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Richter E, Patel P, Babu JR, Wang X, Geetha T. The Importance of Sleep in Overcoming Childhood Obesity and Reshaping Epigenetics. Biomedicines 2024; 12:1334. [PMID: 38927541 PMCID: PMC11201669 DOI: 10.3390/biomedicines12061334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
The development of childhood obesity is a complex process influenced by a combination of genetic predisposition and environmental factors, such as sleep, diet, physical activity, and socioeconomic status. Long-term solutions for decreasing the risk of childhood obesity remain elusive, despite significant advancements in promoting health and well-being in school and at home. Challenges persist in areas such as adherence to interventions, addressing underlying social determinants, and individual differences in response to treatment. Over the last decade, there has been significant progress in epigenetics, along with increased curiosity in gaining insights into how sleep and lifestyle decisions impact an individual's health. Epigenetic modifications affect the expression of genes without causing changes to the fundamental DNA sequence. In recent years, numerous research studies have explored the correlation between sleep and the epigenome, giving a better understanding of DNA methylation, histone modification, and non-coding RNAs. Although significant findings have been made about the influence of sleep on epigenetics, a notable gap exists in the literature concerning sleep-related genes specifically associated with childhood obesity. Consequently, it is crucial to delve deeper into this area to enhance our understanding. Therefore, this review primarily focuses on the connection between sleep patterns and epigenetic modifications in genes related to childhood obesity. Exploring the interplay between sleep, epigenetics, and childhood obesity can potentially contribute to improved overall health outcomes. This comprehensive review encompasses studies focusing on sleep-related genes linked to obesity.
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Affiliation(s)
- Erika Richter
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
| | - Priyadarshni Patel
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jeganathan Ramesh Babu
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL 36849, USA
- Alabama Agricultural Experiment Station, Auburn University, Auburn, AL 36849, USA
| | - Xu Wang
- Alabama Agricultural Experiment Station, Auburn University, Auburn, AL 36849, USA
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Thangiah Geetha
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL 36849, USA
- Alabama Agricultural Experiment Station, Auburn University, Auburn, AL 36849, USA
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Zhang S, Wang R, Zhu X, Zhang L, Liu X, Sun L. Characteristics and expression of lncRNA and transposable elements in Drosophila aneuploidy. iScience 2023; 26:108494. [PMID: 38125016 PMCID: PMC10730892 DOI: 10.1016/j.isci.2023.108494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/28/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Aneuploidy can globally affect the expression of the whole genome, which is detrimental to organisms. Dosage-sensitive regulators usually have multiple intermolecular interactions, and changes in their stoichiometry are responsible for the dysregulation of the regulatory network. Currently, studies on noncoding genes in aneuploidy are relatively rare. We studied the characteristics and expression profiles of long noncoding RNAs (lncRNAs) and transposable elements (TEs) in aneuploid Drosophila. It is found that lncRNAs and TEs are affected by genomic imbalance and appear to be more sensitive to an inverse dosage effect than mRNAs. Several dosage-sensitive lncRNAs and TEs were detected for their expression patterns during embryogenesis, and their biological functions in the ovary and testes were investigated using tissue-specific RNAi. This study advances our understanding of the noncoding sequences in imbalanced genomes and provides a novel perspective for the study of aneuploidy-related human diseases such as cancer.
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Affiliation(s)
- Shuai Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ruixue Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xilin Zhu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Ludan Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xinyu Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lin Sun
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China
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Anoushirvani AA, Jafarian Yazdi A, Amirabadi S, Asouri SA, Shafabakhsh R, Sheida A, Hosseini Khabr MS, Jafari A, Tamehri Zadeh SS, Hamblin MR, Kalantari L, Talaei Zavareh SA, Mirzaei H. Role of non-coding RNAs in neuroblastoma. Cancer Gene Ther 2023; 30:1190-1208. [PMID: 37217790 DOI: 10.1038/s41417-023-00623-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/25/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
Neuroblastoma is known as the most prevalent extracranial malignancy in childhood with a neural crest origin. It has been widely accepted that non-coding RNAs (ncRNAs) play important roles in many types of cancer, including glioma and gastrointestinal cancers. They may regulate the cancer gene network. According to recent sequencing and profiling studies, ncRNAs genes are deregulated in human cancers via deletion, amplification, abnormal epigenetic, or transcriptional regulation. Disturbances in the expression of ncRNAs may act either as oncogenes or as anti-tumor suppressor genes, and can lead to the induction of cancer hallmarks. ncRNAs can be secreted from tumor cells inside exosomes, where they can be transferred to other cells to affect their function. However, these topics still need more study to clarify their exact roles, so the present review addresses different roles and functions of ncRNAs in neuroblastoma.
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Affiliation(s)
- Ali Arash Anoushirvani
- Department of Internal Medicine, Firoozgar Hospital, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Sanaz Amirabadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Sahar Ahmadi Asouri
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University, Kashan, Iran
| | - Rana Shafabakhsh
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University, Kashan, Iran
| | - Amirhossein Sheida
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Maryam Sadat Hosseini Khabr
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Ameneh Jafari
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, P.O. BOX: 15179/64311, Tehran, Iran
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Leila Kalantari
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
| | | | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University, Kashan, Iran.
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Villa GR, Chiocca EA. The Role of Long Noncoding Ribonucleic Acids in Glioblastoma: What the Neurosurgeon Should Know. Neurosurgery 2023; 92:1104-1111. [PMID: 36880757 DOI: 10.1227/neu.0000000000002449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/12/2023] [Indexed: 03/08/2023] Open
Abstract
A significant proportion of the human transcriptome, long noncoding RNAs (lncRNAs) play pivotal roles in several aspects of glioblastoma (GBM) pathophysiology including proliferation, invasion, radiation and temozolomide resistance, and immune modulation. The majority of lncRNAs exhibit tissue- and tumor-specific expression, lending them to be attractive targets for therapeutic translation. In recent years, unprecedented progress has been made toward our understanding of lncRNA in GBM. In this review, we discuss the function of lncRNAs, including specific lncRNAs that have critical roles in key aspects of GBM pathophysiology, and potential clinical relevance of lncRNAs for patients with GBM.
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Affiliation(s)
- Genaro Rodriguez Villa
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston , Massachusetts , USA
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Dimond A, Van de Pette M, Taylor-Bateman V, Brown K, Sardini A, Whilding C, Feytout A, Prinjha RK, Merkenschlager M, Fisher AG. Drug-induced loss of imprinting revealed using bioluminescent reporters of Cdkn1c. Sci Rep 2023; 13:5626. [PMID: 37024615 PMCID: PMC10079848 DOI: 10.1038/s41598-023-32747-6] [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: 12/15/2022] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
Genomic imprinting is an epigenetically mediated mechanism that regulates allelic expression of genes based upon parent-of-origin and provides a paradigm for studying epigenetic silencing and release. Here, bioluminescent reporters for the maternally-expressed imprinted gene Cdkn1c are used to examine the capacity of chromatin-modifying drugs to reverse paternal Cdkn1c silencing. Exposure of reporter mouse embryonic stem cells (mESCs) to 5-Azacytidine, HDAC inhibitors, BET inhibitors or GSK-J4 (KDM6A/B inhibitor) relieved repression of paternal Cdkn1c, either selectively or by inducing biallelic effects. Treatment of reporter fibroblasts with HDAC inhibitors or GSK-J4 resulted in similar paternal Cdkn1c activation, whereas BET inhibitor-induced loss of imprinting was specific to mESCs. Changes in allelic expression were generally not sustained in dividing cultures upon drug removal, indicating that the underlying epigenetic memory of silencing was maintained. In contrast, Cdkn1c de-repression by GSK-J4 was retained in both mESCs and fibroblasts following inhibitor removal, although this impact may be linked to cellular stress and DNA damage. Taken together, these data introduce bioluminescent reporter cells as tools for studying epigenetic silencing and disruption, and demonstrate that Cdkn1c imprinting requires distinct and cell-type specific chromatin features and modifying enzymes to enact and propagate a memory of silencing.
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Affiliation(s)
- Andrew Dimond
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
| | - Mathew Van de Pette
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Victoria Taylor-Bateman
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Karen Brown
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Alessandro Sardini
- Whole Animal Physiology and Imaging, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Chad Whilding
- Microscopy Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Amelie Feytout
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Rab K Prinjha
- Immunology and Epigenetics Research Unit, Research, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, Herts, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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Peng L, Wang C, Tian X, Zhou L, Li K. Finding lncRNA-Protein Interactions Based on Deep Learning With Dual-Net Neural Architecture. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3456-3468. [PMID: 34587091 DOI: 10.1109/tcbb.2021.3116232] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The identification of lncRNA-protein interactions (LPIs) is important to understand the biological functions and molecular mechanisms of lncRNAs. However, most computational models are evaluated on a unique dataset, thereby resulting in prediction bias. Furthermore, previous models have not uncovered potential proteins (or lncRNAs) interacting with a new lncRNA (or protein). Finally, the performance of these models can be improved. In this study, we develop a Deep Learning framework with Dual-net Neural architecture to find potential LPIs (LPI-DLDN). First, five LPI datasets are collected. Second, the features of lncRNAs and proteins are extracted by Pyfeat and BioTriangle, respectively. Third, these features are concatenated as a vector after dimension reduction. Finally, a deep learning model with dual-net neural architecture is designed to classify lncRNA-protein pairs. LPI-DLDN is compared with six state-of-the-art LPI prediction methods (LPI-XGBoost, LPI-HeteSim, LPI-NRLMF, PLIPCOM, LPI-CNNCP, and Capsule-LPI) under four cross validations. The results demonstrate the powerful LPI classification performance of LPI-DLDN. Case study analyses show that there may be interactions between RP11-439E19.10 and Q15717, and between RP11-196G18.22 and Q9NUL5. The novelty of LPI-DLDN remains, integrating various biological features, designing a novel deep learning-based LPI identification framework, and selecting the optimal LPI feature subset based on feature importance ranking.
