Oncogenic B-Raf signaling in melanoma cells controls a network of microRNAs with combinatorial functions

Couts, Kasey L.; Anderson, Emily M.; Gross, Maren M.; Sullivan, Kevin A.; Ahn, Natalie G.

doi:10.1038/onc.2012.209

Cited by 45 publications

(47 citation statements)

References 39 publications

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“…Indeed, individual genetic variability as well as the heterogeneity of the tumors may hamper the identification of functionally relevant deregulated miRNAs. The generation of appropriate cell model systems might help to “read” expression profile data [40-42]. …”

Section: Discussionmentioning

confidence: 99%

miR-199a-3p displays tumor suppressor functions in papillary thyroid carcinoma

et al. 2014

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Thyroid cancer incidence is rapidly increasing. Papillary Thyroid Carcinoma (PTC), the most frequent hystotype, usually displays good prognosis, but no effective therapeutic options are available for the fraction of progressive PTC patients. BRAF and RET/PTC are the most frequent driving genetic lesions identified in PTC. We developed two complementary in vitro models based on RET/PTC1 oncogene, starting from the hypothesis that miRNAs modulated by a driving PTC-oncogene are likely to have a role in thyroid neoplastic processes. Through this strategy, we identified a panel of deregulated miRNAs. Among these we focused on miR-199a-3p and showed its under-expression in PTC specimens and cell lines. We demonstrated that miR-199a-3p restoration in PTC cells reduces MET and mTOR protein levels, impairs migration and proliferation and, more interesting, induces lethality through an unusual form of cell death similar to methuosis, caused by macropinocytosis dysregulation. Silencing MET or mTOR, both involved in survival pathways, does not recapitulate miR-199a-3p-induced cell lethality, thus suggesting that the cooperative regulation of multiple gene targets is necessary. Integrated analysis of miR-199a-3p targets unveils interesting networks including HGF and macropinocytosis pathways. Overall our results indicate miR-199a-3p as a tumor suppressor miRNA in PTC.

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Section: Discussionmentioning

confidence: 99%

miR-199a-3p displays tumor suppressor functions in papillary thyroid carcinoma

et al. 2014

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“…Estimates of miRNA half-life range from 1 to Ͼ200 h in animal cells (60 -62), arguing that targets with extended kinetics are likely to be biologically relevant. In addition, measurements of intracellular miRNA concentrations show 60-to 250-fold increases in response to transfection of 15-50 nM exogenous miRNA (39,63,64), matching the more than 1000-fold changes in endogenous miRNAs quantified under varying cellular (e.g. disease) conditions (65,66).…”

Section: Discussionmentioning

confidence: 99%

“…WM239A cells derived from metastatic melanoma were labeled by SILAC with heavy (H) or light (L) isotopically-labeled ArgϩLys, and transfected with 50 nM of nontargeting (NT) miRNA or miR-22, previously identified as an miRNA whose expression is regulated by oncogenic mutant B-Raf signaling in melanoma (39). Proteins from whole cell lysate were trypsinized and the resulting peptides were analyzed by LC-MS/MS (Fig.…”

