Ontology highlight
ABSTRACT:
PROVIDER: PRJNA481334 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:BRAF, one of three RAF serine/threonine kinases (ARAF, BRAF and CRAF), plays a major role in the RAS-RAF-MEK-ERK mitogen-activated protein kinase (MAPK) signaling pathway, which mediates cellular responses to growth signals. Recently a high frequency (~60%-70%) of activating BRAF mutations (predominantly V600E) has been reported in malignant melanoma. In order to identify the downstream effects of BRAF signaling on melanoma cell growth and gene expression, cDNA microarray analysis was carried out following BRAF siRNA or MEK1/2 inhibitor (U0126) treatment. Keywords: time series, siRNA time series, siRNA, drug treatment
2013-07-07 | E-GEOD-5481 | biostudies-arrayexpress
Project description:Selective RAF inhibitors including vemurafenib (PLX4032) have demonstrated clinical efficacy in mutant BRAF driven metastatic melanoma. The clinical effectiveness of RAF inhibitors depends on near complete abolition of the MAPK pathway output in tumors harboring BRAF mutations. However these compounds paradoxically activate the MAPK pathway in cells bearing oncogenic RAS or elevated upstream receptor signaling. This paradox can promote cellular proliferation and can manifest clinically with progression of secondary malignancies such as cutaneous squamous cell carcinomas (cuSCC). We have identified next generation RAF inhibitors (“paradox breakers”, e.g. PLX7904) that inhibit mutant BRAF cells without activating the MAPK pathway in cells bearing upstream activation. In murine cuSCC B9 cells that express the same HRAS mutation prevalent in squamous tumors from patients treated with RAF inhibitors, the first-generation RAF PLX4032 stimulated in vitro and in vivo growth; by contrast the paradox breaker PLX7904 had no effect. Here we compared the gene expression changes in B9 cells treated overnight with PLX4032 and PLX7904.
2015-10-01 | GSE71109 | GEO
Project description:Melanoma patients treated with oncogenic BRAF inhibitors can develop cutaneous squamous cell carcinoma (cSCC) within weeks of treatment, driven by paradoxical RAS/RAF/MAPK pathway activation. Here, we identify frequent TGFBR1 and TGFBR2 mutations in human vemurafenib-induced skin lesions and in sporadic cSCC. Functional analysis reveals these mutations ablate canonical TGFβ Smad signaling which is localised to bulge stem cells in both normal human and murine skin. MAPK pathway hyperactivation (through BrafV600E or KrasG12D knockin) and TGFβ signaling ablation (through Tgfbr1 deletion) in LGR5+ve stem cells enables rapid cSCC development in the mouse. Mutation of Tp53 (which is commonly mutated in sporadic cSCC) coupled with Tgfbr1 deletion in LGR5+ve cells also results in cSCC development. These findings indicate that LGR5+ve stem cells can act as cells of origin for cSCC and that RAS/RAF/MAPK pathway hyperactivation or Tp53 mutation, coupled with loss of TGFβ signaling, are driving events of skin tumorigenesis.
| EGAS00001001892 | EGA
Project description:BRAF, one of three RAF serine/threonine kinases (ARAF, BRAF and CRAF), plays a major role in the RAS-RAF-MEK-ERK mitogen-activated protein kinase (MAPK) signaling pathway, which mediates cellular responses to growth signals. Recently a high frequency (~60%-70%) of activating BRAF mutations (predominantly V600E) has been reported in malignant melanoma. In order to identify the downstream effects of BRAF signaling on melanoma cell growth and gene expression, cDNA microarray analysis was carried out following BRAF siRNA or MEK1/2 inhibitor (U0126) treatment. Keywords: time series, siRNA
2013-07-07 | GSE5481 | GEO
Project description:Mitogen-activated protein kinase (MAPK) pathway activation is a central step in BRAFV600E-mutant cutaneous melanoma (CM) pathogenesis. In the last years, Spry1 has been frequently described as an upstream regulator of MAPK signaling pathway. However, its specific role in BRAFV600E-mutant CM is still poorly defined. Here, we report that Spry1 knockdown (Spry1KO) in three BRAFV600E-mutant CM cell lines markedly induced cell cycle arrest and apoptosis, repressed cell proliferation in vitro, and impaired tumor growth in vivo. Furthermore, our findings indicated that Spry1KO reduced the expression of several EMT-markers, such as MMP-2 both in vitro and in vivo. These effects were associated with a sustained and deleterious phosphorylation of ERK1/2. In addition, p38 activation along with an increase in basal ROS levels were found in Spry1KO clones compared to parental CM cell lines, suggesting that BRAFV600E-mutant CM may restrain the activity of Spry1 to avoid oncogenic stress and to enable tumor growth. Consistent with this hypothesis, treatment with the BRAF inhibitor (BRAFi) vemurafenib down-regulated Spry1 levels in parental CM cell lines, indicating that Spry1 expression is sustained by MAPK/ERK signaling pathway in a positive feedback loop that safeguards cells from the potentially toxic effects of ERK1/2 hyperactivation. Disruption of this feedback loop rendered Spry1KO cells more susceptible to apoptosis and markedly improved response to BRAFi both in vitro and in vivo, as a consequence of the detrimental effect of ERK1/2 hyperactivation observed upon Spry1 abrogation. Therefore, targeting Spry1 might offer a treatment strategy for BRAFV600E-mutant CM by inducing the toxic effects of ERK-mediated signaling.
