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Khan MM, Kirabo A. Long Noncoding RNA MALAT1: Salt-Sensitive Hypertension. Int J Mol Sci 2024; 25:5507. [PMID: 38791545 PMCID: PMC11122212 DOI: 10.3390/ijms25105507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/06/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Hypertension stands as the leading global cause of mortality, affecting one billion individuals and serving as a crucial risk indicator for cardiovascular morbidity and mortality. Elevated salt intake triggers inflammation and hypertension by activating antigen-presenting cells (APCs). We found that one of the primary reasons behind this pro-inflammatory response is the epithelial sodium channel (ENaC), responsible for transporting sodium ions into APCs and the activation of NADPH oxidase, leading to increased oxidative stress. Oxidative stress increases lipid peroxidation and the formation of pro-inflammatory isolevuglandins (IsoLG). Long noncoding RNAs (lncRNAs) play a crucial role in regulating gene expression, and MALAT1, broadly expressed across cell types, including blood vessels and inflammatory cells, is also associated with inflammation regulation. In hypertension, the decreased transcriptional activity of nuclear factor erythroid 2-related factor 2 (Nrf2 or Nfe2l2) correlates with heightened oxidative stress in APCs and impaired control of various antioxidant genes. Kelch-like ECH-associated protein 1 (Keap1), an intracellular inhibitor of Nrf2, exhibits elevated levels of hypertension. Sodium, through an increase in Sp1 transcription factor binding at its promoter, upregulates MALAT1 expression. Silencing MALAT1 inhibits sodium-induced Keap1 upregulation, facilitating the nuclear translocation of Nrf2 and subsequent antioxidant gene transcription. Thus, MALAT1, acting via the Keap1-Nrf2 pathway, modulates antioxidant defense in hypertension. This review explores the potential role of the lncRNA MALAT1 in controlling the Keap1-Nrf2-antioxidant defense pathway in salt-induced hypertension. The inhibition of MALAT1 holds therapeutic potential for the progression of salt-induced hypertension and cardiovascular disease (CVD).
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Affiliation(s)
- Mohd Mabood Khan
- Department of Medicine, Preston Research Building, Vanderbilt University Medical Centre, Nashville, TN 37232, USA
| | - Annet Kirabo
- Department of Medicine, Preston Research Building, Vanderbilt University Medical Centre, Nashville, TN 37232, USA
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Blood-derived lncRNAs as biomarkers for cancer diagnosis: the Good, the Bad and the Beauty. NPJ Precis Oncol 2022; 6:40. [PMID: 35729321 PMCID: PMC9213432 DOI: 10.1038/s41698-022-00283-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/13/2022] [Indexed: 11/24/2022] Open
Abstract
Cancer ranks as one of the deadliest diseases worldwide. The high mortality rate associated with cancer is partially due to the lack of reliable early detection methods and/or inaccurate diagnostic tools such as certain protein biomarkers. Cell-free nucleic acids (cfNA) such as circulating long noncoding RNAs (lncRNAs) have been proposed as a new class of potential biomarkers for cancer diagnosis. The reported correlation between the presence of tumors and abnormal levels of lncRNAs in the blood of cancer patients has notably triggered a worldwide interest among clinicians and oncologists who have been actively investigating their potentials as reliable cancer biomarkers. In this report, we review the progress achieved (“the Good”) and challenges encountered (“the Bad”) in the development of circulating lncRNAs as potential biomarkers for early cancer diagnosis. We report and discuss the diagnostic performance of more than 50 different circulating lncRNAs and emphasize their numerous potential clinical applications (“the Beauty”) including therapeutic targets and agents, on top of diagnostic and prognostic capabilities. This review also summarizes the best methods of investigation and provides useful guidelines for clinicians and scientists who desire conducting their own clinical studies on circulating lncRNAs in cancer patients via RT-qPCR or Next Generation Sequencing (NGS).
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Matboli M, Hasanin AH, Hussein R, El-Nakeep S, Habib EK, Ellackany R, Saleh LA. Cyanidin 3-glucoside modulated cell cycle progression in liver precancerous lesion, in vivo study. World J Gastroenterol 2021; 27:1435-1450. [PMID: 33911466 PMCID: PMC8047539 DOI: 10.3748/wjg.v27.i14.1435] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/22/2021] [Accepted: 03/26/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cyanidin-3-O-glucoside (cyan) exhibits antioxidant and anticancer properties. The cell cycle proteins and antimitotic drugs might be promising therapeutic targets in hepatocellular carcinoma.
AIM To investigate the effect of cyan administration on cell cycle in hepatic precancerous lesion (PCL) induced by diethylnitrosamine/2-acetylaminofluorene (DEN/2-AAF) in Wistar rats.
METHODS In vivo, DEN/2-AAF-induced hepatic PCL, rats were treated with three doses of cyan (10, 15, and 20 mg/kg/d, for four consecutive days per week for 16 wk). Blood and liver tissue samples were collected for measurement of the followings; alpha fetoprotein (AFP) liver function and RNA panel differential expression was evaluated via real time polymerase chain reaction. Histopathological examination of liver sections stained with H&E and immunohistochemical study using glutathione S-transferase placental (GSTP) and proliferating cell nuclear antigen (PCNA) antibodies were assessed.
RESULTS Cyan administration mitigated the effect of DEN/2-AFF induced PCL, decreased AFP levels, and improved liver function. Remarkably, treatment with cyan dose dependently decreased the long non-coding RNA MALAT1 and tubulin gamma 1 mRNA expressions and increased the levels of miR-125b, all of which are involved in cell cycle and mitotic spindle assembly. Of note, cyan decreased GSTP foci percent area and PCNA positively stained nuclei.
CONCLUSION Our results indicated that cyan could be used as a potential therapeutic agent to inhibit liver carcinogenesis in rat model via modulation of cell cycle.
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Affiliation(s)
- Marwa Matboli
- Department of Biochemistry, Ain Shams Faculty of Medicine, Cairo 11318, Egypt
| | - Amany H Hasanin
- Department of Clinical Pharmacology, Ain Shams Faculty of Medicine, Cairo 11381, Egypt
| | - Reham Hussein
- Department of Clinical Pharmacology, Ain Shams Faculty of Medicine, Cairo 11381, Egypt
| | - Sarah El-Nakeep
- Department of General Internal Medicine, Ain Shams Faculty of Medicine, Cairo 11381, Egypt
| | - Eman K Habib
- Department of Anatomy & Embryology, Ain Shams Faculty of Medicine, Cairo 11318, Egypt
| | - Rawan Ellackany
- Department of Undergraduate, Faculty of Medicine, Modern University for Technology and Information, Cairo 11381, Egypt
| | - Lobna A Saleh
- Department of Clinical Pharmacology, Ain Shams Faculty of Medicine, Cairo 11381, Egypt
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Epigenetic Targets for Oligonucleotide Therapies of Pulmonary Arterial Hypertension. Int J Mol Sci 2020; 21:ijms21239222. [PMID: 33287230 PMCID: PMC7731052 DOI: 10.3390/ijms21239222] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 01/13/2023] Open
Abstract
Arterial wall remodeling underlies increased pulmonary vascular resistance and right heart failure in pulmonary arterial hypertension (PAH). None of the established vasodilator drug therapies for PAH prevents or reverse established arterial wall thickening, stiffening, and hypercontractility. Therefore, new approaches are needed to achieve long-acting prevention and reversal of occlusive pulmonary vascular remodeling. Several promising new drug classes are emerging from a better understanding of pulmonary vascular gene expression programs. In this review, potential epigenetic targets for small molecules and oligonucleotides will be described. Most are in preclinical studies aimed at modifying the growth of vascular wall cells in vitro or normalizing vascular remodeling in PAH animal models. Initial success with lung-directed delivery of oligonucleotides targeting microRNAs suggests other epigenetic mechanisms might also be suitable drug targets. Those targets include DNA methylation, proteins of the chromatin remodeling machinery, and long noncoding RNAs, all of which act as epigenetic regulators of vascular wall structure and function. The progress in testing small molecules and oligonucleotide-based drugs in PAH models is summarized.
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Kohata K, Miyoshi D. RNA phase separation-mediated direction of molecular trafficking under conditions of molecular crowding. Biophys Rev 2020; 12:669-676. [PMID: 32415614 DOI: 10.1007/s12551-020-00696-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/28/2020] [Indexed: 12/14/2022] Open
Abstract
Living cells are highly crowded with large and small biomolecules. The total concentration of biomolecules can reach 400 mg/ml, and 40% of the cell volume is occupied by biomolecules. Droplet formation in cells via liquid-liquid phase separation may play a role in controlling biochemical reactions in this complex molecular environment. Liquid-liquid phase separation generally involves nucleic acids and proteins as anionic and cationic components, respectively. Significant characteristics of droplets, which make them different from protein aggregation or fibril formation, are reversibility of formation and responsiveness to the molecular environment. In this review, we quantitatively describe the molecular environment inside cells and droplets that participate in controlling central dogma reactions. Finally, we discuss the importance of droplets under conditions of molecular crowding within living cells.
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Affiliation(s)
- Kazuki Kohata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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Shang R, Wang M, Dai B, Du J, Wang J, Liu Z, Qu S, Yang X, Liu J, Xia C, Wang L, Wang D, Li Y. Long noncoding RNA SLC2A1-AS1 regulates aerobic glycolysis and progression in hepatocellular carcinoma via inhibiting the STAT3/FOXM1/GLUT1 pathway. Mol Oncol 2020; 14:1381-1396. [PMID: 32174012 PMCID: PMC7266282 DOI: 10.1002/1878-0261.12666] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/02/2020] [Accepted: 03/12/2020] [Indexed: 12/15/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal malignant diseases worldwide. Despite advances in the diagnosis and treatment of HCC, its overall prognosis remains poor. Recent studies have shown that long noncoding RNAs (lncRNAs) play crucial roles in various pathophysiological processes, including liver cancer. In the current study, we report that lncRNA SLC2A1-AS1 is frequently downregulated in HCC samples, as shown by quantitative real-time polymerase chain reaction analysis. SLC2A1-AS1 deletion is significantly associated with recurrence-free survival in HCC. By performing glucose uptake, lactate production and ATP detection assays, we found that SLC2A1-AS1-mediated glucose transporter 1 (GLUT1) downregulation significantly suppressed glycolysis of HCC. In vitro Cell Counting Kit-8, colony formation, transwell assays as well as in vivo tumorigenesis and metastasis assays showed that SLC2A1-AS1 overexpression significantly suppressed proliferation and metastasis in HCC through the transcriptional inhibition of GLUT1. Results from fluorescence in situ hybridization, ChIP and luciferase reporter assays demonstrated that SLC2A1-AS1 exerts its regulatory role on GLUT1 by competitively binding to transketolase and signal transducer and activator of transcription 3 (STAT3) and inhibits the transactivation of Forkhead box M1 (FOXM1) via STAT3, thus resulting in inactivation of the FOXM1/GLUT1 axis in HCC cells. Our findings will be helpful for understanding the function and mechanism of lncRNA in HCC. These data also highlight the crucial role of SLC2A1-AS1 in HCC aerobic glycolysis and progression and pave the way for further research regarding the potential of SLC2A1-AS1 as a valuable predictive biomarker for HCC recurrence.