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Abstract
As sequencing technologies improved, new classes of genes were uncovered. Initially, many of these were considered non-functional given their low protein-coding potential but have now emerged as important regulators of biological processes. One of the new classes of genes are called long noncoding RNAs (lncRNAs). LncRNAs are the largest group of transcribed RNA. As their name suggests, they are non-protein coding genes. To differentiate them from other smaller, noncoding RNAs, lncRNAs are transcripts whose length are greater than 200 nucleotides. According to GENCODE Release 38, there are approximately 18,000 lncRNAs, of which only 4% have a known function. Of the lncRNAs characterized, many of them play regulatory roles in many biological processes, including regulation of gene expression, alternative splicing, chromatin modification, protein activity, and posttranscriptional mechanisms. Compared to protein coding genes, lncRNAs show high cell type specificity. Many lncRNAs have been shown to be expressed in distinct immune cell populations and play RNA-mediated immune-regulatory roles. Many aspects of the immune response, including the duration, magnitude, and subsequent return to homeostasis are carefully controlled. Dysregulation of lncRNAs can result in an uncontrolled immune response, which can lead to a variety of immune-related diseases. This introduction aims to summarize the chapters highlighting the discovery of lncRNAs, their role in the immune response, and their functional characterization, either through interaction with DNA, RNA, and/or proteins in distinct immune cell populations or cells implicated in immune-related diseases. Additionally, the immune regulatory role of lncRNAs will be covered, and how lncRNA localization, sequence and secondary structure can inform function. Delving into this largely unexplored field can identify lncRNAs as potential therapeutic targets.
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Liao W, Xu N, Zhang H, Liao W, Wang Y, Wang S, Zhang S, Jiang Y, Xie W, Zhang Y. Persistent high glucose induced EPB41L4A-AS1 inhibits glucose uptake via GCN5 mediating crotonylation and acetylation of histones and non-histones. Clin Transl Med 2022; 12:e699. [PMID: 35184403 PMCID: PMC8858623 DOI: 10.1002/ctm2.699] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/12/2021] [Accepted: 12/20/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Persistent hyperglycemia decreases the sensitivity of insulin-sensitive organs to insulin, owing to which cells fail to take up and utilize glucose, which exacerbates the progression of type 2 diabetes mellitus (T2DM). lncRNAs' abnormal expression is reported to be associated with the progression of diabetes and plays a significant role in glucose metabolism. Herein, we study the detailed mechanism underlying the functions of lncRNA EPB41L4A-AS1in T2DM. METHODS Data from GEO datasets were used to analyze the expression of EPB41L4A-AS1 between insulin resistance or type 2 diabetes patients and the healthy people. Gene expression was evaluated by qRT-PCR and western blotting. Glucose uptake was measured by Glucose Uptake Fluorometric Assay Kit. Glucose tolerance of mice was detected by Intraperitoneal glucose tolerance tests. Cell viability was assessed by CCK-8 assay. The interaction between EPB41L4A-AS1 and GCN5 was explored by RNA immunoprecipitation, RNA pull-down and RNA-FISH combined immunofluorescence. Oxygen consumption rate was tested by Seahorse XF Mito Stress Test. RESULTS EPB41L4A-AS1 was abnormally increased in the liver of patients with T2DM and upregulated in the muscle cells of patients with insulin resistance and in T2DM cell models. The upregulation was associated with increased TP53 expression and reduced glucose uptake. Mechanistically, through interaction with GCN5, EPB41L4A-AS1 regulated histone H3K27 crotonylation in the GLUT4 promoter region and nonhistone PGC1β acetylation, which inhibited GLUT4 transcription and suppressed glucose uptake by muscle cells. In contrast, EPB41L4A-AS1 binding to GCN5 enhanced H3K27 and H3K14 acetylation in the TXNIP promoter region, which activated transcription by promoting the recruitment of the transcriptional activator MLXIP. This enhanced GLUT4/2 endocytosis and further suppressed glucose uptake. CONCLUSION Our study first showed that the EPB41L4A-AS1/GCN5 complex repressed glucose uptake via targeting GLUT4/2 and TXNIP by regulating histone and nonhistone acetylation or crotonylation. Since a weaker glucose uptake ability is one of the major clinical features of T2DM, the inhibition of EPB41L4A-AS1 expression seems to be a potentially effective strategy for drug development in T2DM treatment.
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Affiliation(s)
- Weijie Liao
- State Key Laboratory of Chemical OncogenomicsTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- Key Lab in Healthy Science and TechnologyDivision of Life ScienceTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- School of Life SciencesTsinghua UniversityBeijingP. R. China
| | - Naihan Xu
- State Key Laboratory of Chemical OncogenomicsTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- Key Lab in Healthy Science and TechnologyDivision of Life ScienceTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- Open FIESTA CenterTsinghua UniversityShenzhenP. R. China
| | - Haowei Zhang
- State Key Laboratory of Chemical OncogenomicsTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- Key Lab in Healthy Science and TechnologyDivision of Life ScienceTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- School of Life SciencesTsinghua UniversityBeijingP. R. China
| | - Weifang Liao
- College of life science and technologyWuhan Polytechnic UniversityWuhanP. R. China
| | - Yanzhi Wang
- State Key Laboratory of Chemical OncogenomicsTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- Key Lab in Healthy Science and TechnologyDivision of Life ScienceTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- School of Life SciencesTsinghua UniversityBeijingP. R. China
| | - Songmao Wang
- State Key Laboratory of Chemical OncogenomicsTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- Key Lab in Healthy Science and TechnologyDivision of Life ScienceTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- School of Life SciencesTsinghua UniversityBeijingP. R. China
| | - Shikuan Zhang
- State Key Laboratory of Chemical OncogenomicsTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- Key Lab in Healthy Science and TechnologyDivision of Life ScienceTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- School of Life SciencesTsinghua UniversityBeijingP. R. China
| | - Yuyang Jiang
- State Key Laboratory of Chemical OncogenomicsTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
| | - Weidong Xie
- State Key Laboratory of Chemical OncogenomicsTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- Key Lab in Healthy Science and TechnologyDivision of Life ScienceTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- Open FIESTA CenterTsinghua UniversityShenzhenP. R. China
| | - Yaou Zhang
- State Key Laboratory of Chemical OncogenomicsTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- Key Lab in Healthy Science and TechnologyDivision of Life ScienceTsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhenP. R. China
- Open FIESTA CenterTsinghua UniversityShenzhenP. R. China
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Rato L, Sousa ACA. The Impact of Endocrine-Disrupting Chemicals in Male Fertility: Focus on the Action of Obesogens. J Xenobiot 2021; 11:163-196. [PMID: 34940512 PMCID: PMC8709303 DOI: 10.3390/jox11040012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/12/2021] [Accepted: 11/23/2021] [Indexed: 12/11/2022] Open
Abstract
The current scenario of male infertility is not yet fully elucidated; however, there is increasing evidence that it is associated with the widespread exposure to endocrine-disrupting chemicals (EDCs), and in particular to obesogens. These compounds interfere with hormones involved in the regulation of metabolism and are associated with weight gain, being also able to change the functioning of the male reproductive axis and, consequently, the testicular physiology and metabolism that are pivotal for spermatogenesis. The disruption of these tightly regulated metabolic pathways leads to adverse reproductive outcomes. The permanent exposure to obesogens has raised serious health concerns. Evidence suggests that obesogens are one of the leading causes of the marked decline of male fertility and key players in shaping the future health outcomes not only for those who are directly exposed but also for upcoming generations. In addition to the changes that lead to inefficient functioning of the male gametes, obesogens induce alterations that are “imprinted” on the genes of the male gametes, establishing a link between generations and contributing to the transmission of defects. Unveiling the molecular mechanisms by which obesogens induce toxicity that may end-up in epigenetic modifications is imperative. This review describes and discusses the suggested molecular targets and potential mechanisms for obesogenic–disrupting chemicals and the subsequent effects on male reproductive health.
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Affiliation(s)
- Luís Rato
- Health School of the Polytechnic Institute of Guarda, 6300-035 Guarda, Portugal
- Correspondence: (L.R.); (A.C.A.S.)
| | - Ana C. A. Sousa
- Department of Biology, School of Science and Technology, University of Évora, 7006-554 Évora, Portugal
- Comprehensive Health Research Centre (CHRC), University of Évora, 7000-671 Évora, Portugal
- Correspondence: (L.R.); (A.C.A.S.)
