Abstract LB-248: BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration.

Abstract

Aberrations of protein-coding genes are a focus of cancer genomics; however, the impact of oncogenes on expression of the ~50% of transcripts without protein-coding potential, including long noncoding RNAs (lncRNAs), has been largely uncharacterized. Activating mutations in the BRAF oncogene are present in >70% of melanomas, 90% of which produce active mutant BRAF(V600E) protein. To define the impacts of oncogenic BRAF on the melanocyte transcriptome, massively parallel cDNA sequencing (RNA-seq) was performed on genetically matched normal human melanocytes with and without BRAF(V600E) expression. To enhance potential disease relevance by verifying expression of altered genes in BRAF-driven cancer tissue, parallel RNA-seq was also undertaken of two BRAF(V600E)-mutant human melanomas. BRAF(V600E) regulated expression of 1027 protein-coding transcripts and 39 annotated lncRNAs, as well as 70 unannotated, potentially novel, intergenic transcripts. These transcripts display both tissue-specific and multi-tissue expression profiles and harbor distinctive regulatory chromatin marks and transcription factor binding sites indicative of active transcription. Coding potential analysis of the 70 unannotated transcripts suggested that most may represent newly identified lncRNAs. BRAF-regulated lncRNA 1 (BANCR) was identified as a recurrently overexpressed, previously unannotated 693-bp transcript on chromosome 9 with a potential functional role in melanoma cell migration. BANCR knockdown reduced melanoma cell migration, and this could be rescued by the chemokine CXCL11. Combining RNA-seq of oncogene-expressing normal cells with RNA-seq of their corresponding human cancers may represent a useful approach to discover new oncogene-regulated RNA transcripts of potential clinical relevance in cancer. Citation Format: Ross J. Flockhart, Dan E. Webster, Kun Qu, Nicholas Mascarenhas, Joanna Kovalski, Markus Kretz, Khavari A. Paul. BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-248. doi:10.1158/1538-7445.AM2013-LB-248

Epigenetic regulation in human melanoma: past and future

“…BANCR was identified as a potential regulator of melanoma cell migration as profound migration defects were observed following BANCR depletion. 74 The mechanism by which BANCR regulates gene expression remains to be identified.…”

Lentiviral-mediated overexpression of long non-coding RNA GAS5 reduces invasion by mediating MMP2 expression and activity in human melanoma cells

“…Some lncRNAs have been implicated in melanoma, such as antisense noncoding RNA in the INK4b locus (ANRIL), bRAF activated non-coding RNA (bANCR), metastasis associated lung adenocarcinoma transcript 1 (MALAT1) and SPRYT-4 intronic transcripts (SPRY4-IT1) (39,(42)(43)(44)(45). Specifically, chromosomal translocation involving the 1q25 locus, which contains GAS5, has been identified in melanoma (42).…”

Long non-coding RNAs drive metastatic progression in melanoma (Review)

“…flockhart et al set out with just this goal in mind as outlined in their recent article, which describes the use of rna-seq on primary human melanocytes transduced with lentivirus expressing either braf v600e or red fluorescent protein control in order to specifically identify differentially expressed lncrnas (69). this approach represents an important shift away from other studies, which have generally focused on lncrnas that are differentially expressed in cancer, without first addressing the cause of the observed differential expression and whether it is driven by oncogenic events or an artefact of tumour heterogeneity and genomic instability.…”

“…finally, transcripts of interest were analysed using a previously described coding potential calculator (cPc) algorithm that discriminates coding from non-coding transcripts (71). this combinatorial approach identified a novel lncrna that is overexpressed in braf v600e -positive melanocytes and melanoma, which the authors termed BRAF-activated non-coding rna (BANCR) (69).…”

“…Gene expression profiling carried out on Colo829 braf v600e -depleted melanoma cells using a cDna microarray revealed that 88 genes were differentially expressed compared with control and significantly genes involved in cell motility were overrepresented among this number ( fig. 1D) (69). in order to gain some functional insight into how BANCR might be regulating cell migration, targets that displayed altered gene expression in BANCR-depleted cells and are associated with cell motility were investigated further.…”