CTAB–Urea Method Purifies RNA from Melanin for cDNA Microarray Analysis

Lagonigro, Maria Stefania; Cecco, Loris De; Carninci, Piero; Stasi, Delia Di; Ranzani, Tiziana; Rodolfo, Monica; Gariboldi, Manuela

doi:10.1111/j.1600-0749.2004.00155.x

Cited by 29 publications

(7 citation statements)

References 10 publications

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“…At day 42, cells from all conditions were collected and genomic DNA was extracted. Since melanin pigment may interfere with DNA-and/or RNA-based molecular profiling 63 , we purified the samples using the OneStep TM PCR inhibitor Removal Kit (Zymo Research). The integrated sgRNAs were then amplified by PCR with primers containing multiplexing barcodes and adaptors and sequenced on the Illumina NextSeq500.…”

Section: Methodsmentioning

confidence: 99%

SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling

et al. 2018

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While multiple mechanisms of BRAFV600-mutant melanoma resistance to targeted MAPK signaling inhibitors (MAPKi) have been reported, the epigenetic regulation of this process remains undetermined. Here, using a CRISPR–Cas9 screen targeting chromatin regulators, we discover that haploinsufficiency of the histone deacetylase SIRT6 allows melanoma cell persistence in the presence of MAPKi. Haploinsufficiency, but not complete loss of SIRT6 promotes IGFBP2 expression via increased chromatin accessibility, H3K56 acetylation at the IGFBP2 locus, and consequent activation of the IGF-1 receptor (IGF-1R) and downstream AKT signaling. Combining a clinically applicable IGF-1Ri with BRAFi overcomes resistance of SIRT6 haploinsufficient melanoma cells in vitro and in vivo. Using matched melanoma samples derived from patients receiving dabrafenib + trametinib, we identify IGFBP2 as a potential biomarker for MAPKi resistance. Our study has not only identified an epigenetic mechanism of drug resistance, but also provides insights into a combinatorial therapy that may overcome resistance to standard-of-care therapy for BRAFV600-mutant melanoma patients.

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Section: Methodsmentioning

confidence: 99%

SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling

et al. 2018

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“…DNA was extracted from the biopsies using QIAamp DNA Mini Kit ® (Qiagen, Chatsworth, CA, USA). Some of the DNA samples also had to undergo further steps to separate DNA from melanin [ 21 , 22 ]. DNA was dissolved in dH 2 O and kept at −20 °C.…”

Section: Methodsmentioning

confidence: 99%

Low BRAF and NRAS expression levels are associated with clinical benefit from DTIC therapy and prognosis in metastatic melanoma

Birkeland

Busch

Berge

et al. 2013

Clin Exp Metastasis

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Metastatic melanoma is characterized by a poor response to chemotherapy. Furthermore, there is a lack of established predictive and prognostic markers. In this single institution study, we correlated mutation status and expression levels of BRAF and NRAS to dacarbazine (DTIC) treatment response as well as progression-free and overall survival in a cohort of 85 patients diagnosed with advanced melanoma. Neither BRAF nor NRAS mutation status correlated to treatment response. However, patients with tumors harboring NRAS mutations had a shorter overall survival (p < 0.001) compared to patients with tumors wild-type for NRAS. Patients having a clinical benefit (objective response or stable disease at 3 months) on DTIC therapy had lower BRAF and NRAS expression levels compared to patients progressing on therapy (p = 0.037 and 0.003, respectively). For BRAF expression, this association was stronger among patients with tumors wild-type for BRAF (p = 0.005). Further, low BRAF as well as NRAS expression levels were associated with a longer progression-free survival in the total population (p = 0.004 and <0.001, respectively). Contrasting low NRAS expression levels, which were associated with improved overall survival in the total population (p = 0.01), low BRAF levels were associated with improved overall survival only among patients with tumors wild-type for BRAF (p = 0.013). These findings indicate that BRAF and NRAS expression levels may influence responses to DTIC as well as prognosis in patients with advanced melanoma.Electronic supplementary materialThe online version of this article (doi:10.1007/s10585-013-9587-4) contains supplementary material, which is available to authorized users.

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“…At the same time, rice CBF2 was expressed in shoots and seeds but not in roots and leaves. Novillo et al [7,20] also reported that CBF2 is induced later than CBF1 and CBF3 during cold acclimation. Novillo et al [20] confirmed that nonacclimated and cold-acclimated CBF2 mutants have higher capacity for tolerating freezing and dehydration than the corresponding WT plants.…”

Section: Discussionmentioning

confidence: 94%

“…Arabidopsis CBF1, CBF2, and CBF3 are major transcriptional factors affecting cold-inducible gene expression [6,7]. CBF4 from Arabidopsis is weakly induced by cold stress [8], whereas DREB2A is induced by drought and salinity [9].…”

Section: Introductionmentioning

confidence: 99%

Isolation and expression characterization of CBF2 in <i>vitis amurensis</i> with stress

Chen¹,

Tao²,

Zhang³

et al. 2013

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The transcription factor VaCBF2, which interacts with C-repeat/DRE and its promoter, was isolated from Vitis amurensis. The VaCBF2 amino acid sequence contained a conserved AP2 domain of 56 amino acids and a potential nuclear localization sequence. The sequence of VaCBF2 showed a high level of homology with other CBF2 family members. Phylogenetic analysis showed that the amino acid sequences may be CBF2 proteins with evolutionary relationship. Quantitative reverse-transcription polymerase chain reaction analysis indicated that the expression of VaCBF2 gene in tissues (roots, stems, leaves, and petioles) was induced by low temperature, high salinity, and application of abscisic acid and salicylic acid in a time-dependent manner but to different extents in the coldhardy V. amurensis and the less cold-hardy Vitis vinifera. The presence of cis-elements such as MYC and ABRE in VaCBF2 promoter further confirmed that this promoter was a component of the CBF transduction pathway involved in plant response to multiple stresses.

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CTAB–Urea Method Purifies RNA from Melanin for cDNA Microarray Analysis

Cited by 29 publications

References 10 publications

SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling

SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling

Low BRAF and NRAS expression levels are associated with clinical benefit from DTIC therapy and prognosis in metastatic melanoma

Isolation and expression characterization of CBF2 in <i>vitis amurensis</i> with stress

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CTAB–Urea Method Purifies RNA from Melanin for cDNA Microarray Analysis

Cited by 29 publications

References 10 publications

SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling

SIRT6 haploinsufficiency induces BRAFV600E melanoma cell resistance to MAPK inhibitors via IGF signalling

Low BRAF and NRAS expression levels are associated with clinical benefit from DTIC therapy and prognosis in metastatic melanoma

Isolation and expression characterization of CBF2 in &lt;i&gt;vitis amurensis&lt;/i&gt; with stress

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Isolation and expression characterization of CBF2 in <i>vitis amurensis</i> with stress