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Thepsuwan T, Rungrassamee W, Sangket U, Whankaew S, Sathapondecha P. Long non-coding RNA profile in banana shrimp, Fenneropenaeus merguiensis and the potential role of lncPV13 in vitellogenesis. Comp Biochem Physiol A Mol Integr Physiol 2021; 261:111045. [PMID: 34358684 DOI: 10.1016/j.cbpa.2021.111045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/30/2021] [Accepted: 07/30/2021] [Indexed: 01/04/2023]
Abstract
The long non-coding RNAs (lncRNAs) have been known to play important roles in several biological processes as well as in reproduction. This study aimed to identify lncRNA in ovary female banana shrimp, Fenneropenaeus merguiensis, and investigate the potential role of lncPV13 in the vitellogenesis. After the in silico identification of the ovarian transcriptome, a total of 24,733 putative lncRNAs were obtained, and only 147 putative lncRNAs were significantly differentially expressed among the ovarian development stages. To validate the in silico identification of lncRNAs, the 16 lncRNAs with the highest differential expression in the transcriptome analysis were evaluated by RT-qPCR. The 6 lncRNAs showed higher expression levels in the mature stage than in the previtellogenic stage and were found in several tissues such as in eyestalks, brains, thoracic ganglia, gills, and muscle. Furthermore, most candidate lncRNAs were amplifiable in Litopenaeus vannamei's and Penaeus monodon's DNA but not in Macrobrachium rosenbergii's DNA, suggesting some lncRNAs are expressed in a species-specific manner among penaeid shrimp. In this study, the lncPV13 was investigated for its vitellogenin regulating function by RNA interference. The result indicates that the lncPV13 expression was suppressed in the ovary on day 7 after the injection of double-stranded RNA specific to lncPV13 (dslncPV13), while vitellogenin (Vg) expression was significantly decreased. In contrast, the gonad inhibiting hormone (GIH) expression was significantly increased in the lncPV13 knockdown shrimp. However, the oocyte proliferation was not significantly different between control and lncPV13 knockdown shrimp. This suggests that lncPV13 regulate Vg synthesis through GIH inhibition. Finally, our findings provide lncRNA information and potential lncRNAs involved in the vitellogenesis of female banana shrimp.
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Affiliation(s)
- Timpika Thepsuwan
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Wanilada Rungrassamee
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Rd., Khlong Luang, Pathum Thani 12120, Thailand
| | - Unitsa Sangket
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand
| | - Sukhuman Whankaew
- Department of Plant Science, Faculty of Technology and Community Development, Thaksin University, Phatthalung Campus, Phatthalung 93210, Thailand
| | - Ponsit Sathapondecha
- Center for Genomics and Bioinformatics Research, Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand.
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Han S, Qi Y, Xu Y, Wang M, Wang J, Wang J, Yuan M, Jia Y, Ma X, Wang Y, Liu X. lncRNA DLEU2 promotes gastric cancer progression through ETS2 via targeting miR-30a-5p. Cancer Cell Int 2021; 21:376. [PMID: 34261460 PMCID: PMC8278695 DOI: 10.1186/s12935-021-02074-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 07/05/2021] [Indexed: 12/24/2022] Open
Abstract
Background Gastric cancer (GC) remains an important cancer worldwide. Further understanding of the molecular mechanisms of gastric carcinogenesis will enhance the diagnosis and treatment of GC. Methods The expression of DLEU2 and ETS2 was analyzed in several GC cell lines using GEPIA online analyze, qRT-PCR and immunohistochemistry. The biological behavior of GC cells was detected by CCK8, clone formation, transwell, wound healing, western blot, and flow cytometry assay. More in-depth mechanisms were studied. Results DLEU2 was significantly up-regulated in GC tissues and cell lines. The expression of DLEU2 was significantly associated with pathological grading and TNM stage of GC patients. Furthermore, knockdown of DLEU2 inhibited the proliferation, migration, and invasion of AGS and MKN-45 cells, while overexpression of DLEU2 promoted the proliferation, migration, and invasion of HGC-27 cells. MiR-30a-5p could directly bind to the 3’ UTR region of ETS2. Moreover, DLEU2 bound to miR-30a-5p through the same binding site, which facilitated the expression of ETS2. Knockdown of DLEU2 reduced the protein level of intracellular ETS2 and inhibited AKT phosphorylation, while overexpression of DLEU2 induced the expression of ETS2 and the phosphorylation of AKT. ETS2 was highly expressed in GC tissues. The expression of ETS2 was significantly associated with age, pathological grading, and TNM stage. ETS2 overexpression promoted cell proliferation and migration of AGS and MKN-45 cells. Furthermore, ETS2 overexpression rescued cell proliferation and migration inhibition induced by DLEU2 down-regulation and miR-30a-5p up-regulation in AGS and MKN-45 cells. Conclusions DLEU2 is a potential molecular target for GC treatment.
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Affiliation(s)
- Shuyi Han
- Jinan Central Hospital Affiliated to Shandong First Medical University, 115 Jie Fang Road, Jinan, 250013, Shandong, People's Republic of China.,Jinan Central Hospital Affiliated to Shandong University, 115 Jie Fang Road, Jinan, 250013, Shandong, P.R. China
| | - Yan Qi
- Department of Clinical Laboratory, Qingdao Municipal Hospital, Qingdao, Shandong, People's Republic of China
| | - Yihui Xu
- Jinan Central Hospital Affiliated to Shandong First Medical University, 115 Jie Fang Road, Jinan, 250013, Shandong, People's Republic of China
| | - Min Wang
- Jinan Central Hospital Affiliated to Shandong First Medical University, 115 Jie Fang Road, Jinan, 250013, Shandong, People's Republic of China
| | - Jun Wang
- Jinan Central Hospital Affiliated to Shandong First Medical University, 115 Jie Fang Road, Jinan, 250013, Shandong, People's Republic of China
| | - Jing Wang
- Binzhou Medical University, Binzhou, Shandong, People's Republic of China
| | - Mingjie Yuan
- Binzhou Medical University, Binzhou, Shandong, People's Republic of China
| | - Yanfei Jia
- Jinan Central Hospital Affiliated to Shandong First Medical University, 115 Jie Fang Road, Jinan, 250013, Shandong, People's Republic of China
| | - Xiaoli Ma
- Jinan Central Hospital Affiliated to Shandong First Medical University, 115 Jie Fang Road, Jinan, 250013, Shandong, People's Republic of China
| | - Yunshan Wang
- Jinan Central Hospital Affiliated to Shandong First Medical University, 115 Jie Fang Road, Jinan, 250013, Shandong, People's Republic of China
| | - Xiangdong Liu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated To Shandong University, Jinan, Shandong, People's Republic of China.
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12
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Li Y, Li J, Chen L, Xu L. The Roles of Long Non-coding RNA in Osteoporosis. Curr Stem Cell Res Ther 2021; 15:639-645. [PMID: 32357819 DOI: 10.2174/1574888x15666200501235735] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/20/2020] [Accepted: 03/25/2020] [Indexed: 12/17/2022]
Abstract
The Human Genome Project (HGP) announced in 2001 that it had sequenced the entire human genome, yielding nearly complete human DNA. About 98.5 percent of the human genome has been found to be non-coding sequences. Long non-coding RNA (lncRNA) is a non-coding RNA with a length between 200 and 100,000 nucleotide units. Because of shallow research on lncRNA, it was believed that it had no biological functions, but exists as a by-product of the transcription process. With the development of high-throughput sequencing technology, studies have shown that lncRNA plays important roles in many processes by participating in epigenetics, transcription, translation and protein modification. Current researches have shown that lncRNA also has an important part in the pathogenesis of osteoporosis. Osteoporosis is a common disorder of bone metabolism, also a major medical and socioeconomic challenge worldwide. It is characterized by a systemic reduction in bone mass and microstructure changes, which increases the risk of brittle fractures. It is more common in postmenopausal women and elderly men. However, the roles of lncRNA and relevant mechanisms in osteoporosis remain unclear. Based on this background, we hereby review the roles of lncRNA in osteoporosis, and how it influences the functions of osteoblasts and osteoclasts, providing reference to clinical diagnosis, treatment and prognosis of osteoporosis.
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Affiliation(s)
- Ying Li
- Lingnan Medical Research Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jinglan Li
- Lingnan Medical Research Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Leilei Chen
- Department of Orthopaedics & Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Liangliang Xu
- Lingnan Medical Research Center, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
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13
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Mushimiyimana I, Tomas Bosch V, Niskanen H, Downes NL, Moreau PR, Hartigan K, Ylä-Herttuala S, Laham-Karam N, Kaikkonen MU. Genomic Landscapes of Noncoding RNAs Regulating VEGFA and VEGFC Expression in Endothelial Cells. Mol Cell Biol 2021; 41:e0059420. [PMID: 33875575 PMCID: PMC8224232 DOI: 10.1128/mcb.00594-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/29/2020] [Accepted: 04/03/2021] [Indexed: 12/26/2022] Open
Abstract
Vascular endothelial growth factors (VEGFs) are best known as key regulators of angiogenesis and lymphangiogenesis. Although VEGFs have been promising therapeutic targets for various cardiovascular diseases, their regulatory landscape in endothelial cells remains elusive. Several studies have highlighted the involvement of noncoding RNAs (ncRNAs) in the modulation of VEGF expression. In this study, we investigated the role of two classes of ncRNAs, long ncRNAs (lncRNAs) and enhancer RNAs (eRNAs), in the transcriptional regulation of VEGFA and VEGFC. By integrating genome-wide global run-on sequencing (GRO-Seq) and chromosome conformation capture (Hi-C) data, we identified putative lncRNAs and eRNAs associated with VEGFA and VEGFC genes in endothelial cells. A subset of the identified putative enhancers demonstrated regulatory activity in a reporter assay. Importantly, we demonstrate that deletion of enhancers and lncRNAs by CRISPR/Cas9 promoted significant changes in VEGFA and VEGFC expression. Transcriptome sequencing (RNA-Seq) data from lncRNA deletions showed downstream factors implicated in VEGFA- and VEGFC-linked pathways, such as angiogenesis and lymphangiogenesis, suggesting functional roles for these lncRNAs. Our study uncovers novel lncRNAs and eRNAs regulating VEGFA and VEGFC that can be targeted to modulate the expression of these important molecules in endothelial cells.
