A novel lncRNA derived from an ultraconserved region: lnc-uc.147, a potential biomarker in luminal A breast cancer.

The human genome contains 481 ultraconserved regions (UCRs), which are genomic stretches of over 200 base pairs conserved among human, rat, and mouse. The majority of these regions are transcriptionally active (T-UCRs), and several have been found to be differentially expressed in tumours. Some T-UCRs have been functionally characterized, but of those few have been associated to breast cancer (BC). Using TCGA data, we found 302 T-UCRs related to clinical features in BC: 43% were associated with molecular subtypes, 36% with oestrogen-receptor positivity, 17% with HER2 expression, 12% with stage, and 10% with overall survival. The expression levels of 12 T-UCRs were further analysed in a cohort of 82 Brazilian BC patients using RT-qPCR. We found that uc.147 is high expressed in luminal A and B patients. For luminal A, a subtype usually associated with better prognosis, high uc.147 expression was associated with a poor prognosis and suggested as an independent prognostic factor. The lncRNA from uc.147 (lnc-uc.147) is located in the nucleus. Northern blotting results show that uc.147 is a 2,8 kb monoexonic trancript, and its sequence was confirmed by RACE. The silencing of uc.147 increases apoptosis, arrests cell cycle, and reduces cell viability and colony formation in BC cell lines. Additionally, we identifed 19 proteins that interact with lnc-uc.147 through mass spectrometry and demonstrated a high correlation of lnc-uc.147 with the neighbour gene expression and miR-18 and miR-190b. This is the first study to analyse the expression of all T-UCRs in BC and to functionally assess the lnc-uc.147.

Highlighting transcribed ultraconserved regions in human diseases.

Ultraconserved regions (UCRs) are 481 DNA segments longer than 200 bp in length that are completely conserved among human, mouse, and rat and, extremely conserved across disparate taxa. More than 90% of UCRs are transcribed (T-UCRs) in normal tissues, but most of them remain uncharacterized. In addition, it was demonstrated that T-UCRs have a tissue-specific expression, and a differential expression profile between tumors and other diseases, which suggests that most of T-UCRs may have an important role in cell processes. However, there is little information about T-UCR characterization or about their molecular mechanisms of action. Taking this into account, in this study, we aim to summarize deregulated T-UCRs in human diseases, emphasizing the ones with stronger functional evidences that are associated with important cell pathways and have a detailed molecular characterization. This article is characterized under: RNA in Disease and Development > RNA in Disease Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.