The long non-coding RNA<i>HOTAIR</i>is transcriptionally activated by HOXA9 and is an independent prognostic marker in patients with malignant glioma

Abstract

The lncRNA <i>HOTAIR</i> has been implicated in several human cancers. Here, we evaluated the molecular alterations and upstream regulatory mechanisms of <i>HOTAIR</i> in glioma, the most common primary brain tumors, and its clinical relevance. <i>HOTAIR</i> gene expression, methylation, copy-number and prognostic value were investigated in human gliomas integrating data from online datasets and our cohorts. High levels of <i>HOTAIR</i> were associated with higher grades of glioma, particularly IDH wild-type cases. Mechanistically, <i>HOTAIR</i> was overexpressed in a gene dosage-independent manner, while DNA methylation levels of particular CpGs in <i>HOTAIR</i> locus were associated with <i>HOTAIR</i> expression levels in GBM clinical specimens and cell lines. Concordantly, the demethylating agent 5-Aza-2'-deoxycytidine affected <i>HOTAIR</i> transcriptional levels in a cell line-dependent manner. Importantly, <i>HOTAIR</i> was frequently co-expressed with <i>HOXA9</i> in high-grade gliomas from TCGA, Oncomine, and our Portuguese and French datasets. Integrated <i>in silico</i> analyses, chromatin immunoprecipitation, and qPCR data showed that HOXA9 binds directly to the promoter of <i>HOTAIR</i>. Clinically, GBM patients with high <i>HOTAIR</i> expression had a significantly reduced overall survival, independently of other prognostic variables. In summary, this work reveals <i>HOXA9</i> as a novel direct regulator of <i>HOTAIR</i>, and establishes <i>HOTAIR</i> as an independent prognostic marker, providing new therapeutic opportunities to treat this highly aggressive cancer.