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Affiliation(s)
- Isidore Mushimiyimana
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Vanesa Tomas Bosch
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nicholas L. Downes
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Pierre R. Moreau
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Seppo Ylä-Herttuala
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
| | - Nihay Laham-Karam
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Minna U. Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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14
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Hao Y, Li C, Zhao T, Liu H. Long Non-Coding RNA GATA3-AS1 Promotes 5-Fluorouracil Resistance of Ovarian Cancer via Mediating miR-6771-3p/SOX4 Target Axis. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ovarian cancer (OC) ranks as the 5th highest cause of cancer-related deaths worldwide. Long non-coding RNAs (lncRNAs) exert significant effects on chemotherapy resistance. The effects of lncRNA GATA3-AS1 on the 5-Fluorouracil (5-FU) resistance in ovarian carcinoma were explored in the
current study. The results showed that GATA3-AS1 was highly expressed in OC tissues and 5-FU resistant OC cells. Moreover, GATA3-AS1 knockdown reduced 50% inhibitory concentration (IC50) of 5-Fluorouracil and promoted cell apoptosis, while GATA3-AS1-overexpression showed the opposite effect.
In vivo experiment and murine xenograft assay indicated GATA3-AS1 knockdown inhibited neoplasm growth, promoted cell apoptosis, and altered the expression level of apoptosis-associated proteins. GATA3-AS1 promoted SOX4 expression, a well-known transcription factor regulating apoptosis,
via targeting miR-6771-3p. In summary, our findings suggested GATA3-AS1 was associated with OC 5-Fluorouracil viaregulating miR-6771-3p/SOX4, providing novel insights into OC chemoresistance.
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Affiliation(s)
- Yafei Hao
- Department of Gynecology, Taian City Central Hospital, Taian 271000, PR China
| | - Changzhou Li
- Reproductive Medicine Centre, Taian City Central Hospital, Taian 271000, PR China
| | - Teng Zhao
- Department of Gynecology, Ningyang County People’s Hospital, Taian 271400, PR China
| | - Hansheng Liu
- Department of Gynecology, Taian City Central Hospital, Taian 271000, PR China
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15
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Dogan F, Forsyth NR. Telomerase Regulation: A Role for Epigenetics. Cancers (Basel) 2021; 13:cancers13061213. [PMID: 33802026 PMCID: PMC8000866 DOI: 10.3390/cancers13061213] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Maintenance of telomeres is a fundamental step in human carcinogenesis and is primarily regulated by telomerase and the human telomerase reverse transcriptase gene (TERT). Improved understanding of the transcriptional control of this gene may provide potential therapeutic targets. Epigenetic modifications are a prominent mechanism to control telomerase activity and regulation of the TERT gene. TERT-targeting miRNAs have been widely studied and their function explained through pre-clinical in vivo model-based validation studies. Further, histone deacetylase inhibitors are now in pre and early clinical trials with significant clinical success. Importantly, TERT downregulation through epigenetic modifications including TERT promoter methylation, histone deacetylase inhibitors, and miRNA activity might contribute to clinical study design. This review provides an overview of the epigenetic mechanisms involved in the regulation of TERT expression and telomerase activity. Abstract Telomerase was first described by Greider and Blackburn in 1984, a discovery ultimately recognized by the Nobel Prize committee in 2009. The three decades following on from its discovery have been accompanied by an increased understanding of the fundamental mechanisms of telomerase activity, and its role in telomere biology. Telomerase has a clearly defined role in telomere length maintenance and an established influence on DNA replication, differentiation, survival, development, apoptosis, tumorigenesis, and a further role in therapeutic resistance in human stem and cancer cells including those of breast and cervical origin. TERT encodes the catalytic subunit and rate-limiting factor for telomerase enzyme activity. The mechanisms of activation or silencing of TERT remain open to debate across somatic, cancer, and stem cells. Promoter mutations upstream of TERT may promote dysregulated telomerase activation in tumour cells but additional factors including epigenetic, transcriptional and posttranscriptional modifications also have a role to play. Previous systematic analysis indicated methylation and mutation of the TERT promoter in 53% and 31%, respectively, of TERT expressing cancer cell lines supporting the concept of a key role for epigenetic alteration associated with TERT dysregulation and cellular transformation. Epigenetic regulators including DNA methylation, histone modification, and non-coding RNAs are now emerging as drivers in the regulation of telomeres and telomerase activity. Epigenetic regulation may be responsible for reversible silencing of TERT in several biological processes including development and differentiation, and increased TERT expression in cancers. Understanding the epigenetic mechanisms behind telomerase regulation holds important prospects for cancer treatment, diagnosis and prognosis. This review will focus on the role of epigenetics in telomerase regulation.
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Affiliation(s)
- Fatma Dogan
- The Guy Hilton Research Laboratories, School of Pharmacy and Bioengineering, Faculty of Medicine and Health Sciences, Keele University, Stoke on Trent ST4 7QB, UK;
| | - Nicholas R. Forsyth
- The Guy Hilton Research Laboratories, School of Pharmacy and Bioengineering, Faculty of Medicine and Health Sciences, Keele University, Stoke on Trent ST4 7QB, UK;
- School of Medicine, Tongji University, Shanghai 200092, China
- Correspondence:
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16
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Ebrahimpour A, Sarfi M, Rezatabar S, Tehrani SS. Novel insights into the interaction between long non-coding RNAs and microRNAs in glioma. Mol Cell Biochem 2021; 476:2317-2335. [PMID: 33582947 DOI: 10.1007/s11010-021-04080-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/25/2021] [Indexed: 02/07/2023]
Abstract
Glioma is the most common brain tumor of the central nervous system. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been identified to play a vital role in the initiation and progression of glioma, including tumor cell proliferation, survival, apoptosis, invasion, and therapy resistance. New documents emerged, which indicated that the interaction between long non-coding RNAs and miRNAs contributes to the tumorigenesis and pathogenesis of glioma. LncRNAs can act as competing for endogenous RNA (ceRNA), and molecular sponge/deregulator in regulating miRNAs. These interactions stimulate different molecular signaling pathways in glioma, including the lncRNAs/miRNAs/Wnt/β-catenin molecular signaling pathway, the lncRNAs/miRNAs/PI3K/AKT/mTOR molecular signaling pathway, the lncRNAs-miRNAs/MAPK kinase molecular signaling pathway, and the lncRNAs/miRNAs/NF-κB molecular signaling pathway. In this paper, the basic roles and molecular interactions of the lncRNAs and miRNAs pathway glioma were summarized to better understand the pathogenesis and tumorigenesis of glioma.
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Affiliation(s)
- Anahita Ebrahimpour
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Sarfi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Setareh Rezatabar
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Sadra Samavarchi Tehrani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran. .,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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17
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PRKAR1B-AS2 Long Noncoding RNA Promotes Tumorigenesis, Survival, and Chemoresistance via the PI3K/AKT/mTOR Pathway. Int J Mol Sci 2021; 22:ijms22041882. [PMID: 33668685 PMCID: PMC7918312 DOI: 10.3390/ijms22041882] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/23/2021] [Accepted: 01/28/2021] [Indexed: 12/19/2022] Open
Abstract
Many long noncoding RNAs have been implicated in tumorigenesis and chemoresistance; however, the underlying mechanisms are not well understood. We investigated the role of PRKAR1B-AS2 long noncoding RNA in ovarian cancer (OC) and chemoresistance and identified potential downstream molecular circuitry underlying its action. Analysis of The Cancer Genome Atlas OC dataset, in vitro experiments, proteomic analysis, and a xenograft OC mouse model were implemented. Our findings indicated that overexpression of PRKAR1B-AS2 is negatively correlated with overall survival in OC patients. Furthermore, PRKAR1B-AS2 knockdown-attenuated proliferation, migration, and invasion of OC cells and ameliorated cisplatin and alpelisib resistance in vitro. In proteomic analysis, silencing PRKAR1B-AS2 markedly inhibited protein expression of PI3K-110α and abrogated the phosphorylation of PDK1, AKT, and mTOR, with no significant effect on PTEN. The RNA immunoprecipitation detected a physical interaction between PRKAR1B-AS2 and PI3K-110α. Moreover, PRKAR1B-AS2 knockdown by systemic administration of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine nanoparticles loaded with PRKAR1B-AS2–specific small interfering RNA enhanced cisplatin sensitivity in a xenograft OC mouse model. In conclusion, PRKAR1B-AS2 promotes tumor growth and confers chemoresistance by modulating the PI3K/AKT/mTOR pathway. Thus, targeting PRKAR1B-AS2 may represent a novel therapeutic approach for the treatment of OC patients.
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18
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Abstract
Long noncoding RNAs (lncRNAs) are involved in many regulatory mechanisms in practically every step of the RNA cycle, from transcription to RNA stability and translation. They are a highly heterogeneous class of molecules in terms of site of production, interaction networks, and functions. More and more databases are available on the web with the aim to make public information about lncRNA accessible to the scientific community. Here we review the most interesting resources with the purpose to organize a compendium of useful tools to interrogate before studying a lncRNA of interest.
