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Chromatin remodellers Brg1 and Bptf are required for normal gene expression and progression of oncogenic Braf-driven mouse melanoma

Abstract

Somatic oncogenic mutation of BRAF coupled with inactivation of PTEN constitute a frequent combination of genomic alterations driving the development of human melanoma. Mice genetically engineered to conditionally express oncogenic BrafV600E and inactivate Pten in melanocytes following tamoxifen treatment rapidly develop melanoma. While early-stage melanomas comprised melanin-pigmented Mitf and Dct-expressing cells, expression of these and other melanocyte identity genes was lost in later stage tumours that showed histological and molecular characteristics of de-differentiated neural crest type cells. Melanocyte identity genes displayed loss of active chromatin marks and RNA polymerase II and gain of heterochromatin marks, indicating epigenetic reprogramming during tumour progression. Nevertheless, late-stage tumour cells grown in culture re-expressed Mitf, and melanocyte markers and Mitf together with Sox10 coregulated a large number of genes essential for their growth. In this melanoma model, somatic inactivation that the catalytic Brg1 (Smarca4) subunit of the SWI/SNF complex and the scaffolding Bptf subunit of the NuRF complex delayed tumour formation and deregulated large and overlapping gene expression programs essential for normal tumour cell growth. Moreover, we show that Brg1 and Bptf coregulated many genes together with Mitf and Sox10. Together these transcription factors and chromatin remodelling complexes orchestrate essential gene expression programs in mouse melanoma cells.

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Data availability

All sequencing data in this paper have been submitted to the Geo database under the accession number. SuperSeries GSE129621.

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Acknowledgements

We thank R. Marais for the BrafLSL-V600E mice, D. Metzger for floxed Smarca4 and Pten mice, C. Wu for Bptf floxed mice, all the staff of the IGBMC high-throughput sequencing facility, a member of “France Génomique” consortium (ANR10-INBS-09-08). This work was supported by grants from the CNRS, the INSERM, Ligue National Contre le Cancer; Institut National du Cancer; ITMO-Cancer, Agence National de la Recherche, ANR10-Labex-0030-INRT. PL was supported by fellowships from the Ministère de l’enseignement supérieur et de la recherche and Fondation ARC pour la recherche sur le cancer. ID and LL are “équipes labellisées” of the Ligue Nationale contre le Cancer.

Author information

PL and SC performed and analysed all of the wet lab experiments. PL and GM generated and maintained the mouse lines. PL and GD performed the bioinformatics analysis. IM performed the tail and tumour genotyping. PS performed histopathology analysis, LL provided mice, performed histology analysis and analysed the data, ML and WY provided samples from the lymph nodes and skin sections, ID, PL, SC and LL conceived experiments, analysed the data and wrote the paper.

Correspondence to Irwin Davidson.

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