Life, Death, and Function: The Primate-Specific Long Non-Coding RNA Transcriptome

生命、死亡和功能：灵长类动物特异性长非编码 RNA 转录组

• 批准号: 8754784
• 负责人: Leonard Lipovich
• 金额: $ 230.2万
• 依托单位: WAYNE STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-26 至 2019-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8754784
• 关键词: Accounting; Achievement; Apoptosis; Biological; Biological Assay; Cancer Biology; Cataloging; Catalogs; Cell Death; Cell Proliferation; Cell Survival; Cell physiology; Cells; Cellular biology; Cessation of life; Code; Custom; DNA; Data; Disease; Elements; Encyclopedia of DNA Elements; Estrogen Receptor alpha; Estrogens; Evolution; Functional RNA; Gene Expression; Gene Expression Profile; Generations; Genes; Genome; Genomics; Health; Human; Human Genome; Human Genome Project; Left; Life; MCF7 cell; Malignant Neoplasms; Messenger RNA; MicroRNAs; Mutation; Normal Cell; Nuclear Hormone Receptors; Organism; Pathogenesis; Pathway interactions; Peptides; Primates; Property; Proteins; RNA; RNA Interference; Regulator Genes; Rest; Role; System; Testing; Therapeutic; Translating; Translations; Work; cell growth; clinically relevant; fascinate; functional outcomes; genome sequencing; human disease; in vitro Model; interest; malignant breast neoplasm; novel; overexpression; public health relevance; response; therapeutic target

DESCRIPTION (provided by applicant): The completion of the Human Genome Project left an enduring mystery: Why do protein-coding genes account for only a tiny fraction of the genome sequence? What functional elements reside in the rest of the genome? Nearly a decade later, in 2012, the ENCODE (Encyclopedia of DNA Elements) Consortium, in which I participate, revealed the extraordinary abundance of long non-coding RNA (lncRNA) genes in the human genome (Derrien et al 2012). This achievement builds, in part, on my prior work (Jia et al 2010). In contrast to microRNAs, lncRNAs act through diverse and heterogeneous mechanisms, as both positive and negative regulators of gene expression. Among the properties of lncRNAs, their low interspecies conservation is particularly intriguing: nearly 5,000 human lncRNAs are not conserved beyond primates. This is interesting and important because, traditionally, protein-coding genes conserved in evolution were thought to be responsible for most functional outcomes in normal cellular processes and in disease. However, evolutionary lineage-specific biological and pathological responses and mechanisms are increasingly clear. Do non-conserved lncRNAs have lineage- and species-specific functions in human disease? To investigate this, I will examine the functions of evolutionarily non-conserved human lncRNAs in a biologically and clinically relevant system: human MCF7 cells, an established in-vitro model of estrogen receptor alpha positive breast cancer. To generate preliminary data, I utilized my custom human lncRNA microarray (Lipovich et al 2012) to interrogate lncRNAs for estrogen responsiveness in MCF7 cells. I identified 127 estrogen-responsive lncRNAs, analyzing 18 by RNAi and overexpression, followed by a panel of six phenotypic assays. Knockdown of estrogen- induced, and overexpression of estrogen-repressed, primate-specific lncRNAs reduced cell viability and proliferation, and in several cases caused cell death. This finding prompted my central hypothesis: certain primate-specific lncRNAs shift human cells along the apoptosis-proliferation axis. In this project, I will pursue this hypothesis and expand upon it. I ill extend the six functional assays to all 127 leads. I will employ second- and third-generation RNAseq, instead of microarrays, to impute the complete MCF7 estrogen- responsive lncRNAome. I will identify novel primate-specific lncRNAs from RNAseq data and subject them to my optimized workflow of system perturbations and phenotypic assays. Having shown ectopic translation of some lncRNAs within the framework of the ENCODE Consortium (B¿nfai et al 2012), I will also test whether primate-specific functional lncRNAs act directly as RNAs, not via translated peptides. The results will approach a fascinating new question with the potential to initiate a paradigm shift in cancer biology: Is human cancer, to an extent, a primate-specific disease caused by non-conserved lncRNAs? Implementation of this proposal will result in the first ever conservation-unbiased, high-throughput assignment of cellular functions to primate-specific lncRNAs in a major nuclear hormone receptor pathway that is highly relevant to cancer therapeutics.

