TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

Vergoulis, Thanasis; Vlachos, Ioannis S.; Alexiou, Panagiotis; Γεωργακίλας, Γεώργιος; Maragkakis, Manolis; Reczko, Martin; Gerangelos, Stefanos; Koziris, Nectarios; Dalamagas, Theodore; Hatzigeorgiou, Artemis G.

doi:10.1093/nar/gkr1161

Cited by 491 publications

(405 citation statements)

References 26 publications

(35 reference statements)

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“…In DIANA Lab's TarBase, only a correlation between miR-21 and MMP9 was found. The aforementioned analyses are current as of September 2014, and the list of miRNA databases is based on those used by Vergoulis et al (26).…”

Section: Discussionmentioning

confidence: 99%

Expression of MMP9, SERPINE1 and miR-134 as prognostic factors in esophageal cancer

et al. 2016

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Abstract. Esophageal cancer (EC) is a malignant tumor with a typically poor prognosis for patients. It is well known that certain microRNA (miRNA/miR) genes can regulate other genes responsible for carcinogenesis. In the present study, a group of these genes (miR-21, miR-134, miR-205 and miR-495) and genes connected with cancer-related pathways (MET, MMP9, PDGFA and SERPINE1) were chosen for analysis in order to find a potential correlation between their expression and the clinicopathological factors of EC. Esophageal tumors and adjacent non-cancerous tissue specimens were collected from a total of 63 patients and embedded in paraffin. Commercial arrays were used on KYSE-30, KYSE-150 and KYSE-270 EC cell lines in order to find genes of different expression profiles compared with those acquired from the control Het-1A cell line. Quantitative polymerase chain reaction was used on formalin-fixed, paraffin-embedded samples in order to analyze the expression of the genes chosen in the earlier step. The results were analyzed by the Kruskal-Wallis and Mann-Whitney U tests, Spearman's rank correlation coefficient, Kaplan-Meier methods and the long-rank test. Only miR-495 was not expressed in the analyzed samples. The expression of MMP9 and SERPINE1 was significantly coefficient with age range (P=0.011 and P=0.044, respectively) according to the Kruskal-Wallis test. The Spearman's rank-order correlation measurement showed that there was a coefficient correlation between age and miR-134 expression. The same measurement demonstrated a correlation between age range and MMP9 expression. The expression of miR-134 and MMP9 were also found to be correlated. In all cases, a value of P<0.049 was recorded. Overall, the present study demonstrated that MMP9, SERPINE1 and miR-134 were the most prognostic genes in Caucasian patients with EC.

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Section: Discussionmentioning

confidence: 99%

Expression of MMP9, SERPINE1 and miR-134 as prognostic factors in esophageal cancer

et al. 2016

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“…A reduction in miR-let-7a might have negative effects on development of CRC. Caspase 3 (CASP3) is a validated target gene of miR-let-7a (Vergoulis et al 2012) as an effector of apoptosis, too. Tsang and Kwok (2008) could demonstrate an inverse interaction between miR-let7a and CASP3 in HepG2 and A431 cells, and Medina et al (1997) showed an induction of CASP3 activity by butyrate and TSA in Jurkat cells and LIM 1215 colon cancer cells.…”

Section: Discussionmentioning

confidence: 99%

Influence of miRNA-106b and miRNA-135a on butyrate-regulated expression of p21 and Cyclin D2 in human colon adenoma cells