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19
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Seale AP, Malintha GHT, Celino-Brady FT, Head T, Belcaid M, Yamaguchi Y, Lerner DT, Baltzegar DA, Borski RJ, Stoytcheva ZR, Breves JP. Transcriptional regulation of prolactin in a euryhaline teleost: Characterisation of gene promoters through in silico and transcriptome analyses. J Neuroendocrinol 2020; 32:e12905. [PMID: 32996203 PMCID: PMC8612711 DOI: 10.1111/jne.12905] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 07/31/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022]
Abstract
The sensitivity of prolactin (Prl) cells of the Mozambique tilapia (Oreochromis mossambicus) pituitary to variations in extracellular osmolality enables investigations into how osmoreception underlies patterns of hormone secretion. Through the actions of their main secretory products, Prl cells play a key role in supporting hydromineral balance of fishes by controlling the major osmoregulatory organs (ie, gill, intestine and kidney). The release of Prl from isolated cells of the rostral pars distalis (RPD) occurs in direct response to physiologically relevant reductions in extracellular osmolality. Although the particular signal transduction pathways that link osmotic conditions to Prl secretion have been identified, the processes that underlie hyposmotic induction of prl gene expression remain unknown. In this short review, we describe two distinct tilapia gene loci that encode Prl177 and Prl188 . From our in silico analyses of prl177 and prl188 promoter regions (approximately 1000 bp) and a transcriptome analysis of RPDs from fresh water (FW)- and seawater (SW)-acclimated tilapia, we propose a working model for how multiple transcription factors link osmoreceptive processes with adaptive patterns of prl177 and prl188 gene expression. We confirmed via RNA-sequencing and a quantitative polymerase chain reaction that multiple transcription factors emerging as predicted regulators of prl gene expression are expressed in the RPD of tilapia. In particular, gene transcripts encoding pou1f1, stat3, creb3l1, pbxip1a and stat1a were highly expressed; creb3l1, pbxip1a and stat1a were elevated in fish acclimated to SW vs FW. Combined, our in silico and transcriptome analyses set a path for resolving how adaptive patterns of Prl secretion are achieved via the integration of osmoreceptive processes with the control of prl gene transcription.
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Affiliation(s)
- Andre P. Seale
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai’i at Mānoa, Honolulu, HI, USA
| | | | - Fritzie T. Celino-Brady
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai’i at Mānoa, Honolulu, HI, USA
| | - Tony Head
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai’i at Mānoa, Honolulu, HI, USA
| | - Mahdi Belcaid
- Hawai’i Institute of Marine Biology, University of Hawai’i at Mānoa, Kaneohe, HI, USA
| | - Yoko Yamaguchi
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue, Japan
| | - Darren T. Lerner
- University of Hawai’i Sea Grant College Program, University of Hawai’i at Mānoa, Honolulu, HI, USA
| | - David A. Baltzegar
- Genomic Sciences Laboratory, Office of Research and Innovation, North Carolina State University, Raleigh, NC, USA
| | - Russell J. Borski
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Zoia R. Stoytcheva
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai’i at Mānoa, Honolulu, HI, USA
| | - Jason P. Breves
- Department of Biology, Skidmore College, Saratoga Springs, NY, USA
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20
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Yuan L, Yu L, Zhang J, Zhou Z, Li C, Zhou B, Hu X, Xu G, Tang Y. Long non‑coding RNA H19 protects H9c2 cells against hypoxia‑induced injury by activating the PI3K/AKT and ERK/p38 pathways. Mol Med Rep 2020; 21:1709-1716. [PMID: 32319634 PMCID: PMC7057826 DOI: 10.3892/mmr.2020.10978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 07/12/2019] [Indexed: 12/18/2022] Open
Abstract
Myocardial ischemia/reperfusion injury often leads to adverse cardiovascular outcomes due to severe hypoxia. The present study aimed to evaluate the effects and mechanism of long non-coding RNA H19 (H19) on rat H9c2 cells with hypoxia-induced injury. H9c2 cells were infected with lentiviruses to express H19 or H19-targeting short hairpin RNA (shRNA), or their respective controls, at a multiplicity of infection of 1:100. H19 expression was determined by reverse transcription-quantitative PCR. Hypoxic injury was induced and assessed by analyzing the level of apoptosis, the cell cycle distribution and the mitochondrial membrane potential using flow cytometry in the different groups. The expression of the PI3K/AKT and the ERK/p38 signaling pathways were analyzed using western blotting. It was found that hypoxia stimulated apoptosis, induced G1 phase cell cycle arrest and increased the mitochondrial depolarization rate in H9c2 cells. When compared with the hypoxic model group, the H19 overexpression group had a significantly reduced rate of apoptosis (P=0.016), a smaller G1 population and a higher S phase population (P=0.018 and P=0.031, respectively), and a reduced mitochondrial depolarization rate (P=0.036). By contrast, the H19 shRNA group exhibited the opposite trends, suggesting that hypoxia-induced injury was alleviated by the overexpression of H19 and was aggravated by the knockdown of H19. The present mechanistic studies revealed that H19 may decrease hypoxia-induced cell injury by activating the PI3K/AKT and ERK/p38 pathways. The results of the present study suggested that H19 may alleviate hypoxia-induced myocardial cell injury through the activation of the PI3K/AKT and ERK/p38 pathways.
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Affiliation(s)
- Linhui Yuan
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Leitao Yu
- Department of Thyroid Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jing Zhang
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhidong Zhou
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Chang Li
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Bin Zhou
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Xiaolan Hu
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Guohai Xu
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yanhua Tang
- Department of Cardiac Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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21
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Ahmad A, Lin H, Shatabda S. Locate-R: Subcellular localization of long non-coding RNAs using nucleotide compositions. Genomics 2020; 112:2583-2589. [PMID: 32068122 DOI: 10.1016/j.ygeno.2020.02.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 11/11/2019] [Accepted: 02/12/2020] [Indexed: 12/12/2022]
Abstract
Knowledge of the sub-cellular localization of the most diverse class of transcribed RNA, long non-coding RNAs (lncRNAs) will lead us to identify different types of cancers and other diseases as lncRNAs play key role in related cellular functions. In recent days with the exponential growth of known records, it becomes essential to establish new machine learning based techniques to identify the new one due to faster and cheaper solutions provided compared to laboratory methods. In this paper, we propose Locate-R, a novel method for predicting the sub-cellular location of lncRNAs. We have used only n-gapped l-mer composition and l-mer composition as features and select best 655 features to build the model. This model is based locally deep support vector machines which significantly enhance the prediction accuracy with respect to exiting state-of-the-art methods. Our predictor is readily available for use as a stand-alone web application from: http://locate-r.azurewebsites.net/.
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Affiliation(s)
- Ahsan Ahmad
- Department of Computer Science and Engineering, United International University, Plot 2, United City, Madani Avenue, Satarkul, Badda, Dhaka 1212, Bangladesh
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, China
| | - Swakkhar Shatabda
- Department of Computer Science and Engineering, United International University, Plot 2, United City, Madani Avenue, Satarkul, Badda, Dhaka 1212, Bangladesh.
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22
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Xia Q, Li J, Yang Z, Zhang D, Tian J, Gu B. Long non-coding RNA small nucleolar RNA host gene 7 expression level in prostate cancer tissues predicts the prognosis of patients with prostate cancer. Medicine (Baltimore) 2020; 99:e18993. [PMID: 32049793 PMCID: PMC7035107 DOI: 10.1097/md.0000000000018993] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Long non-coding small nucleolar RNA host gene 7 (lncRNA SNHG7) is located on chromosome 9q34.3 in length of 984 bp. SNHG7 has been found to play the role of oncogene in varieties of cancers, and its dysregulation has been found to be associated with carcinogenesis and progression. In the present study, we examined the expression of SNHG7 in prostate cancer tissues and in paired adjacent normal prostate tissues, and we further explored the clinical significance and prognostic value of SNHG7 in prostate cancer patients.A total of 127 prostate cancer tissues were collected from prostate cancer patients who underwent radical prostatectomy between April 2011 and March 2019 at the department of urology, Pudong New Area People's Hospital. Real-time quantitative polymerase chain reaction experiment was performed to detect the relative expressions of SNHG7 in the prostate cancer tissues and normal prostate tissues. The Kaplan-Meier method was used to create survival curves and the log-rank test was used to determine statistical significance. A Cox proportional hazard analysis was used to evaluate the prognostic factors in univariate and multivariate analyses.Compared with paired adjacent normal prostatic tissues, SNHG7 expression was increased in prostate cancer tissues (P < .001). Increased SNHG7 expression correlated with Gleason score (P = .021), bone metastasis (P = .013), pelvic lymph node metastasis (P = .008), and TNM stage (P = .007). Multivariate Cox regression analyses revealed increased SNHG7 expression was independently associated with a poor prognosis of prostate cancer patients (hazard ratio [HR] = 2.839, 95% confidence interval [CI] = 1.921-8.382, P = .038).This study showed that lncRNA-SNHG7 was overexpressed in prostate cancer tissues, and it might contributes to the development and progression of prostate cancer. Furthermore, the SNHG7 expression was associated with the prognosis of prostate cancer, suggesting a potential target for the treatment and prognosis of prostate cancer. Nevertheless, the underlying modulatory mechanism by which SNHG7 aggravates prostate cancer progression need to be further studied.
