The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset

Abstract

The most common mutation in melanoma, BRAF(V600E), activates the BRAF serine/threonine kinase and causes excessive MAPK pathway activity1,2. BRAF(V600E)mutations are also present in benign melanocytic nevi3, highlighting the importance of additional genetic alterations in the genesis of malignant tumors. Such changes include recurrent copy number variations that result in the amplification of oncogenes4,5. For certain amplifications, the large number of genes in the interval has precluded an understanding of cooperating oncogenic events. Here, we have used a zebrafish melanoma model to test genes in a recurrently amplified region on chromosome 1 for the ability to cooperate with BRAF(V600E) and accelerate melanoma. SETDB1, an enzyme that methylates histone H3 on lysine 9 (H3K9), was found to significantly accelerate melanoma formation in the zebrafish. Chromatin immunoprecipitation coupled with massively parallel DNA sequencing (ChIP-Seq) and gene expression analyses revealed target genes, including Hox genes, that are transcriptionally dysregulated in response to elevated SETDB1. Our studies establish SETDB1 as an oncogene in melanoma and underscore the role of chromatin factors in regulating tumorigenesis.

Epigenetic regulation in human melanoma: past and future

“…SETDB1 catalyzes the trimethylation of histone H3K9 and thereby promotes the repression of target genes. 44 Unlike BRAF V600E , which is present in both melanoma and benign nevi, 45 SETDB1 protein is elevated in melanoma but not in benign nevi or normal melanocytes. 44 This indicates that an unknown trigger may lead to the upregulation of SETDB1.…”

“…44 Unlike BRAF V600E , which is present in both melanoma and benign nevi, 45 SETDB1 protein is elevated in melanoma but not in benign nevi or normal melanocytes. 44 This indicates that an unknown trigger may lead to the upregulation of SETDB1. The genes that are targeted by elevated levels of SETDB1 remain unknown.…”

The Immune Signaling Adaptor LAT Contributes to the Neuroanatomical Phenotype of 16p11.2 BP2-BP3 CNVs

“…19 Macrocephaly during infancy is a recurrent observation in ASD, while HC defects in general are common features of neurodevelopmental disorders. 20,21 For these phenotypes, the measurement of the head size of zebrafish embryos has served as a relevant and useful proxy to identify genes whose dosage imbalance contributes to the neuropathology. We used this approach to demonstrate that the major driver of the 16p11.2 600 kb BP4-BP5 CNV head phenotype was KCTD13 (MIM: 608947), in epistasis with MVP (MIM: 605088) and MAPK3 (MIM: 601795), 18,22 while similar studies helped understand the genetic architecture of other CNVs.…”

Screening for Melanoma Modifiers using a Zebrafish Autochthonous Tumor Model

“…Create Gateway middle entry clones by PCR amplifying the full-length open reading frame of genes of interest (GOI) and recombining into pDONR 221 using BP clonase II (Invitrogen). Use Multisite Gateway technology (Invitrogen) to recombine p5E_mitfa, pME_GOI, Tol2kit #302 p3E_SV40polyA 6 and miniCoopR 5 to place genes of interest under the mitfa promoter in the miniCoopR vector ( Figure 1A). );p53(lf);mitfa(lf)triply homozygous zebrafish embryos as previously described 7 .…”