BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration
BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration
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DOI：
10.1101/gr.140061.112
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发表时间：
2012-06-01
期刊：
影响因子：
7
通讯作者：
Khavari, Paul A.
中科院分区：
文献类型：
--
作者：
Flockhart, Ross J.;Webster, Dan E.;Khavari, Paul A.
蛋白质编码基因的异常是癌症基因组学研究的热点，然而，近50%的无蛋白质编码能力的转录本，包括长非编码RNA(IncRNAs)，癌基因对其表达的影响在很大程度上还不清楚。BRAF癌基因的激活突变存在于70%的黑色素瘤中，其中90%会产生活性突变的BRAF(V600E)蛋白。为了确定致癌基因BRAF(V600E)对黑素细胞转录组的影响，我们对表达BRAF(V600E)和表达BRAF(V600E)的基因匹配的正常人黑素细胞进行了大规模平行cDNA测序(RNA-SEQ)。为了通过验证改变的基因在BRAF驱动的癌症组织中的表达来增强潜在的疾病相关性，还对两个BRAF(V600E)突变的人类黑色素瘤进行了平行的RNA-SEQ。BRAF(V600E)调控IO27蛋白编码转录本和39个带注释的IncRNAs以及70个未注释的、潜在的新的基因间转录本的表达。这些转录本显示组织特异性和多组织表达谱，并含有独特的调控染色质标记和转录因子结合位点，表明活跃的转录。对70个未注释转录本的编码潜力分析表明，大多数转录本可能代表新发现的IncRNAs。BRAF调节的IncRNA1(BANCR)是位于9号染色体上的一个重复过表达的693个碱基的转录本，在黑色素瘤细胞的迁移中具有潜在的功能。BANCR基因敲除减少了黑色素瘤细胞的迁移，这可以被趋化因子CXCLII拯救。将表达癌基因的正常细胞的RNA-seq与相应的人类癌症的RNA-seq相结合，可能是发现新的癌基因调控的具有潜在临床意义的RNA转录本的有用途径。
Aberrations of protein-coding genes are a focus of cancer genomics; however, the impact of oncogenes on expression of the similar to 50% of transcripts without protein-coding potential, including long noncoding RNAs (IncRNAs), 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 IO27 protein-coding transcripts and 39 annotated IncRNAs, 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 IncRNAs. BRAF-regulated IncRNA 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 CXCLII. 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.