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Gabriel AF, Costa MC, Enguita FJ. Interactions Among Regulatory Non-coding RNAs Involved in Cardiovascular Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:79-104. [PMID: 32285406 DOI: 10.1007/978-981-15-1671-9_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Non-coding RNAs (ncRNAs) are important regulatory players in human cells that have been shown to modulate different cellular processes and biological functions through controlling gene expression, being also involved in pathological conditions such as cardiovascular diseases. Among them, long non-coding RNAs (lncRNAs) and circular (circRNAs) could act as competing endogenous RNAs (ceRNAs) sequestering other ncRNAs. This entangled network of interactions has been reported to trigger the decay of the targeted ncRNAs having important roles in gene regulation. Growing evidences have been demonstrated that the regulatory mechanism underlying the crosstalk between different ncRNA species, namely lncRNAs, circRNAs and miRNAs has also an important role in the pathophysiological processes of cardiovascular diseases. In this chapter, the main regulatory relationship among lncRNAs, circRNAs and miRNAs were summarized and their role in the control and development of cardiovascular diseases was highlighted.
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Affiliation(s)
- André F Gabriel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Marina C Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal. .,Cardiomics Unit, Centro de Cardiologia da Universidade de Lisboa (CCUL), Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
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Wang Q, Han CL, Wang KL, Sui YP, Li ZB, Chen N, Fan SY, Shimabukuro M, Wang F, Meng FG. Integrated analysis of exosomal lncRNA and mRNA expression profiles reveals the involvement of lnc-MKRN2-42:1 in the pathogenesis of Parkinson's disease. CNS Neurosci Ther 2019; 26:527-537. [PMID: 31814304 PMCID: PMC7163584 DOI: 10.1111/cns.13277] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/14/2019] [Accepted: 11/22/2019] [Indexed: 12/19/2022] Open
Abstract
Background Parkinson's disease (PD) is a common movement disorder for which diagnosis mainly depends on the medical history and clinical symptoms. Exosomes are now considered an additional mechanism for intercellular communication, allowing cells to exchange proteins, lipids, and genetic material. Long noncoding (lnc) RNA in exosomes plays a critical role in many diseases, including neurodegenerative disease. Aim To study expression differences for lncRNAs in peripheral blood exosomes of PD patients compared with healthy individuals and to look for lncRNAs that might be related to the pathogenesis of PD. Materials and Methods We recruited PD patients along with age‐ and sex‐matched healthy individuals as healthy controls and evaluated levels of lncRNAs extracted from exosomes in plasma samples via next‐generation sequencing and real‐time quantitative PCR. Correlation analysis was conducted for the clinical characteristics of PD patients and the expression of selected lncRNAs. Results We found 15 upregulated and 24 downregulated exosomal lncRNAs in the PD group. According to bioinformatics analyses, we chose lnc‐MKRN2‐42:1 for further study. Interestingly, lnc‐MKRN2‐42:1 was positively correlated with the MDS‐UPDRS III score for PD patients. Conclusion Our study suggested that lnc‐MKRN2‐42:1 may be involved in the occurrence and development of PD.
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Affiliation(s)
- Qiao Wang
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Chun-Lei Han
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Kai-Liang Wang
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Yun-Peng Sui
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Zhi-Bao Li
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Ning Chen
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shi-Ying Fan
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Michitomo Shimabukuro
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Neurostimulation, Beijing, China
| | - Feng Wang
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Fan-Gang Meng
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Neurostimulation, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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25
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Zhang H, Shi G, Hu Q, Zhang H, Zheng M, Jiang K, Gu M. Transcriptional dissection of differentially expressed long non-coding RNAs and messenger RNAs reveals the potential molecular mechanism after kidney transplantation. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:458. [PMID: 31700894 DOI: 10.21037/atm.2019.08.60] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Background Kidney transplantation has given benefits to patients, although the associated genetic mechanisms are unclear. The present study aimed to understand the changes in gene expression and genetic pathways after kidney transplantation with the administration of immunosuppressive drugs. Methods The transcriptome data of blood samples from kidney transplantation recipients, obtained by RNA-seq, were reannotated to a more complete human genome (GRCh38/hg38). We compared the differentially expressed genes (DEGs) at pretransplant and 1 week, 3 months and 6 months posttransplant; researched the temporal variation of the DEGs; and constructed a long non-coding RNA (lncRNA)-messenger RNA (mRNA) network. Results We found that compared to that at pretransplantation, 1,766 genes and 3,530 genes were upregulated and downregulated, respectively, at 1 week after kidney transplantation, and the number of DEGs declined over time. These DEGs were separated into 16 clusters, and the temporal variation expression was established by the average expression of the DEGs. A pathway analysis suggested that the immune reaction was attenuated and that the expression of ribosome-related proteins was reduced. Conclusions The lncRNA-mRNA network had 235 connections between 138 lncRNAs and 170 mRNAs. This work generated a gene profile based on temporal variation and revealed a significantly altered lncRNA-mRNA axis contributing to molecular regulation, suggesting the potential gene mechanism of kidney transplantation and the effects of immunosuppressive drugs.
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Affiliation(s)
- Hengcheng Zhang
- Department of Urology, Jiangsu Provincial Hospital, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Guodong Shi
- Pancreas Center, Department of General Surgery, Jiangsu Provincial Hospital, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.,Pancreas Institute of Nanjing Medical University, Nanjing 210029, China
| | - Qingqiao Hu
- Department of Nuclear Medicine, Jiangsu Provincial Hospital, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Henglu Zhang
- Department of Endocrinology and Metabolism, Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huaian 223001, China
| | - Ming Zheng
- Department of Urology, Jiangsu Provincial Hospital, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Kuirong Jiang
- Pancreas Center, Department of General Surgery, Jiangsu Provincial Hospital, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China.,Pancreas Institute of Nanjing Medical University, Nanjing 210029, China
| | - Min Gu
- Department of Urology, Jiangsu Provincial Hospital, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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Su ZD, Huang Y, Zhang ZY, Zhao YW, Wang D, Chen W, Chou KC, Lin H. iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC. Bioinformatics 2019; 34:4196-4204. [PMID: 29931187 DOI: 10.1093/bioinformatics/bty508] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/19/2018] [Indexed: 12/20/2022] Open
Abstract
Motivation Long non-coding RNAs (lncRNAs) are a class of RNA molecules with more than 200 nucleotides. They have important functions in cell development and metabolism, such as genetic markers, genome rearrangements, chromatin modifications, cell cycle regulation, transcription and translation. Their functions are generally closely related to their localization in the cell. Therefore, knowledge about their subcellular locations can provide very useful clues or preliminary insight into their biological functions. Although biochemical experiments could determine the localization of lncRNAs in a cell, they are both time-consuming and expensive. Therefore, it is highly desirable to develop bioinformatics tools for fast and effective identification of their subcellular locations. Results We developed a sequence-based bioinformatics tool called 'iLoc-lncRNA' to predict the subcellular locations of LncRNAs by incorporating the 8-tuple nucleotide features into the general PseKNC (Pseudo K-tuple Nucleotide Composition) via the binomial distribution approach. Rigorous jackknife tests have shown that the overall accuracy achieved by the new predictor on a stringent benchmark dataset is 86.72%, which is over 20% higher than that by the existing state-of-the-art predictor evaluated on the same tests. Availability and implementation A user-friendly webserver has been established at http://lin-group.cn/server/iLoc-LncRNA, by which users can easily obtain their desired results. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhen-Dong Su
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan Huang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhao-Yue Zhang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Ya-Wei Zhao
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dong Wang
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wei Chen
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Department of Physics, School of Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China.,Gordon Life Science Institute, Boston, MA, USA
| | - Kuo-Chen Chou
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Gordon Life Science Institute, Boston, MA, USA
| | - Hao Lin
- Key Laboratory for Neuro-Information of Ministry of Education, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.,Gordon Life Science Institute, Boston, MA, USA
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Zhang L, Mao J. Long-Chain Noncoding RNA PVT1 Gene Polymorphisms Are Associated with the Risk and Prognosis of Colorectal Cancer in the Han Chinese Population. Genet Test Mol Biomarkers 2019; 23:728-736. [PMID: 31509024 DOI: 10.1089/gtmb.2019.0078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: To investigate the association between long-chain noncoding RNA (lncRNA) plasmacytoma variant translocation 1 (PVT1) gene polymorphisms and the risk and prognosis of colorectal cancer (CRC) in the Han Chinese population. Methods: A cohort of 225 Han Chinese CRC patients and 225 healthy controls was analyzed for the PVT1 gene genotypes at the loci rs1221464062, rs1366023633, rs1252200336, and rs1273526412. The levels of PVT1 mRNA, hsa-miR-455-5p, and hsa-miR-455-3p in both cancerous tissues and paracancerous normal tissues of the CRC patients were determined by reverse transcription polymerase chain reaction. The survival rate of CRC patients was recorded after 3 years of follow-up. Results: The risk of developing CRC in subjects with the ID genotype of the PVT1 gene locus rs1252200336 was 2.71 times higher compared with the type II genotype; and the D allele was a risk factor for CRC. The survival of CRC patients with the ID/DD genotypes of the PVT1 gene rs1252200336 locus was significantly lower compared with the II genotype. In both the cancerous tissues and the paracancerous normal tissues of CRC patients, the level of lncRNA PVT1 was negatively correlated with the hsa-miR-455-5p and hsa-miR-455-3p levels. In subjects carrying the ID/DD genotypes of the PVT1 gene rs1252200336 locus, the level of the lncRNA PVT1 in cancerous tissues was significantly higher compared with the II genotype, whereas the hsa-miR-455-3p level was significantly lower compared with the II genotype. Conclusion: The PVT1 gene rs1252200336 locus polymorphisms are associated with the risk of developing CRC in the Han Chinese population. The rs1252200336 locus deletion mutation (D) may impact the binding of hsa-miR-455-5p to the lncRNA PVT1 and its role in the development and progression of CRC.