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Affiliation(s)
- Runze Shang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Miao Wang
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Bin Dai
- Department of General Surgery, General Hospital of the Central Theater Command of the People's Liberation Army, Wuhan, China
| | - Jianbing Du
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Jianlin Wang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Zekun Liu
- State Key Laboratory of Cancer Biology, Cell Engineering Research Center & Department of Cell Biology, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Shibin Qu
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Xisheng Yang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Jingjing Liu
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Congcong Xia
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Lin Wang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Desheng Wang
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University (Air Force Medical University), Xi'an, China
| | - Yu Li
- School of Life Science, Northwestern Polytechnical University, Xi'an, China
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MALAT1: a therapeutic candidate for a broad spectrum of vascular and cardiorenal complications. Hypertens Res 2019; 43:372-379. [PMID: 31853043 DOI: 10.1038/s41440-019-0378-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 01/26/2023]
Abstract
Cardiovascular and renal complications cover a wide array of diseases. The most commonly known overlapping complications include cardiac and renal fibrosis, cardiomyopathy, cardiac hypertrophy, hypertension, and cardiorenal failure. The known or reported causes for the abovementioned complications include injury, ischemia, infection, and metabolic stress. To date, various targets have been reported and investigated in detail that are considered to be the cause of these complications. In the past 5 years, the role of noncoding RNAs has emerged in the area of cardiovascular and renal research, especially in relation to metabolic stress. The long noncoding RNA MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) has shown immense promise among the long noncoding RNA targets for treating cardiorenal complications. In this review, we shed light on the role of MALAT1 as a primary and novel target in treating cardiovascular and renal diseases as a whole.
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Wheway G, Lord J, Baralle D. Splicing in the pathogenesis, diagnosis and treatment of ciliopathies. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194433. [PMID: 31698098 DOI: 10.1016/j.bbagrm.2019.194433] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/12/2019] [Accepted: 09/17/2019] [Indexed: 12/12/2022]
Abstract
Primary cilia are essential signalling organelles found on the apical surface of epithelial cells, where they coordinate chemosensation, mechanosensation and light sensation. Motile cilia play a central role in establishing fluid flow in the respiratory tract, reproductive tract, brain ventricles and ear. Genetic defects affecting the structure or function of cilia can lead to a broad range of developmental and degenerative diseases known as ciliopathies. Splicing contributes to the pathogenesis, diagnosis and treatment of ciliopathies. Tissue-specific alternative splicing contributes to the tissue-specific manifestation of ciliopathy phenotypes, for example the retinal-specific effects of some genetic defects, due to specific transcript expression in the highly specialised ciliated cells of the retina, the photoreceptor cells. Ciliopathies can arise both as a result of genetic variants in spliceosomal proteins, or as a result of variants affecting splicing of specific cilia genes. Here we discuss the opportunities and challenges in diagnosing ciliopathies using RNA sequence analysis and the potential for treating ciliopathies in a relatively mutation-neutral way by targeting splicing. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Human Development and Health, United Kingdom of Great Britain and Northern Ireland; University Hospital Southampton NHS Foundation Trust, United Kingdom of Great Britain and Northern Ireland
| | - Jenny Lord
- Faculty of Medicine, University of Southampton, Human Development and Health, United Kingdom of Great Britain and Northern Ireland; University Hospital Southampton NHS Foundation Trust, United Kingdom of Great Britain and Northern Ireland
| | - Diana Baralle
- Faculty of Medicine, University of Southampton, Human Development and Health, United Kingdom of Great Britain and Northern Ireland; University Hospital Southampton NHS Foundation Trust, United Kingdom of Great Britain and Northern Ireland.
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9
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Li X, Chen N, Zhou L, Wang C, Wen X, Jia L, Cui J, Hoffman AR, Hu JF, Li W. Genome-wide target interactome profiling reveals a novel EEF1A1 epigenetic pathway for oncogenic lncRNA MALAT1 in breast cancer. Am J Cancer Res 2019; 9:714-729. [PMID: 31105998 PMCID: PMC6511647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023] Open
Abstract
Breast cancer is the most common cancer in women worldwide, accounting for approximately 500,000 deaths each year. MALAT1 is a highly conserved long noncoding RNA (lncRNA), and its increased expression is associated with relapse and metastatic progression in breast cancer. We performed RNA reverse transcription-associated trap sequencing (RAT-seq) to characterize the genome-wide target interaction network for MALAT1 and showed that MALAT1 interacted with multiple pathway target genes that are closely related to tumor progression and metastasis. Notably, MALAT1 bound to the promoter regulatory element of the translation elongation factor 1-alpha 1 gene EEF1A1. Knockdown of MALAT1 by shRNA caused significant downregulation of EEF1A1 in breast cancer MDA-MB231 and SKRB3 cells. Using a luciferase reporter assay, we showed that knockdown of MALAT1 reduced the promoter activity of EEF1A1 in these two breast cancer cells. Chromatin immunoprecipitation (ChIP) assay indicated that MALAT1 regulated EEF1A1 by altering the histone 3 lysine 4 (H3K4) epigenotype in the gene promoter. MALAT1 was overexpressed in breast cancer tissues and breast cancer cells. Knockdown of MALAT1 reduced cell proliferation and invasion by arresting cells at the G0/G1 phase. Ectopic overexpression of EEF1A1 reversed the altered tumor phenotypes induced by MALAT1 shRNA treatment. These data suggest an epigenetic mechanism by which MALAT1 lncRNA facilitates a pro-metastatic phenotype in breast cancer by trans-regulating EEF1A1.
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Affiliation(s)
- Xueli Li
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
| | - Naifei Chen
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
| | - Lei Zhou
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
- Stanford University Medical School, Palo Alto Veterans Institute for ResearchPalo Alto, CA 94304, USA
| | - Cong Wang
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
| | - Xue Wen
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
| | - Lin Jia
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
- Stanford University Medical School, Palo Alto Veterans Institute for ResearchPalo Alto, CA 94304, USA
| | - Jiuwei Cui
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
| | - Andrew R Hoffman
- Stanford University Medical School, Palo Alto Veterans Institute for ResearchPalo Alto, CA 94304, USA
| | - Ji-Fan Hu
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
- Stanford University Medical School, Palo Alto Veterans Institute for ResearchPalo Alto, CA 94304, USA
| | - Wei Li
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
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Wang Y, Zhang X, Wang Z, Hu Q, Wu J, Li Y, Ren X, Wu T, Tao X, Chen X, Li X, Xia J, Cheng B. LncRNA-p23154 promotes the invasion-metastasis potential of oral squamous cell carcinoma by regulating Glut1-mediated glycolysis. Cancer Lett 2018; 434:172-183. [PMID: 30026052 DOI: 10.1016/j.canlet.2018.07.016] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 02/09/2023]
Abstract
The dysregulation of glycolysis has been suggested to lead to alteration of cell drug resistance signals, proliferation and metastasis. Emerging evidence indicates that lncRNAs play a key role in the cellular processes of tumor cells, including glycolysis, growth, and movement. However, the role and potential mechanism of lncRNAs in glycolysis-mediated metastasis has not been explored. In this study, we identified a novel lncRNA lnc-p23154 which is associated with OSCC patient metastasis and the promotion of OSCC cell migration and invasion in vitro and in vivo. Furthermore, we found that lnc-p23154 also participates in OSCC glycolysis by facilitating Glut1 expression. Rescue of lnc-p23154 reversed the suppression of OSCC cell migration and invasion induced by Glut1 knockdown. In addition, lnc-p23154 is mainly located in the nucleus and binds to the promoter region of miR-378a-3p, which represses Glut1 expression by targeting to its 3'UTR directly. Therefore, we concluded that lnc-p23154 may play an important role in Glut1-mediated glycolysis by inhibiting miR-378a-3p transcription and accelerate OSCC metastasis.
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Affiliation(s)
- Yun Wang
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaojie Zhang
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhi Wang
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qinchao Hu
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jie Wu
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuanyuan Li
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xianyue Ren
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tong Wu
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoan Tao
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaobing Chen
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaoxu Li
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Juan Xia
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Bin Cheng
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China.
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Zhao M, Wang S, Li Q, Ji Q, Guo P, Liu X. MALAT1: A long non-coding RNA highly associated with human cancers. Oncol Lett 2018; 16:19-26. [PMID: 29928382 PMCID: PMC6006327 DOI: 10.3892/ol.2018.8613] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 03/21/2017] [Indexed: 12/18/2022] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a well-known lncRNA associated with numerous diseases, particularly cancer, has received increased attention. The expression of MALAT1 was determined to be upregulated in numerous types of tumors and MALAT1 exhibited effects on tumor cell proliferation, migration, invasion and apoptosis. The abnormal expression of MALAT1 was identified in almost in every organ of the digestive system. MALAT1 performed an important role in the pathological alterations of organs that are associated with sex hormones and several reproductive system cancers. MALAT1 participates in molecular pathways. In the clinical application of MALAT1, MALAT1 was considered as a potential biomarker for the diagnosis and prediction of cancers, and may also serve as therapeutic target for treatment of specific tumors. This review summarizes the abnormal expression of MALAT1 in cancer, its significant effect on the primary features of cancer, as well as the underlying molecular mechanisms of MALAT1 in various cancers. According to studies on MALAT1, we introduce the upstream and downstream substances associated with the function of MALAT1. These reviewed studies promote the clinical application of MALAT1 in the aspect of diagnosis and treatment of different cancers, and may help point out new study directions for MALAT1.
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Affiliation(s)
- Miaomiao Zhao
- Department of Traditional Chinese Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China.,Department of Oncology, Zhengzhou Traditional Chinese Medicine Hospital, Zhengzhou 450007, P.R. China
| | - Songpo Wang
- Department of Traditional Chinese Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Qi Li
- Department of Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, P.R. China
| | - Qing Ji
- Department of Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, P.R. China
| | - Piaoting Guo
- Department of Traditional Chinese Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
| | - Xiaowei Liu
- Department of Traditional Chinese Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, P.R. China
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Vieweger M, Nesbitt DJ. Synergistic SHAPE/Single-Molecule Deconvolution of RNA Conformation under Physiological Conditions. Biophys J 2018; 114:1762-1775. [PMID: 29694857 PMCID: PMC5937115 DOI: 10.1016/j.bpj.2018.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/06/2018] [Accepted: 02/20/2018] [Indexed: 11/24/2022] Open
Abstract
Structural RNA domains are widely involved in the regulation of biological functions, such as gene expression, gene modification, and gene repair. Activity of these dynamic regions depends sensitively on the global fold of the RNA, in particular, on the binding affinity of individual conformations to effector molecules in solution. Consequently, both the 1) structure and 2) conformational dynamics of noncoding RNAs prove to be essential in understanding the coupling that results in biological function. Toward this end, we recently reported observation of three conformational states in the metal-induced folding pathway of the tRNA-like structure domain of Brome Mosaic Virus, via single-molecule fluorescence resonance energy transfer studies. We report herein selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE)-directed structure predictions as a function of metal ion concentrations ([Mn+]) to confirm the three-state folding model, as well as test 2° structure models from the literature. Specifically, SHAPE reactivity data mapped onto literature models agrees well with the secondary structures observed at 0-10 mM [Mg2+], with only minor discrepancies in the E hairpin domain at low [Mg2+]. SHAPE probing and SHAPE-directed structure predictions further confirm the stepwise unfolding pathway previously observed in our single-molecule studies. Of special relevance, this means that reduction in the metal-ion concentration unfolds the 3' pseudoknot interaction before unfolding the long-range stem interaction. This work highlights the synergistic power of combining 1) single-molecule Förster resonance energy transfer and 2) SHAPE-directed structure-probing studies for detailed analysis of multiple RNA conformational states. In particular, single-molecule guided deconvolution of the SHAPE reactivities permits 2° structure predictions of isolated RNA conformations, thereby substantially improving on traditional limitations associated with current structure prediction algorithms.
