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| Status |
Public on Dec 31, 2022 |
| Title |
An epigenetic switch controls the expression of an alternative NR2F2 isoform that unleashes a pro-metastatic program in melanoma |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
Metastatic melanoma develops once transformed melanocytic cells begin to de-differentiate into migratory and invasive melanoma cells with neural crest cell (NCC)-like and epithelial-to mesenchymal transition (EMT)-like features. However, it is still unclear how transformed melanocytes assume a metastatic melanoma cell state. Here, we define DNA-methylation changes that accompany metastatic progression in melanoma patients and discover Nuclear Receptor Subfamily 2 Group F, Member 2 – isoform 2 (NR2F2-Iso2) as an epigenetically regulated metastasis driver. NR2F2-Iso2 is transcribed from an alternative transcriptional start site (TSS) and it is truncated at the N-terminal end which encodes the NR2F2 DNA-binding domain. We find that NR2F2-Iso2 expression is turned off by DNA methylation when NCCs differentiate into melanocytes. Conversely, this process is reversed during metastatic melanoma progression, when NR2F2-Iso2 becomes increasingly hypomethylated and re-expressed. Our functional and molecular studies suggest that NR2F2-Iso2 drives metastatic melanoma progression by modulating the activity of full-length NR2F2 (Isoform 1) over EMT- and NCC associated target genes. Our findings indicate that DNA-methylation changes play a crucial role during metastatic melanoma progression, and their control of NR2F2 activity allows transformed melanocytes to acquire NCC-like and EMT-like features. This epigenetically regulated transcriptional plasticity facilitates cell state transitions and metastatic spread.
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| Overall design |
DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2011.2) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.
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| Web link |
https://pubmed.ncbi.nlm.nih.gov/37015919/
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| Contributor(s) |
Davalos V, Esteller M |
| Citation(s) |
37015919 |
| |
| Submission date |
Aug 11, 2017 |
| Last update date |
Jun 02, 2023 |
| Contact name |
IJC Bioinformatics |
| E-mail(s) |
ijcbioinfo@carrerasresearch.org
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| Organization name |
Josep Carreras Leukemia Research Institute
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| Lab |
Bioinformatics Unit
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| Street address |
Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n
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| City |
Badalona |
| State/province |
Catalonia |
| ZIP/Postal code |
08916 |
| Country |
Spain |
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| Platforms (1) |
| GPL13534 |
Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA397989 |
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