et al. 2015

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Epigenetic and posttranslational modifications of the expression of cell cycle-relevant genes or proteins like p21, e.g., by miRNAs are crucial mechanisms in the development or prevention of colon cancer. The present study investigated the influence of butyrate and trichostatin A (TSA) as histone deacetylase inhibitors on the expression of colon cancer-relevant miRNA (miR-135a, miR-135b, miR-24, miR-106b, miR-let-7a) in LT97 colon adenoma cells as a model of an early stage of colon carcinogenesis. The impact of distinct miRNAs (miR-106b, miR-135a) on butyrate-mediated regulation of p21 and Cyclin D2 gene and protein expression as well as the effect on LT97 cell proliferation (non-transfected, miR-106b and miR-135a mimic transfected) was analyzed. Butyrate and partial TSA reduced the expression of miR-135a, miR-135b, miR-24 and miR-let-7a (*0.5-fold, 24 h) and miR-24, miR-106b and miR-let-7a (*0.5-0.7-fold, 48 h) in LT97 cells. Levels of p21 mRNA and protein were significantly increased by butyrate and TSA (*threefold and 4.5-fold, respectively, 24 h) in non-transfected but not in miR-106b transfected LT97 cells. Levels of Cyclin D2 mRNA were significantly reduced by butyrate and TSA (*0.3-fold, 24 h) in non-transfected and miR-135a-transfected LT97 cells, whereas protein levels were predominantly not influenced. MiR-106b and miR-135a significantly reduced butyrate-/TSA-mediated inhibition of LT97 cell proliferation (72 h). These results indicate that butyrate is able to modify colon cancer-relevant miRNAs like miR-106b and miR-135a which are involved in the regulation of cell cycle-relevant genes like p21 and might influence inhibition of adenoma cell proliferation.

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“…DIANA-MicroT tools are being developed in Artemis Hatzigeorgiou's laboratory for over a decade (Kiriakidou et al, 2004;Sethupathy et al, 2006;Megraw et al, 2007;Maragkakis et al, 2009;Alexiou et al, 2010;Maragkakis et al, 2011;Reczko et al, 2011;Vergoulis et al, 2012;Vlachos et al, 2012;Paraskevopoulou et al, 2013a;Paraskevopoulou et al, 2013b;Paraskevopoulou et al, 2016). MicroT is specifically trained on a positive and a negative set of miRNA binding sites located in 3'-UTR and CDS regions.…”

Section: Targetscan (Http://wwwtargetscanorg/vert_71/)mentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFS3

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This report is the outcome of an EFSA procurement aiming at investigating and summarising the state of knowledge on (I) the mode-of-action of dsRNA and miRNA pathways, (II) the potential for nontarget gene regulation by dsRNA-derived siRNAs or miRNAs, (III) the determination of siRNA pools in plant tissues and the importance of individual siRNAs for silencing. The report is based on a comprehensive and systematic literature search, starting with the identification and retrieval of~190,000 publications related to the research area and further filtered down with keywords to produce focused collections used for subsequent screening of titles and abstracts. The report is comprised of an (I) Introduction to the field of small RNAs, (II) a Data and Methodologies section containing strategies used for literature search and study selection, and (III) the Results of the literature review organized according to the three main procurement tasks. The outcome of the first task reviews dsRNA and miRNA pathways in mammals (including humans), birds, fish, arthropods, annelids, molluscs, nematodes, and plants. Eight taxon-dedicated chapters are based on~1,400 cumulative references chosen from~10,000 inspected titles and abstracts. We review conserved and divergent aspects of small RNA pathways and dsRNA responses in animals and plants including structure and function of key proteins as well as four basic mechanisms: genome-encoded posttranscriptional regulations (miRNA), degradation of RNAs by short interfering RNA pools generated from long dsRNA (RNAi), transcriptional silencing, and sequence-independent responses to dsRNA. The outcome of the second task focuses on base pairing between small RNAs and their target RNAs and predictability of biological effects of small RNAs in animals and plants. The outcome of the last task reviews methodology, siRNA pools, and movement of small RNAs in plants. Potential transfer of small RNAs between species and circulating miRNAs in mammals is described in the final chapter.

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TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

Cited by 491 publications

References 26 publications

Expression of MMP9, SERPINE1 and miR-134 as prognostic factors in esophageal cancer

Expression of MMP9, SERPINE1 and miR-134 as prognostic factors in esophageal cancer

Influence of miRNA-106b and miRNA-135a on butyrate-regulated expression of p21 and Cyclin D2 in human colon adenoma cells

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

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