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Affiliation(s)
- Mario Vieweger
- JILA, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
| | - David J Nesbitt
- JILA, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado; Department of Physics, University of Colorado, Boulder, Colorado.
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13
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Abstract
Majority of the human genome is transcribed into RNAs with absent or limited protein-coding potential. microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are two major families of the non-protein-coding transcripts. miRNAs and lncRNAs can regulate fundamental cellular processes via diverse mechanisms. The expression and function of miRNAs and lncRNAs are tightly regulated in development and physiological homeostasis. Dysregulation of miRNAs and lncRNAs is critical to pathogenesis of human disease. Moreover, recent evidence indicates a cross talk between miRNAs and lncRNAs. Herein we review recent advances in the biology of miRNAs and lncRNAs with respect to the above aspects. We focus on their roles in cancer, respiratory disease, and neurodegenerative disease. The complexity, flexibility, and versatility of the structures and functions of miRNAs and lncRNAs demand integration of experimental and bioinformatics tools to acquire sufficient knowledge for applications of these noncoding RNAs in clinical care.
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Affiliation(s)
- Min Xue
- Xuzhou College of Medicine, Xuzhou, Jiangsu, China
| | - Ying Zhuo
- Kadlec Regional Medical Center, 888 Swift Boulevard, Richland, WA, USA
| | - Bin Shan
- Elson S. Floyd College of Medicine, Washington State University Spokane, 1495, Spokane, WA, 99210-1495, USA.
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14
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Jin H, Du XJ, Zhao Y, Xia DL. XIST/miR-544 axis induces neuropathic pain by activating STAT3 in a rat model. J Cell Physiol 2018; 233:5847-5855. [PMID: 29219175 DOI: 10.1002/jcp.26376] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/29/2017] [Indexed: 01/02/2023]
Abstract
An increasing number of studies have reported that lncRNAs are responsible for the development of neuropathic pain. In our current study, chronic constriction injury (CCI) rat models were established and we observed that lncRNA XIST was greatly increased. Knockdown of XIST can relieve pain characteristics including both mechanical and thermal hyperalgesia in CCI rats. Meanwhile, XIST down-regulation could inhibit neuro-inflammation by reducing expression of inflammatory cytokines including tumor necrosis factor (TNF)-α, IL-1β, and IL-6 and in CCI rats. By performing bioinformatics technology, miR-544 was predicted to have interactions with XIST and dual-luciferase reporter assays validated the correlation between them. A negative correlation between miR-544 and XIST was observed by carrying out XIST loss or gain of function tests. miR-544 markedly alleviated neuropathic pain development in CCI rats via targeting inflammatory cytokines, which was reversed by XIST over-expression. Moreover, STAT3 was manifested to be a target gene of miR-544 by bioinformatics predictions and it was activated in CCI rats. Over-expression of STAT3 was able to induce neuropathic pain and miR-544 inhibited this process in vivo. Furthermore, XIST increased STAT3 expression by sponging miR-544 in neuropathic pain development. To conclude, our present study indicated that XIST can contribute to neuropathic pain progression in rats through down-regulating miR-544 and up-regulating STAT3. Our results suggested that XIST/miR-544/STAT3 axis can serve as a novel therapeutic target in neuropathic pain development.
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Affiliation(s)
- Hui Jin
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xian-Jin Du
- Department of Emergency, Renmin Hospital of Wuhan University, Wuchang, Wuhan, China
| | - Ying Zhao
- Department of Neurology, Huai'an Second People's Hospital, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Dao-Lin Xia
- Department of Anesthesiology, Peoples Hospital of Xuyi, Xuyi, Jiangsu province, China
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15
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Huang NS, Chi YY, Xue JY, Liu MY, Huang S, Mo M, Zhou SL, Wu J. Long non-coding RNA metastasis associated in lung adenocarcinoma transcript 1 (MALAT1) interacts with estrogen receptor and predicted poor survival in breast cancer. Oncotarget 2018; 7:37957-37965. [PMID: 27191888 PMCID: PMC5122363 DOI: 10.18632/oncotarget.9364] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 04/27/2016] [Indexed: 02/04/2023] Open
Abstract
Metastasis associated in lung adenocarcinoma transcript 1 (MALAT1), a lncRNA that was first recognized as a prognostic parameter for patient survival of stage I lung cancer, is up-regulated in multiple human malignancies, including breast cancer. However, the mechanism of its function remained elusive. In the current study, by examining MALAT1 expression on mRNA level, we demonstrated that compared with MCF10A, MALAT1 expression was up-regulated in the majority of breast cancer cell lines (9/12). In 26 pairs of estrogen receptor (ER)-positive breast cancer samples, MALAT1 expression was significantly up-regulated compared with adjacent normal tissues (P = 0.012). Furthermore, of 204 breast cancer patients, high MALAT1 expression was associated with positive ER (P = 0.023) and progesterone receptor (PR) (P = 0.024) status. Further analysis using TCGA database revealed that ER and its target genes PGR and CCND1, were overexpressed in MALAT1 altered group compared with unaltered group, both on the mRNA and protein level. Lastly, we verified MALAT1's prognostic value in breast cancer. At the cut-off value of 75%, MALAT1 was the only independent prognostic factor of recurrence-free survival (RFS) in ER-negative patients in a multivariate Cox regression model (hazard ratio [HR] = 2.83, 95% confidence interval [CI] 1.02–7.83). MALAT1 overexpression was also associated with poor RFS in tamoxifen treated ER-positive breast cancer patients, which might serve as a potential biomarker to predict endocrine treatment sensitivity.
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Affiliation(s)
- Nai-Si Huang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, China.,Department of Oncology, Shanghai Medical College, Fudan University, China
| | - Ya-Yun Chi
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, China.,Department of Oncology, Shanghai Medical College, Fudan University, China
| | - Jing-Yan Xue
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, China.,Department of Oncology, Shanghai Medical College, Fudan University, China
| | - Meng-Ying Liu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, China.,Department of Oncology, Shanghai Medical College, Fudan University, China
| | - Sheng Huang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, China.,Department of Oncology, Shanghai Medical College, Fudan University, China
| | - Miao Mo
- Department of Oncology, Shanghai Medical College, Fudan University, China.,Department of Clinical Statistics, Fudan University Shanghai Cancer Center, China
| | - Shu-Ling Zhou
- Department of Oncology, Shanghai Medical College, Fudan University, China.,Department of Pathology, Fudan University Shanghai Cancer Center, China
| | - Jiong Wu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, China.,Department of Oncology, Shanghai Medical College, Fudan University, China.,Collaborative Innovation Center of Cancer Medicine, China
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16
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Cheng Y, Imanirad P, Jutooru I, Hedrick E, Jin UH, Rodrigues Hoffman A, Leal de Araujo J, Morpurgo B, Golovko A, Safe S. Role of metastasis-associated lung adenocarcinoma transcript-1 (MALAT-1) in pancreatic cancer. PLoS One 2018; 13:e0192264. [PMID: 29389953 PMCID: PMC5794178 DOI: 10.1371/journal.pone.0192264] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/12/2018] [Indexed: 12/28/2022] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript-1 (MALAT-1) is a long non-coding RNA (lncRNA) that is a negative prognostic factor for patients with pancreatic cancer and several other tumors. In this study, we show that knockdown of MALAT-1 in Panc1 and other pancreatic cancer cell lines decreases cell proliferation, survival and migration. We previously observed similar results for the lncRNAs HOTTIP and HOTAIR in Panc1 cells; however, RNAseq comparison of genes regulated by MALAT-1 shows minimal overlap with HOTTIP/HOTAIR-regulated genes. Analysis of changes in gene expression after MALAT-1 knockdown shows that this lncRNA represses several tumor suppressor-like genes including N-myc downregulated gene-1 (NDRG-1), a tumor suppressor in pancreatic cancer that is also corepressed by EZH2 (a PRC2 complex member). We also observed that Specificity proteins Sp1, Sp3 and Sp4 are overexpressed in Panc1 cells and Sp knockdown or treatment with small molecules that decrease Sp proteins expression also decrease MALAT-1 expression. We also generated Kras-overexpressing p53L/L;LSL-KrasG12DL/+;p48Cre+/- (p53L/L/KrasG12D) and p53L/+;LSLKrasG12DL/+;p48Cre+/- (p53L/+/KrasG12D) mice which are p53 homo- and heterozygous, respectively. These mice rapidly develop pancreatic ductal adenocarcinoma-like tumors and were crossed with MALAT-1-/- mice. We observed that the loss of one or two MALAT-1 alleles in these Ras overexpressing mice does not significantly affect the time to death; however, the loss of MALAT-1 in the p53-/+ (heterozygote) mice slightly increases their lifespan.
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Affiliation(s)
- Yating Cheng
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, United States of America
| | - Parisa Imanirad
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, United States of America
| | - Indira Jutooru
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, United States of America
| | - Erik Hedrick
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, United States of America
| | - Un-Ho Jin
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, United States of America
| | - Aline Rodrigues Hoffman
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States of America
| | - Jeann Leal de Araujo
- Department of Veterinary Pathobiology, Texas A&M University, College Station, TX, United States of America
| | - Benjamin Morpurgo
- Texas A&M Institute for Genomic Medicine, Texas A&M University, College Station, TX, United States of America
| | - Andrei Golovko
- Texas A&M Institute for Genomic Medicine, Texas A&M University, College Station, TX, United States of America
| | - Stephen Safe
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, TX, United States of America
- * E-mail:
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17
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Functional and prognostic significance of long non-coding RNA MALAT1 as a metastasis driver in ER negative lymph node negative breast cancer. Oncotarget 2018; 7:40418-40436. [PMID: 27250026 PMCID: PMC5130017 DOI: 10.18632/oncotarget.9622] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/09/2016] [Indexed: 12/15/2022] Open
Abstract
MALAT1 (metastasis associated lung adenocarcinoma transcript1) is a conserved long non-coding RNA, known to regulate gene expression by modulating transcription and post-transcriptional pre-mRNA processing of a large number of genes. MALAT1 expression is deregulated in various tumors, including breast cancer. However, the significance of such abnormal expression is yet to be fully understood. In this study, we demonstrate that regulation of aggressive breast cancer cell traits by MALAT1 is not predicted solely based on an elevated expression level but is context specific. By performing loss- and gain-of-function studies, both under in vitro and in vivo conditions, we demonstrate that MALAT1 facilitates cell proliferation, tumor progression and metastasis of triple-negative breast cancer (TNBC) cells despite having a comparatively lower expression level than ER or HER2-positive breast cancer cells. Furthermore, MALAT1 regulates the expression of several cancer metastasis-related genes, but displays molecular subtype specific correlations with such genes. Assessment of the prognostic significance of MALAT1 in human breast cancer (n=1992) revealed elevated MALAT1 expression was associated with decreased disease-specific survival in ER negative, lymph node negative patients of the HER2 and TNBC molecular subtypes. Multivariable analysis confirmed MALAT1 to have independent prognostic significance in the TNBC lymph node negative patient subset (HR=2.64, 95%CI 1.35 − 5.16, p=0.005). We propose that the functional significance of MALAT1 as a metastasis driver and its potential use as a prognostic marker is most promising for those patients diagnosed with ER negative, lymph node negative breast cancer who might otherwise mistakenly be stratified to have low recurrence risk.