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Affiliation(s)
- Lei Zhang
- Department of Anorectal Surgery, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jiehong Mao
- Department of Anorectal Surgery, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
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28
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Hennessy EJ. Cardiovascular Disease and Long Noncoding RNAs: Tools for Unraveling the Mystery Lnc-ing RNA and Phenotype. ACTA ACUST UNITED AC 2019; 10:e001556. [PMID: 28768752 DOI: 10.1161/circgenetics.117.001556] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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29
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Singh A, Shannon CP, Kim YW, Yang CX, Balshaw R, Cohen Freue GV, Gauvreau GM, FitzGerald JM, Boulet LP, O'Byrne PM, Tebbutt SJ. Novel Blood-based Transcriptional Biomarker Panels Predict the Late-Phase Asthmatic Response. Am J Respir Crit Care Med 2019; 197:450-462. [PMID: 29087730 DOI: 10.1164/rccm.201701-0110oc] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE The allergen inhalation challenge is used in clinical trials to test the efficacy of new treatments in attenuating the late-phase asthmatic response (LAR) and associated airway inflammation in subjects with allergic asthma. However, not all subjects with allergic asthma develop the LAR after allergen inhalation. Blood-based transcriptional biomarkers that can identify such individuals may help in subject recruitment for clinical trials as well as provide novel molecular insights. OBJECTIVES To identify blood-based transcriptional biomarker panels that can predict an individual's response to allergen inhalation challenge. METHODS We applied RNA sequencing to total RNA from whole blood (n = 36) collected before and after allergen challenge and generated both genome-guided and de novo datasets: genes, gene-isoforms (University of California, Santa Cruz, UCSC Genome Browser), Ensembl, and Trinity. Candidate biomarker panels were validated using the NanoString platform in an independent cohort of 33 subjects. MEASUREMENTS AND MAIN RESULTS The Trinity biomarker panel consisting of known and novel biomarker transcripts had an area under the receiver operating characteristic curve of greater than 0.70 in both the discovery and validation cohorts. The Trinity biomarker panel was useful in predicting the response of subjects that elicited different responses (accuracy between 0.65 and 0.71) and subjects that elicit a dual response (accuracy between 0.70 and 0.75) upon repeated allergen inhalation challenges. CONCLUSIONS Interestingly, the biomarker panel containing novel transcripts successfully validated compared with panels with known, well-characterized genes. These biomarker-blood tests may be used to identify subjects with asthma who develop the LAR, and may also represent members of novel molecular mechanisms that can be targeted for therapy.
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Affiliation(s)
- Amrit Singh
- 1 Centre for Heart Lung Innovation, St. Paul's Hospital.,3 Department of Pathology and Laboratory Medicine.,2 Prevention of Organ Failure Centre of Excellence, Vancouver, British Columbia, Canada
| | - Casey P Shannon
- 2 Prevention of Organ Failure Centre of Excellence, Vancouver, British Columbia, Canada
| | - Young Woong Kim
- 1 Centre for Heart Lung Innovation, St. Paul's Hospital.,2 Prevention of Organ Failure Centre of Excellence, Vancouver, British Columbia, Canada
| | - Chen Xi Yang
- 1 Centre for Heart Lung Innovation, St. Paul's Hospital.,2 Prevention of Organ Failure Centre of Excellence, Vancouver, British Columbia, Canada
| | - Robert Balshaw
- 4 Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Gail M Gauvreau
- 6 Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - J Mark FitzGerald
- 8 Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,7 Vancouver Coastal Health Research Institute, Vancouver General Hospital, Vancouver, British Columbia, Canada; and
| | | | - Paul M O'Byrne
- 6 Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Scott J Tebbutt
- 1 Centre for Heart Lung Innovation, St. Paul's Hospital.,8 Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,2 Prevention of Organ Failure Centre of Excellence, Vancouver, British Columbia, Canada
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Razavi M, Ghorbian S. Up-regulation of long non-coding RNA-PCAT-1 promotes invasion and metastasis in esophageal squamous cell carcinoma. EXCLI JOURNAL 2019; 18:422-428. [PMID: 31338011 PMCID: PMC6635722 DOI: 10.17179/excli2018-1847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 06/14/2019] [Indexed: 12/16/2022]
Abstract
Long non-coding RNA prostate cancer associated transcript-1 ncRNA (lncRNA-PCAT-1) plays an important role in the progression of prostate cancer. The present investigation was aimed to evaluate the potential roles of the lncRNA-PCAT-1 gene expression changes in esophageal squamous cell carcinoma (ESCC) between Iranian population. In the case-control investigation, we have analyzed a total of 150 fresh tissue samples, compromising of 75 cancerous tissues and 75 adjacent normal tissues from patients with ESCC. We used quantitative Real-time polymerase chain reaction (qRT-PCR) to evaluate the lncRNA-PCAT-1 gene expression levels in ESCC patients and correlation between the lncRNA-PCAT-1 expression changes and clinical characteristics. Our findings showed that the lncRNA-PCAT-1 gene was up-regulated in cancerous tissues compared with the adjacent non-cancerous tissues (p=0.0016). In addition, the results revealed a significant correlation between up-regulating of lncRNA-PCAT-1 and hot liquid drinking (p =0.017). These findings offer the potential roles of lncRNA-PCAT-1 in the pathogenesis of ESCC and may consider as a candidate prognostic biomarker for ESCC in an Iranian population.
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Affiliation(s)
- Maryam Razavi
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
| | - Saeid Ghorbian
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
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Lin T, Hou PF, Meng S, Chen F, Jiang T, Li ML, Shi ML, Liu JJ, Zheng JN, Bai J. Emerging Roles of p53 Related lncRNAs in Cancer Progression: A Systematic Review. Int J Biol Sci 2019; 15:1287-1298. [PMID: 31223287 PMCID: PMC6567798 DOI: 10.7150/ijbs.33218] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/12/2019] [Indexed: 12/11/2022] Open
Abstract
p53 is the major mediator of the tumor suppressor response. It participates in apoptosis and senescence and can respond to DNA damage. As a crucial sequence-specific transcription factor, p53 regulates the expression of many genes, such as small noncoding RNAs (ncRNAs), microRNAs, and long ncRNAs (lncRNAs). Given the emergence of novel and high-throughput sequencing technologies, many lncRNAs have been discovered. LncRNAs may function as vital gene regulators in a variety of biological processes through extensive mechanisms. Recently, lncRNAs have been demonstrated to be associated with the p53 regulatory pathway. In this review, we discuss the current and fast growing knowledge about the influence of lncRNAs to the p53 signaling pathway, the different mechanisms by which they affect gene expression in cancer. Our findings show that p53-associated lncRNAs may be used as biomarkers for cancer diagnosis or targets for disease therapy.
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Affiliation(s)
- Tian Lin
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Ping-Fu Hou
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Sen Meng
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Fang Chen
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Tao Jiang
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Min-Le Li
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Mei-Lin Shi
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jin-Jin Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Jun-Nian Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
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Machtinger R, Zhong J, Mansur A, Adir M, Racowsky C, Hauser R, Brennan K, Karlsson O, Baccarelli AA. Placental lncRNA Expression Is Associated With Prenatal Phthalate Exposure. Toxicol Sci 2019; 163:116-122. [PMID: 29385630 DOI: 10.1093/toxsci/kfy013] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Phthalates are endocrine-disrupting chemicals that can cross the placenta and affect the fetal epigenome. Among various epigenetic regulators of gene expression, long noncoding RNAs (lncRNAs) are important players that may also be involved in the manifestation of endocrine-disrupting chemical toxicity. We sought to explore the association between maternal urinary phthalate metabolite concentrations and lncRNA expression in human placenta to better understand potential mechanisms through which lncRNAs participate in mediating phthalate toxicity. Ten patients with uncomplicated dichorionic diamniotic twin pregnancies at term were included in this study. Urinary (n = 10) and placenta samples (n = 20) were collected for all participants. Urinary samples were analyzed for 15 phthalate metabolites and 2 phthalate alternative metabolites. Real-time PCR arrays were used to identify and quantify 87 lncRNAs from the placental samples. We tested the Spearman correlation matrix to compare prenatal phthalate measures against placental lncRNA levels. lncRNA levels showed large variations across samples, with no significant differences in lncRNA expression within twin pairs. Mono-(carboxynonyl) phthalate demonstrated consistently strong correlations with most lncRNAs. The strongest correlation was observed between mono-hydroxyisobutyl phthalate and LOC91450 (Rspearman = 0.88, p < .001). This correlation remained significant after Bonferroni adjustment. Other strong correlations were observed between mono-isobutyl phthalate, DPP10 and HOTTIP (Rspearman = -0.91, p < .001). AIRN, DACT3.AS1, DLX6, DPP10, HOTTIP, LOC143666, and LOC91450 were strongly correlated with the greatest number of phthalate metabolites. Further studies are needed to validate these results and understand if the altered expression of lncRNAs in human placenta has clinical significance.