2020-05-26 | E-MTAB-7886 | biostudies-arrayexpress
Project description:The most common oncogenic mutations in multiple myeloma (MM) affect N- and K-RAS leading to constitutive activation of RAS-dependent signaling. Signal transduction via RAS, Raf and MAPK has been well described as a canonical pathway. In accordance with this assumption, we showed that the activity of the MEK/ERK module is strictly dependent on pan-Raf activity. However, inhibition of MEK/ERK has no or only minor effects on MM cell survival, whereas oncogenic Ras and pan-Raf critically contribute to survival of multiple myeloma cells. Therefore, we aimed to learn more about Raf-dependent but MEK-independent signaling effectors. We analyzed gene expression profiles in INA-6 cells after either pan-Raf inhibition with SB-590885 or MEK inhibition with PD-325901.
2016-11-21 | GSE75078 | GEO
Project description:BRAF is the most frequently mutated gene in melanoma. Constitutive activation of mutant BRAFV600E leads to aberrant Ras-independent MAPK signaling and cell transformation. Inhibition of mutant BRAF is a current front-line therapy for such cases, with improved survival compared with chemotherapy. Unfortunately, reactivation of MAPK signaling by several mechanisms has been shown to cause drug resistance and disease recurrence. In this work, we describe the co-occurrence of an in-frame deletion within an amplified BRAFV600E locus, and a missense point mutation of the transcriptional repressor BCORL1, in vemurafenib-resistant A375 melanoma cells. Functional data confirmed that truncated p47BRAFV600E and mutant BCORL1Q1076H both contribute to resistance. Interestingly, either endogenous BCORL1 silencing or ectopic BCORL1Q1076H expression mimicked the effects of a CRISPR/Cas9-edited BCORL1Q1076H locus, suggesting a change-of-function mutation. Transcriptomic data confirmed this hypothesis. Finally, we show that the pan-RAF inhibitor sorafenib is not affected by expression of BRAF deletion variant and effectively synergizes with vemurafenib to block resistant cells, suggesting a possible intervention for this class of mutants.
2018-11-27 | GSE107370 | GEO
Project description:This is a Phase 1b/2, multi-center, open label umbrella study of patients ≥12 years of age with recurrent, progressive, or refractory melanoma or other solid tumors with alterations in the key proteins of the RAS/RAF/MEK/ERK pathway, referred to as the MAPK pathway.
| 2385126 | ecrin-mdr-crc
Project description:Pappalardo2016 - PI3K/AKT and MAPK Signaling
Pathways in Melanoma Cancer
This model is described in the article:
Computational Modeling of
PI3K/AKT and MAPK Signaling Pathways in Melanoma Cancer.
Pappalardo F, Russo G, Candido S,
Pennisi M, Cavalieri S, Motta S, McCubrey JA, Nicoletti F, Libra
M.
PLoS ONE 2016; 11(3): e0152104
Abstract:
Malignant melanoma is an aggressive tumor of the skin and
seems to be resistant to current therapeutic approaches.
Melanocytic transformation is thought to occur by sequential
accumulation of genetic and molecular alterations able to
activate the Ras/Raf/MEK/ERK (MAPK) and/or the PI3K/AKT (AKT)
signalling pathways. Specifically, mutations of B-RAF activate
MAPK pathway resulting in cell cycle progression and apoptosis
prevention. According to these findings, MAPK and AKT pathways
may represent promising therapeutic targets for an otherwise
devastating disease.Here we show a computational model able to
simulate the main biochemical and metabolic interactions in the
PI3K/AKT and MAPK pathways potentially involved in melanoma
development. Overall, this computational approach may
accelerate the drug discovery process and encourages the
identification of novel pathway activators with consequent
development of novel antioncogenic compounds to overcome tumor
cell resistance to conventional therapeutic agents. The source
code of the various versions of the model are available as S1
Archive.
This model is hosted on
BioModels Database
and identified by:
MODEL1609190000.
To cite BioModels Database, please use:
BioModels Database:
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quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-09-25 | BIOMD0000000666 | BioModels
Project description:Ras and its downstream cascades transmit cellular signals, resulting in increased transcription of a large number of genes involved in cell growth and division. Research on long non-coding transcripts regulated by the Ras signaling cascade is still in its infancy. Long non-coding RNAs (lncRNAs) are operationally defined as transcripts that are larger than 200 nt that do not appear to have protein-coding potential. Using a custom-designed lncRNA microarray, we identified a novel lncRNA (oncogenic Ras-induced lncRNA 1, Orilnc1) whose expression is significantly induced by activation of Ras. Further molecular studies demonstrated that the expression of Orilnc1 is regulated by the Ras-Raf-MEK-ERK signaling cascade via the transcriptional factor AP1. Importantly, Orilnc1 is highly expressed in BRAF mutant cancers such as BRAF-driven melanoma. Inhibition of Orilnc1 expression by small RNA interference (siRNA) significantly blocked tumor cell proliferation and growth in vitro and in vivo. Finally, we observed that blocking Orilnc1 reduced expression levels of cell cycle related genes such as Cyclin E1 and induced G1/S arrest in tumor cells. Taken together, Orilnc1 may function as a novel non-protein mediator to respond the Ras/Raf activation and could serve as a potential therapeutic target for RAS or BRAF-driven cancers such as melanoma.
2017-09-05 | GSE90044 | GEO