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18
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Liu D, Zhu Y, Pang J, Weng X, Feng X, Guo Y. Knockdown of long non-coding RNA MALAT1 inhibits growth and motility of human hepatoma cells via modulation of miR-195. J Cell Biochem 2017; 119:1368-1380. [PMID: 28722813 DOI: 10.1002/jcb.26297] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 07/18/2017] [Indexed: 12/20/2022]
Abstract
The metastasis-associated lung adenocarcinoma transcription 1 (Malat1) is a long non-coding RNA (lncRNA), exerts oncogenic role in multiple cancers, including hepatocellular carcinoma (HCC). This study was aimed to investigate its posttranscriptional regulation in HCC cells. RT-PCR was performed to monitor the expression levels of Malat1 in normal liver and HCC cell lines. The expression of Malat1, microRNA (miR)-195, and epidermal growth factor receptor (EGFR) in HepG2 and MHCC97 cells was respectively or synchronously altered by transfection. Then the changes in cell viability, apoptotic cell rate, cell cycle distribution, migration, and invasion were respectively assessed. As a result, we found that Malat1 was highly expressed in HCC cell lines when compared to normal liver cells. Malat1 silence suppressed HCC cells viability, migration and invasion, induced apoptosis, and arrested more cells in G0/G1 phase. Malat1 acted as a circular endogenous RNA (ceRNA) for miR-195. Malat1 silence could not suppress HCC cell growth and motility when miR-195 was knocked down. EGFR was a direct target of miR-195. miR-195 overexpression could not suppress HCC cell growth and motility when the 3'UTR site of EGFR was overexpressed. Furthermore, Malat1 silence blocked the activation of PI3K/AKT and JAK/STAT pathways, while EGFR overexpression activated them. Our study demonstrates Malat1-miR-195-EGFR axis plays a critical role in HCC cells which provided a better understanding of Malat1 in HCC.
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Affiliation(s)
- Dingli Liu
- Department of Infectious Diseases, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Yun Zhu
- Department of Infectious Diseases, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Jinke Pang
- Department of Infectious Diseases, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Xie Weng
- Department of Infectious Diseases, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Xiaorong Feng
- Department of Infectious Diseases, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Yabing Guo
- Department of Infectious Diseases, Nanfang Hospital of Southern Medical University, Guangzhou, China
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19
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Pruszko M, Milano E, Forcato M, Donzelli S, Ganci F, Di Agostino S, De Panfilis S, Fazi F, Bates DO, Bicciato S, Zylicz M, Zylicz A, Blandino G, Fontemaggi G. The mutant p53-ID4 complex controls VEGFA isoforms by recruiting lncRNA MALAT1. EMBO Rep 2017; 18:1331-1351. [PMID: 28652379 PMCID: PMC5538427 DOI: 10.15252/embr.201643370] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 05/08/2017] [Accepted: 05/16/2017] [Indexed: 12/21/2022] Open
Abstract
The abundant, nuclear-retained, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been associated with a poorly differentiated and aggressive phenotype of mammary carcinomas. This long non-coding RNA (lncRNA) localizes to nuclear speckles, where it interacts with a subset of splicing factors and modulates their activity. In this study, we demonstrate that oncogenic splicing factor SRSF1 bridges MALAT1 to mutant p53 and ID4 proteins in breast cancer cells. Mutant p53 and ID4 delocalize MALAT1 from nuclear speckles and favor its association with chromatin. This enables aberrant recruitment of MALAT1 on VEGFA pre-mRNA and modulation of VEGFA isoforms expression. Interestingly, VEGFA-dependent expression signatures associate with ID4 expression specifically in basal-like breast cancers carrying TP53 mutations. Our results highlight a key role for MALAT1 in control of VEGFA isoforms expression in breast cancer cells expressing gain-of-function mutant p53 and ID4 proteins.
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Affiliation(s)
- Magdalena Pruszko
- Department of Molecular Biology, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland
| | - Elisa Milano
- Oncogenomic and Epigenetic Unit, Italian National Cancer Institute "Regina Elena", Rome, Italy
| | - Mattia Forcato
- Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy
| | - Sara Donzelli
- Oncogenomic and Epigenetic Unit, Italian National Cancer Institute "Regina Elena", Rome, Italy
| | - Federica Ganci
- Oncogenomic and Epigenetic Unit, Italian National Cancer Institute "Regina Elena", Rome, Italy
| | - Silvia Di Agostino
- Oncogenomic and Epigenetic Unit, Italian National Cancer Institute "Regina Elena", Rome, Italy
| | - Simone De Panfilis
- Centre for Life Nano Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - David O Bates
- Division of Cancer and Stem Cells, Cancer Biology, School of Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Silvio Bicciato
- Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy
| | - Maciej Zylicz
- Department of Molecular Biology, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Alicja Zylicz
- Department of Molecular Biology, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, Italian National Cancer Institute "Regina Elena", Rome, Italy
| | - Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, Italian National Cancer Institute "Regina Elena", Rome, Italy
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20
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Zheng B, Jeong S, Zhu Y, Chen L, Xia Q. miRNA and lncRNA as biomarkers in cholangiocarcinoma(CCA). Oncotarget 2017; 8:100819-100830. [PMID: 29246025 PMCID: PMC5725067 DOI: 10.18632/oncotarget.19044] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/19/2017] [Indexed: 12/16/2022] Open
Abstract
The microRNAs are a group of 20 nucleotides-long non-coding RNAs. By binding to the 3'UTR region of target mRNA, microRNAs can perform extensive actions mediating gene expression at post-trancriptional stages. It makes microRNAs serve as very crucial regulators in various biological progress including carcinogenesis. Long non-coding RNAs, however, are a subgroup of RNA with the length of 200 nucleotides. Unlike microRNAs, long non-coding RNAs can form secondary of tertiary domain based on their length. With the ability of directly interacting with DNA, RNA, protein, long non-coding RNAs have promoting or inhibitive functions in gene expression regulation. Furthermore, the abnormal expression of certain long non-coding RNAs has roused people's interest in the role of long non-coding RNAs in tumorigenesis. Although the connection between microRNA/long non-coding RNA and CCA has been a hot field to researchers, the link between molecular mechanism and clinical outcome has been barely built. This review takes a retrospect at the latest researches on the link between microRNA/long non-coding RNA and cholangiocarcinoma and the potential of microRNA/long non-coding RNA serving as distinctive biomarkers for CCA in clinical practice.
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Affiliation(s)
- Bo Zheng
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai 200438, P.R. China.,National Center for Liver Cancer, Shanghai 201805, P.R. China
| | - Seogsong Jeong
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Yanjing Zhu
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai 200438, P.R. China.,National Center for Liver Cancer, Shanghai 201805, P.R. China
| | - Lei Chen
- International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Institute, Second Military Medical University, Shanghai 200438, P.R. China.,National Center for Liver Cancer, Shanghai 201805, P.R. China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
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21
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Rao AKDM, Rajkumar T, Mani S. Perspectives of long non-coding RNAs in cancer. Mol Biol Rep 2017; 44:203-218. [PMID: 28391434 DOI: 10.1007/s11033-017-4103-6] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/31/2017] [Indexed: 01/17/2023]
Abstract
A recent advance in transcriptomics has spawned the 'Decade of non-coding RNAs' by potentiating the growing numbers of long non-coding RNA in cancer. LncRNA involvement in cancer denotes its significance beyond our perception as they participate in tumor suppression and promoting oncogenesis, which raises them as a mighty class of effectors or regulators. Aberrantly expressed lncRNAs interact with major protein and coding partners, which ultimately deregulate normal cellular processes and drive the cell towards malignant state. Identification of theses interactions are utmost important as lncRNAs can be ideal targets for therapy. Dysregulation of lncRNAs by genomic alterations like single nucleotide variations and gene fusions are also potential modulators of their secondary structure. In this review, we discuss the various molecular interactions of lncRNAs with major bio-molecules and genetic variations in lncRNA genes and their importance in cancer. This systematic review outlines the vivid role of lncRNAs in cancer context and opens up future conceptual applications.
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Affiliation(s)
| | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), No:38, Sardar Patel Road, Adyar, Chennai, Tamil Nadu, 600036, India
| | - Samson Mani
- Department of Molecular Oncology, Cancer Institute (WIA), No:38, Sardar Patel Road, Adyar, Chennai, Tamil Nadu, 600036, India.
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22
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Liu S, Mitra R, Zhao MM, Fan W, Eischen CM, Yin F, Zhao Z. The Potential Roles of Long Noncoding RNAs (lncRNA) in Glioblastoma Development. Mol Cancer Ther 2016; 15:2977-2986. [PMID: 27784795 DOI: 10.1158/1535-7163.mct-16-0320] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/17/2016] [Accepted: 09/20/2016] [Indexed: 01/06/2023]
Abstract
Long noncoding RNA (lncRNA) may contribute to the initiation and progression of tumor. In this study, we first systematically compared lncRNA and mRNA expression between glioblastoma and paired normal brain tissues using microarray data. We found 27 lncRNA and 82 mRNA significantly upregulated in glioblastoma, as well as 198 lncRNA and 285 mRNA significantly downregulated in glioblastoma. We identified 138 coexpressed lncRNA-mRNA pairs from these differentially expressed lncRNA and genes. Subsequent pathway analysis of the lncRNA-paired genes indicated that EphrinB-EPHB, p75-mediated signaling, TNFα/NF-κB, and ErbB2/ErbB3 signaling pathways might be altered in glioblastoma. Specifically, lncRNA RAMP2-AS1 had significant decrease of expression in glioblastoma tissues and showed coexpressional relationship with NOTCH3, an important tumor promoter in many neoplastic diseases. Our follow up experiment indicated that (i) an overexpression of RAMP2-AS1 reduced glioblastoma cell proliferation in vitro and also reduced glioblastoma xenograft tumors in vivo; (ii) NOTCH3 and RAMP2-AS1 coexpression rescued the inhibitory action of RAMP2-AS1 in glioblastoma cells; and (iii) RNA pull-down assay revealed a direct interaction of RAMP2-AS1 with DHC10, which may consequently inhibit, as we hypothesize, the expression of NOTCH3 and its downstream signaling molecule HES1 in glioblastoma. Taken together, our data revealed that lncRNA expression profile in glioblastoma tissue was significantly altered; and RAMP2-AS1 might play a tumor suppressive role in glioblastoma through an indirect inhibition of NOTCH3 Our results provided some insights into understanding the key roles of lncRNA-mRNA coregulation in human glioblastoma and the mechanisms responsible for glioblastoma progression and pathogenesis. Mol Cancer Ther; 15(12); 2977-86. ©2016 AACR.
