RMEL3, a novel BRAF V600E -associated long noncoding RNA, is required for MAPK and PI3K signaling in melanoma

// Lucas Goedert 1, 2, * , Cristiano G. Pereira 1, * , Jason Roszik 3, * , Jessica R. Placa 2, 4 , Cibele Cardoso 1 , Guo Chen 3 , Wanleng Deng 3 , Vashisht Gopal Yennu-Nanda 3 , Wilson A. Silva Jr. 2, 5 , Michael A. Davies 4 , Enilza M. Espreafico 1 1 Department of Celland Molecular Biology, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil 2 National Institute of Science and Technology in Stem Cell and Cell Therapy and Center for Cell-Based Therapy, Ribeirao Preto, Sao Paulo, Brazil 3 Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America 4 Clinical Oncology, Stem Cell and Cell Therapy Program, Ribeirao Preto Medical School, Ribeirao Preto, Sao Paulo, Brazil 5 Department of Genetics, Ribeirao Preto Medical School, and Center for Integrative System Biology (CISBi-NAP/USP), University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil * These authors have contributed equally to this work Correspondence to: Enilza M. Espreafico, e-mail: emesprea@fmrp.usp.br Keywords: lncRNA, ncRNA, TCGA, ENSG00000250961, ENST00000506106.1 Received: August 28, 2015     Accepted: April 16, 2016     Published: May 4, 2016 ABSTRACT Previous work identified RMEL3 as a lncRNA with enriched expression in melanoma. Analysis of The Cancer Genome Atlas (TCGA) data confirmed RMEL3 enriched expression in melanoma and demonstrated its association with the presence of BRAF V600E. RMEL3 siRNA-mediated silencing markedly reduced (95%) colony formation in different BRAF V600Emelanoma cell lines. Multiple genes of the MAPK and PI3K pathways found to be correlated with RMEL3 in TCGA samples were experimentally confirmed. RMEL3 knockdown led to downregulation of activators or effectors of these pathways, including FGF2, FGF3, DUSP6, ITGB3 and GNG2. RMEL3 knockdown induces gain of protein levels of tumor suppressor PTEN and the G1/S cyclin- Cdk inhibitorsp21 and p27, as well as a decrease of pAKT (T308), BRAF, pRB (S807, S811) and cyclin B1. Consistently, knockdown resulted in an accumulation of cells in G1 phase and subG0/G1 in an asynchronously growing population. Thus, TCGA data and functional experiments demonstrate that RMEL3 is required for MAPK and PI3K signaling, and its knockdown decrease BRAF V600Emelanoma cell survival and proliferation.