Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil.
Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA.
RNA Biol. 2021 Oct 15;18(sup1):416-429. doi: 10.1080/15476286.2021.1952757. Epub 2021 Aug 13.
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.
人类基因组包含 481 个超保守区域（UCRs），这些区域是人类、大鼠和小鼠之间超过 200 个碱基对的基因组片段保守。这些区域中的大多数是转录活跃的（T-UCRs），并且已经发现一些在肿瘤中存在差异表达。一些 T-UCRs 已经具有功能特征，但其中很少与乳腺癌（BC）相关。使用 TCGA 数据，我们在 BC 中发现了 302 个与临床特征相关的 T-UCR：43%与分子亚型相关，36%与雌激素受体阳性相关，17%与 HER2 表达相关，12%与分期相关，10%与总生存期相关。在 82 名巴西 BC 患者的队列中，使用 RT-qPCR 进一步分析了 12 个 T-UCR 的表达水平。我们发现 uc.147 在 luminal A 和 B 患者中高表达。对于 luminal A，一种通常与更好的预后相关的亚型，高 uc.147 表达与不良预后相关，并被认为是一个独立的预后因素。uc.147 的 lncRNA（lnc-uc.147）位于核内。Northern 印迹结果显示 uc.147 是一个 2.8 kb 的单外显子转录物，其序列通过 RACE 得到确认。uc.147 的沉默增加了 BC 细胞系的细胞凋亡，使细胞周期停滞，并降低了细胞活力和集落形成。此外，我们通过质谱鉴定了 19 种与 lnc-uc.147 相互作用的蛋白质，并证明 lnc-uc.147 与邻近基因的表达以及 miR-18 和 miR-190b 高度相关。这是第一项分析 BC 中所有 T-UCR 表达并对 lnc-uc.147 进行功能评估的研究。
