanding of miRNAs that are differentially modulated and pathologically involved in GBM as well as the current state of miRNA‐based therapeutics. As the role of miRNAs in GBM becomes more well understood and novel delivery methods are developed and optimized, miRNA‐based therapies could provide a critical step forward in cancer treatment.

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Analysis of microRNA-target interactions across diverse cancer types

Cited by 188 publications

References 47 publications

Genome-wide DNA methylome analysis reveals novel epigenetically dysregulated non-coding RNAs in human breast cancer

Genome-wide DNA methylome analysis reveals novel epigenetically dysregulated non-coding RNAs in human breast cancer

ENDOCRINE TUMOURS: Advances in the molecular pathogenesis of thyroid cancer: lessons from the cancer genome

MicroRNAs in glioblastoma multiforme pathogenesis and therapeutics

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