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Affiliation(s)
- Shuang Liu
- Department of Neurosurgery, Navy General Hospital, PLA. Beijing, 100048, China
| | - Ramkrishna Mitra
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Ming-Ming Zhao
- Department of Neurosurgery, Navy General Hospital, PLA. Beijing, 100048, China
| | - Wenhong Fan
- Department of Recombinant Drugs, National Institutes for Food and Drug Control, Beijing, 100050, China
| | - Christine M Eischen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Feng Yin
- Department of Neurosurgery, Navy General Hospital, PLA. Beijing, 100048, China
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA.,Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN 37212, USA.,Center for Precision Health, School of Biomedical University, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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23
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Iempridee T. Long non-coding RNA H19 enhances cell proliferation and anchorage-independent growth of cervical cancer cell lines. Exp Biol Med (Maywood) 2016; 242:184-193. [PMID: 27633578 DOI: 10.1177/1535370216670542] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNA H19 is aberrantly expressed in multiple malignancies and its expression levels correlate with recurrence, metastasis, and patient survival. Despite numerous reports documenting the role of H19 in carcinogenesis, its contribution to cervical cancer development is still largely unknown. In this study, I observed that H19 expression was elevated in cervical cancer cell lines and could be detected in extracellular vesicles in the culture medium. In addition, I demonstrated, by overexpression and knockdown experiments, that H19 promoted cell proliferation and multicellular tumor spheroid formation without significantly affecting apoptosis and cell migration. Finally, treatment with transforming growth factor beta and hypoxia-mimetic CoCl2 could modulate H19 levels in a cell line-specific manner. These findings indicate that H19 promotes both anchorage-specific and -independent growth of cervical cancer cell lines and may serve as a potential target for cancer diagnosis and therapy.
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Affiliation(s)
- Tawin Iempridee
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathum Thani 12120, Thailand
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24
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Al-Tobasei R, Paneru B, Salem M. Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout. PLoS One 2016; 11:e0148940. [PMID: 26895175 PMCID: PMC4764514 DOI: 10.1371/journal.pone.0148940] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 01/23/2016] [Indexed: 02/07/2023] Open
Abstract
The ENCODE project revealed that ~70% of the human genome is transcribed. While only 1–2% of the RNAs encode for proteins, the rest are non-coding RNAs. Long non-coding RNAs (lncRNAs) form a diverse class of non-coding RNAs that are longer than 200nt. Emerging evidence indicates that lncRNAs play critical roles in various cellular processes including regulation of gene expression. LncRNAs show low levels of gene expression and sequence conservation, which make their computational identification in genomes difficult. In this study, more than two billion Illumina sequence reads were mapped to the genome reference using the TopHat and Cufflinks software. Transcripts shorter than 200nt, with more than 83–100 amino acids ORF, or with significant homologies to the NCBI nr-protein database were removed. In addition, a computational pipeline was used to filter the remaining transcripts based on a protein-coding-score test. Depending on the filtering stringency conditions, between 31,195 and 54,503 lncRNAs were identified, with only 421 matching known lncRNAs in other species. A digital gene expression atlas revealed 2,935 tissue-specific and 3,269 ubiquitously-expressed lncRNAs. This study annotates the lncRNA rainbow trout genome and provides a valuable resource for functional genomics research in salmonids.
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Affiliation(s)
- Rafet Al-Tobasei
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States of America
| | - Bam Paneru
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States of America
| | - Mohamed Salem
- Computational Science Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States of America
- Department of Biology and Molecular Biosciences Program, Middle Tennessee State University, Murfreesboro, TN, 37132, United States of America
- * E-mail:
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Zong X, Nakagawa S, Freier SM, Fei J, Ha T, Prasanth SG, Prasanth KV. Natural antisense RNA promotes 3' end processing and maturation of MALAT1 lncRNA. Nucleic Acids Res 2016; 44:2898-908. [PMID: 26826711 PMCID: PMC4824109 DOI: 10.1093/nar/gkw047] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 01/17/2016] [Indexed: 01/09/2023] Open
Abstract
The RNase P-mediated endonucleolytic cleavage plays a crucial role in the 3′ end processing and cellular accumulation of MALAT1, a nuclear-retained long noncoding RNA that promotes malignancy. The regulation of this cleavage event is largely undetermined. Here we characterize a broadly expressed natural antisense transcript at the MALAT1 locus, designated as TALAM1, that positively regulates MALAT1 levels by promoting the 3′ end cleavage and maturation of MALAT1 RNA. TALAM1 RNA preferentially localizes at the site of transcription, and also interacts with MALAT1 RNA. Depletion of TALAM1 leads to defects in the 3′ end cleavage reaction and compromises cellular accumulation of MALAT1. Conversely, overexpression of TALAM1 facilitates the cleavage reaction in trans. Interestingly, TALAM1 is also positively regulated by MALAT1 at the level of both transcription and RNA stability. Together, our data demonstrate a novel feed-forward positive regulatory loop that is established to maintain the high cellular levels of MALAT1, and also unravel the existence of sense-antisense mediated regulatory mechanism for cellular lncRNAs that display RNase P-mediated 3′ end processing.
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Affiliation(s)
- Xinying Zong
- Department of Cell and Developmental Biology, University of Illinois Urbana, IL 61801, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama 351-0198, Japan
| | | | - Jingyi Fei
- Center for Physics of living cells, Department of Physics, University of Illinois, Urbana, IL, USA
| | - Taekjip Ha
- Center for Physics of living cells, Department of Physics, University of Illinois, Urbana, IL, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois Urbana, IL 61801, USA
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26
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Vieweger M, Holmstrom ED, Nesbitt DJ. Single-Molecule FRET Reveals Three Conformations for the TLS Domain of Brome Mosaic Virus Genome. Biophys J 2015; 109:2625-2636. [PMID: 26682819 PMCID: PMC4699858 DOI: 10.1016/j.bpj.2015.10.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/01/2015] [Accepted: 10/07/2015] [Indexed: 12/28/2022] Open
Abstract
Metabolite-dependent conformational switching in RNA riboswitches is now widely accepted as a critical regulatory mechanism for gene expression in bacterial systems. More recently, similar gene regulation mechanisms have been found to be important for viral systems as well. One of the most abundant and best-studied systems is the tRNA-like structure (TLS) domain, which has been found to occur in many plant viruses spread across numerous genera. In this work, folding dynamics for the TLS domain of Brome Mosaic Virus have been investigated using single-molecule fluorescence resonance energy transfer techniques. In particular, burst fluorescence methods are exploited to observe metal-ion ([M(n+)])-induced folding in freely diffusing RNA constructs resembling the minimal TLS element of brome mosaic virus RNA3. The results of these experiments reveal a complex equilibrium of at least three distinct populations. A stepwise, or consecutive, thermodynamic model for TLS folding is developed, which is in good agreement with the [M(n+)]-dependent evolution of conformational populations and existing structural information in the literature. Specifically, this folding pathway explains the metal-ion dependent formation of a functional TLS domain from unfolded RNAs via two consecutive steps: 1) hybridization of a long-range stem interaction, followed by 2) formation of a 3'-terminal pseudoknot. These two conformational transitions are well described by stepwise dissociation constants for [Mg(2+)] (K1 = 328 ± 30 μM and K2 = 1092 ± 183 μM) and [Na(+)] (K1 = 74 ± 6 mM and K2 = 243 ± 52 mM)-induced folding. The proposed thermodynamic model is further supported by inhibition studies of the long-range stem interaction using a complementary DNA oligomer, which effectively shifts the dynamic equilibrium toward the unfolded conformation. Implications of this multistep conformational folding mechanism are discussed with regard to regulation of virus replication.
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Affiliation(s)
- Mario Vieweger
- Joint Institute for Laboratory Astrophysics, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
| | - Erik D Holmstrom
- Joint Institute for Laboratory Astrophysics, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
| | - David J Nesbitt
- Joint Institute for Laboratory Astrophysics, University of Colorado and National Institute of Standards and Technology, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado.
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27
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Zheng J, Dong P, Mao Y, Chen S, Wu X, Li G, Lu Z, Yu F. lincRNA-p21 inhibits hepatic stellate cell activation and liver fibrogenesis via p21. FEBS J 2015; 282:4810-21. [PMID: 26433205 DOI: 10.1111/febs.13544] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/19/2015] [Accepted: 09/29/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Jianjian Zheng
- Wenzhou Key Laboratory of Surgery; The First Affiliated Hospital of Wenzhou Medical University; China
| | - Peihong Dong
- Department of Infectious Diseases; The First Affiliated Hospital of Wenzhou Medical University; China
| | - Yuqing Mao
- Department of Gastroenterology; Jinshan Hospital of Fudan University; Shanghai China
| | - Shaolong Chen
- Department of Infectious Diseases; Huashan Hospital; Fudan University; Shanghai China
| | - Xiaoli Wu
- Department of Gastroenterology; The First Affiliated Hospital of Wenzhou Medical University; Wenzhou China
| | - Guojun Li
- Department of Hepatology; Ningbo Yinzhou Second Hospital; China
| | - Zhongqiu Lu
- Department of Emergency; The First Affiliated Hospital of Wenzhou Medical University; China
| | - Fujun Yu
- Department of Infectious Diseases; The First Affiliated Hospital of Wenzhou Medical University; China
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28
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Abstract
Since their initial discovery in the early 1990s, microRNAs have now become the focus of a multitude of lines of investigation ranging from basic biology to translational applications in the clinic. Previously believed to be of no biological relevance, microRNAs regulate processes fundamental to human health and disease. In diseases of the lung, microRNAs have been implicated in developmental programming, as drivers of disease, potential therapeutic targets, and clinical biomarkers; however, several obstacles must be overcome for us to fully realize their potential therapeutic use. Here, we provide for the clinician an overview of microRNA biology in selected diseases of the lung with a focus on their potential clinical application.
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29
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Crea F, Clermont PL, Parolia A, Wang Y, Helgason CD. The non-coding transcriptome as a dynamic regulator of cancer metastasis. Cancer Metastasis Rev 2015; 33:1-16. [PMID: 24346158 PMCID: PMC3988524 DOI: 10.1007/s10555-013-9455-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Since the discovery of microRNAs, non-coding RNAs (NC-RNAs) have increasingly attracted the attention of cancer investigators. Two classes of NC-RNAs are emerging as putative metastasis-related genes: long non-coding RNAs (lncRNAs) and small nucleolar RNAs (snoRNAs). LncRNAs orchestrate metastatic progression through several mechanisms, including the interaction with epigenetic effectors, splicing control and generation of microRNA-like molecules. In contrast, snoRNAs have been long considered “housekeeping” genes with no relevant function in cancer. However, recent evidence challenges this assumption, indicating that some snoRNAs are deregulated in cancer cells and may play a specific role in metastasis. Interestingly, snoRNAs and lncRNAs share several mechanisms of action, and might synergize with protein-coding genes to generate a specific cellular phenotype. This evidence suggests that the current paradigm of metastatic progression is incomplete. We propose that NC-RNAs are organized in complex interactive networks which orchestrate cellular phenotypic plasticity. Since plasticity is critical for cancer cell metastasis, we suggest that a molecular interactome composed by both NC-RNAs and proteins orchestrates cancer metastasis. Interestingly, expression of lncRNAs and snoRNAs can be detected in biological fluids, making them potentially useful biomarkers. NC-RNA expression profiles in human neoplasms have been associated with patients’ prognosis. SnoRNA and lncRNA silencing in pre-clinical models leads to cancer cell death and/or metastasis prevention, suggesting they can be investigated as novel therapeutic targets. Based on the literature to date, we critically discuss how the NC-RNA interactome can be explored and manipulated to generate more effective diagnostic, prognostic, and therapeutic strategies for metastatic neoplasms.