Section: Protein Abundance Changes In Response To Mir-22-mentioning

confidence: 99%

Dosage and Temporal Thresholds in microRNA Proteomics*

Lee

Wang

Houel

et al. 2015

Molecular & Cellular Proteomics

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MicroRNAs (miRNAs) modulate protein and mRNA expression through translational repression and/or mRNA decay. In this study, we combined SILAC-based proteomics and RNAseq to identify primary targets based on measurements of protein and mRNA repression and analysis of transcript 3UTR sequences. The primary target set was used to compare different prediction algorithms, revealing higher stringency of selection by Targetscan and PITA compared with miRanda, at the expense of higher false negatives. A key finding was that significant and unexpected variations occurred in the kinetics of repression as well as the sensitivity to exogeneous miRNA concentration. Bimodal thresholds were observed, which distinguished responses to low (10 nM) versus high (50 -100 nM) miRNA, as well as the onset of repression at early (12-18 h) versus late (36 -48 h) times. Similar behavior was seen at the transcript level with respect to kinetics of repression. The differential thresholds were most strongly correlated with ⌬⌬G, the net free energy of miRNA-target interactions, which mainly reflected inverse correlations with ⌬G open , the free energy of forming 3UTR secondary structures, at or nearby the miRNA seed matching sites. Thus, our working model is that protein binding or other competitive mechanisms variably interfere with the accessibility of miRISC to the transcript binding site. In addition, biphasic responses were observed in a subset of proteins that were partially down-regulated at early times, and further down-regulated at later times. Taken together, our findings provide evidence for varying modes of miRNA target repression, which lead to different thresholds of target responses with respect to kinetics and concentration, and predict that certain transcripts will show graded responses in sensitivity and fold-change under cellular conditions that lead to varying steady state miRNA levels. Molecular & Cellular Proteomics 14: 10.1074/mcp.M114.043851, 289-302, 2015. microRNAs (miRNAs)1 are small noncoding RNAs that modulate cellular protein levels, impacting a wide range of processes ranging from cellular development and differentiation to cancer, metabolic disorder, and other human diseases (1-5). Mature miRNAs interact with Argonaute (AGO) family proteins to form miRNA-induced silencing complexes (miRISCs) (6, 7), which in turn attenuate protein expression through translational repression and/or mRNA decay mechanisms. In animal cells, miRISC interacts with mRNA-bound poly(A) binding protein C (PABPC) through a complex between AGO and the GW182 trinucleotide-repeat-containing protein. This interaction recruits deadenylation, 5Ј-decapping, and mRNA degrading enzymes, and also blocks eukaryotic translation initiation factor G (eIFG) binding to confer translational repression (8 -11). Although the degree of protein or mRNA repression by miRNAs is often moderate (1.5-to 4-fold), fine-tuning at this level can be enough to shift cell and organismal phenotypes, or to set thresholds for gene and protein expression changes which control...

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“…Changes in miRNAs expression levels are known to play a key-role in various human cancers (20,21), including melanoma (22). Gene-expression profiling studies previously showed that a network of miRNAs is controlled by BRAF/MEK/ ERK signaling (23). In this paper we identify a mechanism of drug resistance in BRAF mutated melanoma centered around a poorly characterized miRNA, miR-579-3p.…”

Section: Significancementioning

confidence: 95%

“…Significance Analysis of Microarrays performed on melanomas and normal melanocytes recently resulted in the identification of 32 differentially expressed miRNAs (41). Moreover a highly sensitive microarray profiling showed that a network of 420 miRNAs is controlled by B-Raf/MEK/ERK signaling (23). More recently, detailed investigations of individual microRNAs have demonstrated the involvement of miR-125b, miR-365, and miR-425 as tumor suppressors in metastatic melanoma, and of miR-3151 as oncomiR (refs.…”

Section: Mir-579-3p Is Down-regulated In Melanoma Patients Who Developedmentioning

confidence: 99%

miR-579-3p controls melanoma progression and resistance to target therapy

Fattore

Mancini

Acunzo

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

101

115

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Therapy of melanoma patients harboring activating mutations in the BRAF (V-raf murine sarcoma viral oncogene homolog B1) oncogene with a combination of BRAF and MEK inhibitors is plagued by the development of drug resistance. Mutational events, as well as adaptive mechanisms, contribute to the development of drug resistance. In this context we uncover here the role of a miRNA, miR-579-3p. We first show that low expression of miR-579-3p is a negative prognostic factor correlating with poor survival. Expression levels of miR-579-3p decrease from nevi to stage III/IV melanoma samples and even further in cell lines resistant to BRAF/MEK inhibitors. Mechanistically, we demonstrate that miR-579-3p acts as an oncosuppressor by targeting the 3′UTR of two oncoproteins: BRAF and an E3 ubiquitin protein ligase, MDM2. Moreover miR-579-3p ectopic expression impairs the establishment of drug resistance in human melanoma cells. Finally, miR-579-3p is strongly down-regulated in matched tumor samples from patients before and after the development of resistance to targeted therapies.miRNA | melanoma | targeted therapy | drug resistance

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Oncogenic B-Raf signaling in melanoma cells controls a network of microRNAs with combinatorial functions

Cited by 45 publications

References 39 publications

miR-199a-3p displays tumor suppressor functions in papillary thyroid carcinoma

miR-199a-3p displays tumor suppressor functions in papillary thyroid carcinoma

Dosage and Temporal Thresholds in microRNA Proteomics*

miR-579-3p controls melanoma progression and resistance to target therapy

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