描述(申请人提供)：人类基因组计划的完成留下了一个永恒的谜团：为什么蛋白质编码基因只占基因组序列的一小部分？基因组的其余部分有哪些功能元件？近十年后的2012年，我参加的ENCODE(DNA元素百科全书)联盟揭示了人类基因组中异常丰富的长非编码RNA(LncRNA)基因(Derrien等人，2012)。这一成就在一定程度上建立在我之前的工作基础上(贾跃亭等人，2010年)。与microRNAs不同，lncRNAs通过不同和不同的机制发挥作用，既是基因表达的正性调节因子，也是负性调节因子。在lncRNA的特性中，它们的低种间保守性特别耐人寻味：近5000 人类的IncRNA在灵长类以外并不保守。这很有趣，也很重要，因为在传统上，进化过程中保守的蛋白质编码基因被认为是正常细胞过程和疾病中大多数功能结果的原因。然而，进化谱系特异性的生物和病理反应和机制日益明确。非保守的lncRNA在人类疾病中是否具有谱系和物种特异性的功能？为了研究这一点，我将研究进化上非保守的人类lncRNAs在一个生物学和临床相关的系统中的功能：人类MCF7细胞，一个已建立的雌激素受体α阳性乳腺癌的体外模型。为了生成初步数据，我利用我定制的人类LncRNA微阵列(Lipovich等人，2012)询问LncRNA在MCF7细胞中的雌激素反应性。我确定了127个对雌激素有反应的LncRNAs，通过RNAi和过度表达分析了18个，然后进行了六种表型分析。雌激素诱导的抑制和雌激素抑制的灵长类特异的lncRNAs的过度表达降低了细胞的活力和增殖，并在一些情况下导致细胞死亡。这一发现引发了我的中心假设：某些灵长类特有的lncRNAs使人类细胞沿着凋亡-增殖轴移动。在这个项目中，我将继续探讨这一假设，并对其进行扩展。我会将六种功能分析扩展到所有127个导联。我将使用第二代和第三代RNAseq，而不是微阵列，来计算完整的MCF7雌激素反应LncRNAome。我将从RNAseq数据中识别新的灵长类特有的lncRNAs，并将它们置于我的系统扰动和表型分析的优化工作流程中。在展示了ENCODE联盟框架内一些lncRNAs的异位翻译后(Bénfai等人，2012)，我还将测试灵长类特有的功能性lncRNAs是否直接作为RNA起作用，而不是 通过翻译的多肽。这一结果将探讨一个有趣的新问题，有可能引发癌症生物学的范式转变：在某种程度上，人类癌症是由非保守的lncRNA引起的灵长类特有疾病吗？这一提议的实施将导致有史以来第一次无偏见地、高通量地将细胞功能分配给与癌症治疗高度相关的主要核激素受体途径中的灵长类动物特有的lncRNA。

项目成果

Unintended target effect of anti-BCL-2 DNAi.

抗 BCL-2 DNAi 的意外靶点效应。

• DOI: 10.2147/cmar.s139105
• 发表时间: 2017
• 期刊: Cancer management and research
• 影响因子: 3.3
• 作者: Ebrahim,AbdulShukkur;Kandouz,Mustapha;Emara,Nada;Sugalski,AmaraB;Lipovich,Leonard;Al-Katib,AyadM
• 通讯作者: Al-Katib,AyadM

Pangolin genomes and the evolution of mammalian scales and immunity.

穿山甲基因组与哺乳动物鳞片和免疫的进化

• DOI: 10.1101/gr.203521.115
• 发表时间: 2016-10
• 期刊: Genome research
• 影响因子: 7
• 作者: Choo SW;Rayko M;Tan TK;Hari R;Komissarov A;Wee WY;Yurchenko AA;Kliver S;Tamazian G;Antunes A;Wilson RK;Warren WC;Koepfli KP;Minx P;Krasheninnikova K;Kotze A;Dalton DL;Vermaak E;Paterson IC;Dobrynin P;Sitam FT;Rovie-Ryan JJ;Johnson WE;Yusoff AM;Luo SJ;Karuppannan KV;Fang G;Zheng D;Gerstein MB;Lipovich L;O'Brien SJ;Wong GJ
• 通讯作者: Wong GJ

Primate-specific oestrogen-responsive long non-coding RNAs regulate proliferation and viability of human breast cancer cells.

• DOI: 10.1098/rsob.150262
• 发表时间: 2016-12
• 期刊: Open biology
• 影响因子: 5.8
• 作者: Lin CY;Kleinbrink EL;Dachet F;Cai J;Ju D;Goldstone A;Wood EJ;Liu K;Jia H;Goustin AS;Kosir MA;Thepsuwan P;Lipovich L
• 通讯作者: Lipovich L

Pseudogene-derived lncRNAs: emerging regulators of gene expression.

• DOI: 10.3389/fgene.2014.00476
• 发表时间: 2014
• 期刊: Frontiers in genetics
• 影响因子: 3.7
• 作者: Milligan MJ;Lipovich L
• 通讯作者: Lipovich L

The long non-coding RNA NEAT1 is responsive to neuronal activity and is associated with hyperexcitability states.

• DOI: 10.1038/srep40127
• 发表时间: 2017-01-05
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Barry G;Briggs JA;Hwang DW;Nayler SP;Fortuna PR;Jonkhout N;Dachet F;Maag JL;Mestdagh P;Singh EM;Avesson L;Kaczorowski DC;Ozturk E;Jones NC;Vetter I;Arriola-Martinez L;Hu J;Franco GR;Warn VM;Gong A;Dinger ME;Rigo F;Lipovich L;Morris MJ;O'Brien TJ;Lee DS;Loeb JA;Blackshaw S;Mattick JS;Wolvetang EJ
• 通讯作者: Wolvetang EJ