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Affiliation(s)
- Francesco Crea
- Experimental Therapeutics, BC Cancer Research Centre, Vancouver, BC, Canada,
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Abstract
The identification and characterization of long noncoding RNA in a variety of tissues represent major achievements that contribute to our understanding of the molecular mechanisms controlling gene expression. In particular, long noncoding RNA play crucial roles in the epigenetic regulation of the adaptive response to environmental cues via their capacity to target chromatin modifiers to specific locus. In addition, these transcripts have been implicated in controlling splicing, translation and degradation of messenger RNA. Long noncoding RNA have also been shown to act as decoy molecules for microRNA. In the heart, a few long noncoding RNA have been demonstrated to regulate cardiac commitment and differentiation during development. Furthermore, recent findings suggest their involvement as regulators of the pathophysiological response to injury in the adult heart. Their high cellular specificity makes them attractive target molecules for innovative therapies and ideal biomarkers.
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Affiliation(s)
- Thierry Pedrazzini
- Unité de cardiologie expérimentale, département de médecine, centre hospitalier universitaire vaudois, 1011 Lausanne, Suisse
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31
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Liu JH, Chen G, Dang YW, Li CJ, Luo DZ. Expression and prognostic significance of lncRNA MALAT1 in pancreatic cancer tissues. Asian Pac J Cancer Prev 2015; 15:2971-7. [PMID: 24815433 DOI: 10.7314/apjcp.2014.15.7.2971] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) have been recently observed in various human cancers. However, the role of lncRNAs in pancreatic duct adenocarcinoma (PDAC) remains unclarified. The aim of this study was to detect the expression of lncRNA MALAT1 in PDAC formalin-fixed, paraffin embedded (FFPE) tissues and to investigate the clinical significance of the MALAT1 level. METHODS The expression of MALAT1 was examined in 45 PDAC and 25 adjacent non-cancerous FFPE tissues, as well as in five PDAC cell lines and a normal pancreatic epithelium cell line HPDE6c-7, using qRT-PCR. The relationship between MALAT1 level and clinicopathological parameters of PDAC was analyzed with the Kaplan-Meier method and Cox proportional hazards model. RESULTS The relative level of MALAT1 was significantly higher in PDAC compared to the adjacent normal pancreatic tissues (p=0.009). When comparing the MALAT1 level in the cultured cell lines, remarkably higher expression of MALAT1 was found in aspc-1 PDAC cells compared with the immortal pancreatic duct epithelial cell line HPDE6c-7 (q=7.573, p<0.05). Furthermore, MALAT1 expression level showed significant correlation with tumor size (r=0.35, p=0.018), tumor stage (r=0.439, p=0.003) and depth of invasion (r=0.334, p=0.025). Kaplan-Meier analysis revealed that patients with higher MALAT1 expression had a poorer disease free survival (p=0.043). Additionally, multivariate analysis indicated that overexpression of MALAT1, as well as the tumor location and nerve invasion, was an independent predictor of disease-specific survival of PDAC. CONCLUSION MALAT1 might be considered as a potential prognostic indicator and may be a target for diagnosis and gene therapy for PDAC.
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Affiliation(s)
- Jiang-Hua Liu
- Department of Emergency, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China E-mail :
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32
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Comer BS, Ba M, Singer CA, Gerthoffer WT. Epigenetic targets for novel therapies of lung diseases. Pharmacol Ther 2014; 147:91-110. [PMID: 25448041 DOI: 10.1016/j.pharmthera.2014.11.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 11/06/2014] [Indexed: 12/13/2022]
Abstract
In spite of substantial advances in defining the immunobiology and function of structural cells in lung diseases there is still insufficient knowledge to develop fundamentally new classes of drugs to treat many lung diseases. For example, there is a compelling need for new therapeutic approaches to address severe persistent asthma that is insensitive to inhaled corticosteroids. Although the prevalence of steroid-resistant asthma is 5-10%, severe asthmatics require a disproportionate level of health care spending and constitute a majority of fatal asthma episodes. None of the established drug therapies including long-acting beta agonists or inhaled corticosteroids reverse established airway remodeling. Obstructive airways remodeling in patients with chronic obstructive pulmonary disease (COPD), restrictive remodeling in idiopathic pulmonary fibrosis (IPF) and occlusive vascular remodeling in pulmonary hypertension are similarly unresponsive to current drug therapy. Therefore, drugs are needed to achieve long-acting suppression and reversal of pathological airway and vascular remodeling. Novel drug classes are emerging from advances in epigenetics. Novel mechanisms are emerging by which cells adapt to environmental cues, which include changes in DNA methylation, histone modifications and regulation of transcription and translation by noncoding RNAs. In this review we will summarize current epigenetic approaches being applied to preclinical drug development addressing important therapeutic challenges in lung diseases. These challenges are being addressed by advances in lung delivery of oligonucleotides and small molecules that modify the histone code, DNA methylation patterns and miRNA function.
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Affiliation(s)
- Brian S Comer
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL, 36688, USA
| | - Mariam Ba
- Department of Pharmacology, University of Nevada School of Medicine, Reno, NV 89557, USA
| | - Cherie A Singer
- Department of Pharmacology, University of Nevada School of Medicine, Reno, NV 89557, USA
| | - William T Gerthoffer
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL, 36688, USA.
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33
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Fritah S, Niclou SP, Azuaje F. Databases for lncRNAs: a comparative evaluation of emerging tools. RNA (NEW YORK, N.Y.) 2014; 20:1655-65. [PMID: 25323317 PMCID: PMC4201818 DOI: 10.1261/rna.044040.113] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 07/28/2014] [Indexed: 05/26/2023]
Abstract
The vast majority of the human transcriptome does not code for proteins. Advances in transcriptome arrays and deep sequencing are giving rise to a fast accumulation of large data sets, particularly of long noncoding RNAs (lncRNAs). Although it is clear that individual lncRNAs may play important and diverse biological roles, there is a large gap between the number of existing lncRNAs and their known relation to molecular/cellular function. This and related information have recently been gathered in several databases dedicated to lncRNA research. Here, we review the content of general and more specialized databases on lncRNAs. We evaluate these resources in terms of the quality of annotations, the reporting of validated or predicted molecular associations, and their integration with other resources and computational analysis tools. We illustrate our findings using known and novel cancer-related lncRNAs. Finally, we discuss limitations and highlight potential future directions for these databases to help delineating functions associated with lncRNAs.
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Affiliation(s)
- Sabrina Fritah
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Centre de Recherche Public de la Santé (CRP-Santé), Luxembourg L-1526, Luxembourg
| | - Simone P Niclou
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Centre de Recherche Public de la Santé (CRP-Santé), Luxembourg L-1526, Luxembourg
| | - Francisco Azuaje
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Centre de Recherche Public de la Santé (CRP-Santé), Luxembourg L-1526, Luxembourg
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Functional linc-POU3F3 is overexpressed and contributes to tumorigenesis in glioma. Gene 2014; 554:114-9. [PMID: 25445282 DOI: 10.1016/j.gene.2014.10.038] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/15/2014] [Accepted: 10/23/2014] [Indexed: 12/11/2022]
Abstract
Growing number of long intergenic noncoding RNAs (lincRNAs) have recently been identified in mammals as new modulators in cancer origination and progression involved in a broad range of biological processes. Long intergenic noncoding RNA POU3F3 (linc-POU3F3) has been characterized as a highly conserved functional transcription regulator in esophageal squamous cell carcinoma. The contributions of this lincRNA to glioblastoma remain unknown. In this present study, we investigated the expression pattern and functional role of linc-POU3F3 in glioma by using real-time PCR and gain-/loss-of-function studies. The results revealed that linc-POU3F3 levels were extraordinarily associated with the tumor WHO grade. In related biochemical assays, overexpression of linc-POU3F3 promotes cell viability and proliferation in glioma cells, whereas knockdown of linc-POU3F3 showed the opposite effect. As expected, we also found that linc-POU3F3 expression was negatively correlated with the mRNA level of POU3F3 (the evolutionarily conserved neighbor gene of linc-POU3F3). Our results indicate that linc-POU3F3 might affect glioma development via altering expression level of POU3F3, and lead us to believe that linc-POU3F3 may also have a crucial regulatory role in glioma progression.
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35
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Carpenter S, Ricci EP, Mercier BC, Moore MJ, Fitzgerald KA. Post-transcriptional regulation of gene expression in innate immunity. Nat Rev Immunol 2014; 14:361-76. [PMID: 24854588 DOI: 10.1038/nri3682] [Citation(s) in RCA: 268] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Innate immune responses combat infectious microorganisms by inducing inflammatory responses, antimicrobial pathways and adaptive immunity. Multiple genes within each of these functional categories are coordinately and temporally regulated in response to distinct external stimuli. The substantial potential of these responses to drive pathological inflammation and tissue damage highlights the need for rigorous control of these responses. Although transcriptional control of inflammatory gene expression has been studied extensively, the importance of post-transcriptional regulation of these processes is less well defined. In this Review, we discuss the regulatory mechanisms that occur at the level of mRNA splicing, mRNA polyadenylation, mRNA stability and protein translation, and that have instrumental roles in controlling both the magnitude and duration of the inflammatory response.
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Affiliation(s)
- Susan Carpenter
- 1] Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. [2]
| | - Emiliano P Ricci
- 1] Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. [2]
| | - Blandine C Mercier
- 1] Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. [2]
| | - Melissa J Moore
- Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Katherine A Fitzgerald
- 1] Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. [2] Centre of Molecular Inflammation Research, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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36
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Clark BS, Blackshaw S. Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease. Front Genet 2014; 5:164. [PMID: 24936207 PMCID: PMC4047558 DOI: 10.3389/fgene.2014.00164] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 05/18/2014] [Indexed: 01/17/2023] Open
Abstract
Comprehensive analysis of the mammalian transcriptome has revealed that long non-coding RNAs (lncRNAs) may make up a large fraction of cellular transcripts. Recent years have seen a surge of studies aimed at functionally characterizing the role of lncRNAs in development and disease. In this review, we discuss new findings implicating lncRNAs in controlling development of the central nervous system (CNS). The evolution of the higher vertebrate brain has been accompanied by an increase in the levels and complexities of lncRNAs expressed within the developing nervous system. Although a limited number of CNS-expressed lncRNAs are now known to modulate the activity of proteins important for neuronal differentiation, the function of the vast majority of neuronal-expressed lncRNAs is still unknown. Topics of intense current interest include the mechanism by which CNS-expressed lncRNAs might function in epigenetic and transcriptional regulation during neuronal development, and how gain and loss of function of individual lncRNAs contribute to neurological diseases.
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Affiliation(s)
- Brian S Clark
- Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine Baltimore, MD, USA
| | - Seth Blackshaw
- Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Ophthalmology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Department of Neurology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Center for High-Throughput Biology, Johns Hopkins University School of Medicine Baltimore, MD, USA ; Institute for Cell Engineering, Johns Hopkins University School of Medicine Baltimore, MD, USA
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37
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MALAT1 promotes cell proliferation in gastric cancer by recruiting SF2/ASF. Biomed Pharmacother 2014; 68:557-64. [PMID: 24857172 DOI: 10.1016/j.biopha.2014.04.007] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/16/2014] [Indexed: 12/17/2022] Open
Abstract
The functions of long non-coding RNAs (lncRNAs) in gastric cancer (GC) remain largely unknown. MALAT1 is a kind of lncRNA that had been validated as a pivotal metastasis and prognosis mark in lung adenocarcinoma. In this study, we found that MALAT1 was aberrantly highly expressed in GC cell lines (SGC-7901, MKN-45 and SUN-16), and induced specific distribution and over-expression of SF2/ASF in nucleolus. Knock-down of MALAT1 or SF2/ASF in SGC-7901 cells respectively induced significant arrest of cell cycle in G0/G1 phase along with a remarkable suppression of cell proliferation, and the nuclear distribution and expression of SF2/ASF was significantly impaired when MALAT1 was depleted. However, over-expression of SF2/ASF exhibited no effect on rescuing the cell proliferation suppression by MALAT1 depletion. These results suggest that MALAT1 may function as a promoter of GC cell proliferation partly by regulating SF2/ASF, and our findings may provide us a likely biomarker and a potential target for GC diagnosis and therapeutic treatment.
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38
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Bai W, Yang J, Yang G, Niu P, Tian L, Gao A. Long non-coding RNA NR_045623 and NR_028291 involved in benzene hematotoxicity in occupationally benzene-exposed workers. Exp Mol Pathol 2014; 96:354-60. [PMID: 24613687 DOI: 10.1016/j.yexmp.2014.02.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 02/28/2014] [Indexed: 01/08/2023]
Abstract
Benzene is an established human hematotoxicant and leukemogen. New insights into the pathogenesis of benzene hematotoxicity are urgently needed. Long non-coding RNA (lncRNA) widely participate in various physiological and pathological processes. It has been shown that lncRNA plays an important role in hematologic malignancy tumorigenesis. However, the expression and biological function of lncRNA during benzene hematotoxicity progress remain largely unknown. An integrated analysis of differentially expressed lncRNA and mRNA was performed to identify genes which were likely to be critical for benzene hematotoxicity through Microarray analysis. Dynamic gene network analysis of the differentially expressed lncRNA and mRNA was constructed and two main lncRNA (NR_045623 and NR_028291) were discovered and two key lncRNA subnets were involved in immune responses, hematopoiesis, B cell receptor signaling pathway and chronic myeloid leukemia. These findings suggested that NR_045623 and NR_028291 might be the key genes associated with benzene hematotoxicity.
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Affiliation(s)
- Wenlin Bai
- Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Jing Yang
- Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Gengxia Yang
- Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Piye Niu
- Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Lin Tian
- Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China
| | - Ai Gao
- Department of Occupational Health and Environmental Health, School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, China.
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39
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Investigation of circulating lncRNAs in B-cell neoplasms. Clin Chim Acta 2014; 431:255-9. [PMID: 24583225 DOI: 10.1016/j.cca.2014.02.010] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 02/07/2023]
Abstract
Long non-coding RNAs (lncRNA) which are longer than 200 base pairs in length, play an important role in cellular machinery. Chronic lymphocytic leukemia (CLL) and multiple myeloma (MM) are neoplasms of B-cells. In our study we aimed to investigate circulating lncRNA levels of CLL and MM patients. For this purpose we selected 5 candidate lncRNAs (TUG1, LincRNA-p21, MALAT1, HOTAIR, and GAS5) where the first two are regulated by p53. Analyses were performed by real-time PCR using cDNA synthesized from plasma RNAs. In both disease groups differential levels of plasma lncRNAs were observed. LincRNA-p21 was the only molecule displaying significant changes in the CLL group while all remaining lncRNAs showed significant differences in the MM group. In the MM group only TUG1 showed higher levels than the healthy volunteers. In conclusion, the expression levels of the candidate lncRNA molecules display a general trend for tissue- and disease-specific expression which can provide important potential biomarkers specific to the particular disease type. However, further studies are necessary to elucidate their involvement in disease development and progression.
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40
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Zhu YP, Bian XJ, Ye DW, Yao XD, Zhang SL, Dai B, Zhang HL, Shen YJ. Long noncoding RNA expression signatures of bladder cancer revealed by microarray. Oncol Lett 2014; 7:1197-1202. [PMID: 24944692 PMCID: PMC3961449 DOI: 10.3892/ol.2014.1843] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 12/23/2013] [Indexed: 01/16/2023] Open
Abstract
Dysregulation of long noncoding RNAs (lncRNAs) has been regarded as a primary feature of several human cancers. However, the genome-wide expression and functional significance of lncRNAs in bladder cancer remains unclear. The aim of this study was to identify aberrantly expressed lncRNAs that may play an important role in contributing to bladder cancer pathogenesis. In this study, we described lncRNAs profiles in four pairs of human bladder cancer and matched normal bladder tissues by microarray. We finally determined 3,324 differentially expressed human lncRNAs and 2,120 differentially expressed mRNAs (≥2-fold change). A total of 110 lncRNAs were significantly differentially expressed between the tumor and the control groups (≥8-fold change). Four lncRNAs (TNXA, CTA-134P22.2, CTC-276P9.1 and KRT19P3) were selected for further confirmation of microarray results using quantitative PCR (qPCR), and a strong correlation was identified between the qPCR results and microarray data. We also observed that numerous lncRNA expression levels were significantly correlated with the expression of tens of protein coding genes by construction of the lncRNA-mRNA co-expression network. Kyoto Encyclopedia of Genes and Genomes annotation showed a significant association with p53, bladder cancer, cell cycle and propanoate metabolism pathway gene expression in the bladder cancer group compared with the normal tissue group, indicating that deregulated lncRNAs may act by regulating protein-coding genes in these pathways. We demonstrated the expression profiles of human lncRNAs in bladder cancer by microarray. We identified a collection of aberrantly expressed lncRNAs in bladder cancer compared with matched normal tissue. It is likely that these deregulated lncRNAs play a key or partial role in the development and/or progression of bladder cancer.
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Affiliation(s)
- Yi-Ping Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, P.R. China ; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Xiao-Jie Bian
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, P.R. China ; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Ding-Wei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, P.R. China ; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Xu-Dong Yao
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, P.R. China ; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Shi-Lin Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, P.R. China ; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Bo Dai
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, P.R. China ; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Hai-Liang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, P.R. China ; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
| | - Yi-Jun Shen
- Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, P.R. China ; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P.R. China
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41
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Singh DK, Prasanth KV. Functional insights into the role of nuclear-retained long noncoding RNAs in gene expression control in mammalian cells. Chromosome Res 2013; 21:695-711. [PMID: 24233053 PMCID: PMC3951185 DOI: 10.1007/s10577-013-9391-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The mammalian genome harbors thousands of long noncoding RNA (lncRNA) genes. Recent studies have indicated the involvement of several of these lncRNAs in the regulation of gene expression. lncRNAs play crucial roles in various biological processes ranging from epigenetic gene regulation, transcriptional control,to post-transcriptional regulation. lncRNAs are localized in various subcellular compartments, and major proportion of these are retained in the cell nucleus and could be broadly classified as nuclear-retained lncRNAs (nrRNAs). Based on the identified functions,members of the nrRNAs execute diverse roles, including providing architectural support to the hierarchical subnuclear organization and influencing the recruitment of chromatin modifier factors to specific chromatin sites. In this review, we will summarize the recently described roles of mammalian nrRNAs in controlling gene expression by influencing chromatin organization, transcription,pre-mRNA processing, nuclear organization, and their involvement in disease.
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Affiliation(s)
- Deepak K. Singh
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL-61801, USA
| | - Kannanganattu V. Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL-61801, USA
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42
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Peart N, Sataluri A, Baillat D, Wagner EJ. Non-mRNA 3' end formation: how the other half lives. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:491-506. [PMID: 23754627 DOI: 10.1002/wrna.1174] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/25/2013] [Accepted: 04/26/2013] [Indexed: 12/27/2022]
Abstract
The release of nascent RNA from transcribing RNA polymerase complexes is required for all further functions carried out by RNA molecules. The elements and processing machinery involved in 3' end formation therefore represent key determinants in the biogenesis and accumulation of cellular RNA. While these factors have been well-characterized for messenger RNA, recent work has elucidated analogous pathways for the 3' end formation of other important cellular RNA. Here, we discuss four specific cases of non-mRNA 3' end formation-metazoan small nuclear RNA, Saccharomyces cerevisiae small nuclear RNA, Schizosaccharomyces pombe telomerase RNA, and the mammalian MALAT1 large noncoding RNA-as models of alternative mechanisms to generate RNA 3' ends. Comparison of these disparate processing pathways reveals an emerging theme of evolutionary ingenuity. In some instances, evidence for the creation of a dedicated processing complex exists; while in others, components are utilized from the existing RNA processing machinery and modified to custom fit the unique needs of the RNA substrate. Regardless of the details of how non-mRNA 3' ends are formed, the lengths to which biological systems will go to release nascent transcripts from their DNA templates are fundamental for cell survival.
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Affiliation(s)
- Natoya Peart
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, TX, USA
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43
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Long noncoding RNA MALAT1 controls cell cycle progression by regulating the expression of oncogenic transcription factor B-MYB. PLoS Genet 2013; 9:e1003368. [PMID: 23555285 PMCID: PMC3605280 DOI: 10.1371/journal.pgen.1003368] [Citation(s) in RCA: 588] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 01/21/2013] [Indexed: 02/07/2023] Open
Abstract
The long noncoding MALAT1 RNA is upregulated in cancer tissues and its elevated expression is associated with hyper-proliferation, but the underlying mechanism is poorly understood. We demonstrate that MALAT1 levels are regulated during normal cell cycle progression. Genome-wide transcriptome analyses in normal human diploid fibroblasts reveal that MALAT1 modulates the expression of cell cycle genes and is required for G1/S and mitotic progression. Depletion of MALAT1 leads to activation of p53 and its target genes. The cell cycle defects observed in MALAT1-depleted cells are sensitive to p53 levels, indicating that p53 is a major downstream mediator of MALAT1 activity. Furthermore, MALAT1-depleted cells display reduced expression of B-MYB (Mybl2), an oncogenic transcription factor involved in G2/M progression, due to altered binding of splicing factors on B-MYB pre-mRNA and aberrant alternative splicing. In human cells, MALAT1 promotes cellular proliferation by modulating the expression and/or pre-mRNA processing of cell cycle–regulated transcription factors. These findings provide mechanistic insights on the role of MALAT1 in regulating cellular proliferation. The mammalian genome encodes large number of long non protein-coding RNAs (lncRNAs). These lncRNAs are suggested to regulate key biological processes (including cellular proliferation and differentiation), and aberrant expression of these is associated with cancer. However, only a few of these lncRNAs have been functionally validated in biological or disease processes. MALAT1, an abundant nuclear-retained lncRNA, is overexpressed in several cancers, and its elevated expression has been associated with hyper-proliferation and metastasis. However, the underlying mechanism behind this deregulation and its association with cancer is poorly understood. Here, we establish the role of MALAT1 in the cell cycle pathway and propose the molecular mechanism of its function during normal cell cycle progression. MALAT1 RNA levels are differentially regulated and critical for normal cell cycle progression. Depletion of MALAT1 results in cell cycle arrest with significantly reduced cellular proliferation, simultaneously leading to activation of p53 and its target genes. Further, the accurate levels of MALAT1 in the cell are extremely crucial for expression and activity of the oncogenic transcription factor B-MYB, which is involved in G2/M progression. Our data indicates that the cancer-associated MALAT1 RNA regulates cellular proliferation by modulating the expression and/or pre-mRNA processing of cell cycle–regulated transcription factors.
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44
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Lakhotia SC. Long non-coding RNAs coordinate cellular responses to stress. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 3:779-96. [PMID: 22976942 DOI: 10.1002/wrna.1135] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Following the initial discovery of the heat shock RNA omega (hsrω) gene of Drosophila melanogaster to be non-coding (nc) and also inducible by cell stress, other stress-inducible long non-coding RNAs (lncRNA) have been described in diverse organisms. In view of the rapid sequence divergence of lncRNAs, present knowledge of stress trasncriptome is limited and fragmented. Several known stress-related lncRNAs, associated with specific nuclear speckled domains or nucleolus, provide structural base for sequestering diverse RNA-processing/regulatory proteins. Others have roles in transcriptional or translational inhibition during stress or in signaling pathways; functions of several other lncRNAs are not yet known. Most stress-related lncRNAs act primarily by modulating activity of the proteins to which they bind or by sequestering specific sets of proteins away from the active pool. A common emerging theme is that a given lncRNA targets one or more protein/s with key role/s in the cascade of events triggered by the stress and therefore has a widespread integrative effect. Since proteins associate with RNA through short sequence motifs, the overall base sequence of functionally similar ncRNAs is often not conserved except for specific motifs. The rapid evolvability of ncRNA sequences provides elegant modules for adaptability to changing environment as binding of one or the other protein to ncRNA can alter its structure and functions in distinct ways. Thus the stress-related lncRNAs act as hubs in the cellular networks to coordinate activities of the members within and between different networks to maintain cellular homeostasis for survival or to trigger cell death.
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Affiliation(s)
- Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005, India.
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45
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Tripathi V, Song DY, Zong X, Shevtsov SP, Hearn S, Fu XD, Dundr M, Prasanth KV. SRSF1 regulates the assembly of pre-mRNA processing factors in nuclear speckles. Mol Biol Cell 2012; 23:3694-706. [PMID: 22855529 PMCID: PMC3442416 DOI: 10.1091/mbc.e12-03-0206] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
SRSF1 splicing factor and nuclear-localized MALAT1 RNA influence the assembly of nuclear speckles. Depletion of SRSF1 compromises the association of splicing factors to nuclear speckles and influences the levels of other SR proteins. SRSF1 regulates RNA polymerase II–mediated transcription. The mammalian cell nucleus is compartmentalized into nonmembranous subnuclear domains that regulate key nuclear functions. Nuclear speckles are subnuclear domains that contain pre-mRNA processing factors and noncoding RNAs. Many of the nuclear speckle constituents work in concert to coordinate multiple steps of gene expression, including transcription, pre-mRNA processing and mRNA transport. The mechanism that regulates the formation and maintenance of nuclear speckles in the interphase nucleus is poorly understood. In the present study, we provide evidence for the involvement of nuclear speckle resident proteins and RNA components in the organization of nuclear speckles. SR-family splicing factors and their binding partner, long noncoding metastasis-associated lung adenocarcinoma transcript 1 RNA, can nucleate the assembly of nuclear speckles in the interphase nucleus. Depletion of SRSF1 in human cells compromises the association of splicing factors to nuclear speckles and influences the levels and activity of other SR proteins. Furthermore, on a stably integrated reporter gene locus, we demonstrate the role of SRSF1 in RNA polymerase II–mediated transcription. Our results suggest that SR proteins mediate the assembly of nuclear speckles and regulate gene expression by influencing both transcriptional and posttranscriptional activities within the cell nucleus.
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Affiliation(s)
- Vidisha Tripathi
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Eißmann M, Gutschner T, Hämmerle M, Günther S, Caudron-Herger M, Groß M, Schirmacher P, Rippe K, Braun T, Diederichs S, Zörnig M. Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biol 2012; 9:1076-87. [PMID: 22858678 PMCID: PMC3551862 DOI: 10.4161/rna.21089] [Citation(s) in RCA: 324] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The metastasis-associated lung adenocarcinoma transcript 1, MALAT1, is a long non-coding RNA (lncRNA) that has been discovered as a marker for lung cancer metastasis. It is highly abundant, its expression is strongly regulated in many tumor entities including lung adenocarcinoma and hepatocellular carcinoma as well as physiological processes, and it is associated with many RNA binding proteins and highly conserved throughout evolution. The nuclear transcript MALAT-1 has been functionally associated with gene regulation and alternative splicing and its regulation has been shown to impact proliferation, apoptosis, migration and invasion. Here, we have developed a human and a mouse knockout system to study the loss-of-function phenotypes of this important ncRNA. In human tumor cells, MALAT1 expression was abrogated using Zinc Finger Nucleases. Unexpectedly, the quantitative loss of MALAT1 did neither affect proliferation nor cell cycle progression nor nuclear architecture in human lung or liver cancer cells. Moreover, genetic loss of Malat1 in a knockout mouse model did not give rise to any obvious phenotype or histological abnormalities in Malat1-null compared with wild-type animals. Thus, loss of the abundant nuclear long ncRNA MALAT1 is compatible with cell viability and normal development.
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Affiliation(s)
| | - Tony Gutschner
- Helmholtz-University-Group “Molecular RNA Biology & Cancer”; German Cancer Research Center DKFZ & Institute of Pathology; University Hospital Heidelberg; Heidelberg, Germany
| | - Monika Hämmerle
- Helmholtz-University-Group “Molecular RNA Biology & Cancer”; German Cancer Research Center DKFZ & Institute of Pathology; University Hospital Heidelberg; Heidelberg, Germany
- Institute of Pathology; University Hospital Heidelberg; Heidelberg, Germany
| | - Stefan Günther
- Max-Planck-Institute for Heart and Lung Research; Bad Nauheim, Germany
| | - Maïwen Caudron-Herger
- Research Group Genome Organization & Function; German Cancer Research Center DKFZ & BioQuant; Heidelberg, Germany
| | - Matthias Groß
- Helmholtz-University-Group “Molecular RNA Biology & Cancer”; German Cancer Research Center DKFZ & Institute of Pathology; University Hospital Heidelberg; Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology; University Hospital Heidelberg; Heidelberg, Germany
| | - Karsten Rippe
- Research Group Genome Organization & Function; German Cancer Research Center DKFZ & BioQuant; Heidelberg, Germany
| | - Thomas Braun
- Max-Planck-Institute for Heart and Lung Research; Bad Nauheim, Germany
| | - Sven Diederichs
- Helmholtz-University-Group “Molecular RNA Biology & Cancer”; German Cancer Research Center DKFZ & Institute of Pathology; University Hospital Heidelberg; Heidelberg, Germany
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47
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Prasanth KV. Policing cells under stress: noncoding RNAs capture proteins in nucleolar detention centers. Mol Cell 2012; 45:141-2. [PMID: 22284672 DOI: 10.1016/j.molcel.2012.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In this issue of Molecular Cell, Audas et al. (2012) demonstrate that a class of stress-induced noncoding RNAs immobilizes proteins in the nucleolus in response to a specific stimulus.
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Affiliation(s)
- Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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48
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Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis. Int J Mol Sci 2011; 13:97-114. [PMID: 22312241 PMCID: PMC3269675 DOI: 10.3390/ijms13010097] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 12/02/2011] [Accepted: 12/05/2011] [Indexed: 01/22/2023] Open
Abstract
The advent of next generation sequencing revealed that a fraction of transcribed RNAs (short and long RNAs) is non-coding. Long non-coding RNAs (lncRNAs) have a crucial role in regulating gene expression and in epigenetics (chromatin and histones remodeling). LncRNAs may have different roles: gene activators (signaling), repressors (decoy), cis and trans gene expression regulators (guides) and chromatin modificators (scaffolds) without the need to be mutually exclusive. LncRNAs are also implicated in a number of diseases. The huge amount of inhomogeneous data produced so far poses several bioinformatics challenges spanning from the simple annotation to the more complex functional annotation. In this review, we report and discuss several bioinformatics resources freely available and dealing with the study of lncRNAs. To our knowledge, this is the first review summarizing all the available bioinformatics resources on lncRNAs appeared in the literature after the completion of the human genome project. Therefore, the aim of this review is to provide a little guide for biologists and bioinformaticians looking for dedicated resources, public repositories and other tools for lncRNAs functional analysis.
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49
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Meng X, Zhu D, Yang S, Wang X, Xiong Z, Zhang Y, Brachova P, Leslie KK. Cytoplasmic Metadherin (MTDH) provides survival advantage under conditions of stress by acting as RNA-binding protein. J Biol Chem 2011; 287:4485-91. [PMID: 22199357 DOI: 10.1074/jbc.c111.291518] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Overexpression of metadherin (MTDH) has been documented in many solid tumors and is implicated in metastasis and chemoresistance. MTDH has been detected at the plasma membrane as well as in the cytoplasm and nucleus, and the function of MTDH in these locales remains under investigation. In the nucleus, MTDH acts as a transcription co-factor to induce expression of chemoresistance-associated genes. However, MTDH is predominantly cytoplasmic in prostate tumors, and this localization correlates with poor prognosis. Herein, we used endometrial cancer cells as a model system to define a new role for MTDH in the cytoplasm. First, MTDH was primarily localized to the cytoplasm in endometrial cancer cells, and the N-terminal region of MTDH was required to maintain cytoplasmic localization. Next, we identified novel binding partners for cytoplasmic MTDH, including RNA-binding proteins and components of the RNA-induced silencing complex. Nucleic acids were required for the association of MTDH with these cytoplasmic proteins. Furthermore, MTDH interacted with and regulated protein expression of multiple mRNAs, such as PDCD10 and KDM6A. Depletion of cytoplasmic MTDH was associated with increased stress granule formation, reduced survival in response to chemotherapy and the tyrosine kinase inhibitor BIBF1120, Rad51 nuclear accumulation, and cell cycle arrest at G(2)/M. Finally, in vivo tumor formation was abrogated with knockdown of cytoplasmic MTDH. Taken together, our data identify a novel function for cytoplasmic MTDH as an RNA-binding protein. Our findings implicate cytoplasmic MTDH in cell survival and broad drug resistance via association with RNA and RNA-binding proteins.
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Affiliation(s)
- Xiangbing Meng
- Department of Obstetrics and Gynecology, The University of Iowa, Iowa City, Iowa 52242, USA.
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