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Affiliation(s)
- Ronit Machtinger
- Sheba Medical Center, Ramat-Gan and Sackler School of Medicine, Tel-Aviv University, Israel
| | - Jia Zhong
- Department of Environmental Health Sciences, Columbia University, Mailman School of Public Health, New York City, New York, USA
| | - Abdallah Mansur
- Sheba Medical Center, Ramat-Gan and Sackler School of Medicine, Tel-Aviv University, Israel
| | - Michal Adir
- Sheba Medical Center, Ramat-Gan and Sackler School of Medicine, Tel-Aviv University, Israel
| | - Catherine Racowsky
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Russ Hauser
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Kasey Brennan
- Department of Environmental Health Sciences, Columbia University, Mailman School of Public Health, New York City, New York, USA
| | - Oskar Karlsson
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia University, Mailman School of Public Health, New York City, New York, USA
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Choi JY, Shin D, Lee HJ, Oh JD. Comparison of long noncoding RNA between muscles and adipose tissues in Hanwoo beef cattle. Anim Cells Syst (Seoul) 2019; 23:50-58. [PMID: 30834159 PMCID: PMC6394308 DOI: 10.1080/19768354.2018.1512522] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/01/2018] [Accepted: 08/03/2018] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate the expression of mRNA and can affect various biological processes and phenotypes. Currently, studies of lncRNAs in cattle are under way, but their exact function for several tissues has not yet been established. Hanwoo cattle (Bos taurus coreanae) have inhabited the Korean peninsula for about 6000 years and are one of the representative domesticated animals in Korea. As a result of intensive breeding, the meat of Hanwoo cattle is high in marbling content and is preferred by Koreans and other East Asian people. In this study, the expression of lncRNAs was identified in 36 samples from skeletal muscle and three adipose tissues (intramuscular, subcutaneous, and omental) of nine Hanwoo individuals. We identified 76 tissue-specific lncRNAs for each of the four tissues using the differences in expression levels. Through QTL information, we could identify 12 lncRNAs associated with shear force and six lncRNAs associated with body weight, which are two important traits in the Hanwoo population breeding strategy. By the physical position comparison of lncRNA and Bovine transcripts information, we could identify 11 lncRNAs that were in bovine transcripts, and four of the 11 genes related to transcripts of lncRNAs were biologically associated with muscle function. We believe this Hanwoo lncRNAs study will help reveal the lncRNA role in the physiological mechanisms of these four tissues.
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Affiliation(s)
- Jae-Young Choi
- The Animal Molecular Genetics and Breeding Center, Chonbuk National University, Jeonju, Republic of Korea
| | - Donghyun Shin
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju, Republic of Korea
| | - Hyun-Jeong Lee
- Animal Nutritional & Physiology Team, National Institute of Animal Science, Wanju, Republic of Korea
| | - Jae-Don Oh
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju, Republic of Korea
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Song Y, Miao C, Wang J. LncRNA ZEB1-AS1 inhibits renal fibrosis in diabetic nephropathy by regulating the miR-217/MAFB axis. RSC Adv 2019; 9:30389-30397. [PMID: 35557748 PMCID: PMC9088285 DOI: 10.1039/c9ra05602e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022] Open
Abstract
Diabetic nephropathy (DN) is a common chronic microvascular complication of diabetes, characterized by the deposition of extracellular matrix (ECM) proteins.
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Affiliation(s)
- Yan Song
- Department of Nephrology
- People's Hospital of Rizhao
- Rizhao
- China
| | - Chunxia Miao
- Department of Nephrology
- People's Hospital of Rizhao
- Rizhao
- China
| | - Jianwen Wang
- Department of Nephrology
- People's Hospital of Rizhao
- Rizhao
- China
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LncRNAs in TGF-β-Driven Tissue Fibrosis. Noncoding RNA 2018; 4:ncrna4040026. [PMID: 30287731 PMCID: PMC6315857 DOI: 10.3390/ncrna4040026] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/22/2018] [Accepted: 09/28/2018] [Indexed: 02/06/2023] Open
Abstract
Transforming growth factor-β (TGF-β) is a crucial mediator in tissue fibrosis that promotes accumulation of extracellular matrix (ECM), myofibroblasts to epithelial–mesenchymal transition (EMT), endothelial-mesenchymal transition (EndoMT), and apoptosis via canonical and noncanonical signaling pathways. In the past decades, a number of microRNAs have been reported to participate in TGF-β-mediated tissue scarring; however, the roles of long noncoding RNAs (lncRNAs) in fibrogenesis remain largely unknown. Recently, emerging evidence has shown that lncRNAs are involved in the development of different diseases, including cancer, autoimmune diseases, cardiovascular diseases, and fibrotic diseases. In this review, we summarize the current updates of lncRNAs in TGF-β1-driven tissue fibrosis and discuss their therapeutic potential for the treatment of chronic fibrotic diseases.
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LncRNA-NR_033515 promotes proliferation, fibrogenesis and epithelial-to-mesenchymal transition by targeting miR-743b-5p in diabetic nephropathy. Biomed Pharmacother 2018; 106:543-552. [DOI: 10.1016/j.biopha.2018.06.104] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 01/10/2023] Open
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Burris HH, Just AC, Haviland MJ, Neo DT, Baccarelli AA, Dereix AE, Brennan KJ, Rodosthenous RS, Ralston SJ, Hecht JL, Hacker MR. Long noncoding RNA expression in the cervix mid-pregnancy is associated with the length of gestation at delivery. Epigenetics 2018; 13:742-750. [PMID: 30045669 DOI: 10.1080/15592294.2018.1503490] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Infants born preterm are at increased risk of multiple morbidities and mortality. Why some women deliver preterm remains poorly understood. Prior studies have shown that cervical microRNA expression and DNA methylation are associated with the length of gestation. However, no study has examined the role of long noncoding RNAs (lncRNAs) in the cervix during pregnancy. To determine whether expression of lncRNAs is associated with length of gestation at delivery, we analyzed RNA from cervical swabs obtained from 78 women during pregnancy (mean 15.5, SD 5.0, weeks of gestation) who were participating in the Spontaneous Prematurity and Epigenetics of the Cervix (SPEC) Study in Boston, MA, USA. We used a PCR-based platform and found that 9 lncRNAs were expressed in at least 50% of the participants. Of these, a doubling of the expression of TUG1, TINCR, and FALEC was associated with shorter lengths of gestation at delivery [2.8 (95% CI: 0.31, 5.2); 3.3 (0.22, 6.3); and 4.5 (7.3, 1.6) days shorter respectively]. Of the lncRNAs analyzed, none was statistically associated with preterm birth, but expression of FALEC was 2.6-fold higher in women who delivered preterm vs. term (P = 0.051). These findings demonstrate that lncRNAs can be measured in cervical samples obtained during pregnancy and are associated with subsequent length of gestation at delivery. Further, this study supports future work to replicate these findings in other cohorts and perform mechanistic studies to determine the role of lncRNAs in the cervix during pregnancy.
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Affiliation(s)
- Heather H Burris
- a Department of Neonatology, Beth Israel Deaconess Medical Center, Department of Pediatrics , Harvard Medical School , Boston , MA , USA.,b Department of Obstetrics, Gynecology and Reproductive Biology, Beth Israel Deaconess Medical Center , Harvard Medical School , Boston , MA , USA.,c Department of Environmental Health , Harvard TH Chan School of Public Health , Boston , MA , USA.,d Department of Pediatrics , Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
| | - Allan C Just
- e Department of Environmental Medicine & Public Health , Icahn School of Medicine at Mount Sinai , NY , NY , USA
| | - Miriam J Haviland
- b Department of Obstetrics, Gynecology and Reproductive Biology, Beth Israel Deaconess Medical Center , Harvard Medical School , Boston , MA , USA
| | - Dayna T Neo
- b Department of Obstetrics, Gynecology and Reproductive Biology, Beth Israel Deaconess Medical Center , Harvard Medical School , Boston , MA , USA
| | - Andrea A Baccarelli
- f Department of Environmental Health Sciences , Columbia University Mailman School of Public Health , NY , NY , USA
| | - Alexandra E Dereix
- f Department of Environmental Health Sciences , Columbia University Mailman School of Public Health , NY , NY , USA
| | - Kasey J Brennan
- f Department of Environmental Health Sciences , Columbia University Mailman School of Public Health , NY , NY , USA
| | - Rodosthenis S Rodosthenous
- g Cardiology Division, Department of Medicine , Massachusetts General Hospital, Harvard Medical School , Boston , MA , USA
| | - Steven J Ralston
- h Department of Obstetrics and Gynecology , Pennsylvania Hospital, University of Pennsylvania Perelman School of Medicine , Philadelphia , PA , USA
| | - Jonathan L Hecht
- i Department of Pathology, Beth Israel Deaconess Medical Center , Harvard Medical School , Boston , MA , USA
| | - Michele R Hacker
- b Department of Obstetrics, Gynecology and Reproductive Biology, Beth Israel Deaconess Medical Center , Harvard Medical School , Boston , MA , USA.,j Department of Epidemiology , Harvard TH Chan School of Public Health , Boston , MA , USA
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Abstract
Long noncoding RNAs have been implicated in neuropathy. Here, we identify and validate a long noncoding RNA, MRAK009713, as the primary regulator of neuropathic pain in chronic constriction injury (CCI) rats. MRAK009713 expression was markedly increased in CCI rats associated with enhanced pain behaviors, and small interfering RNA against MRAK009713 significantly reduced both mechanical and thermal hyperalgesia in the CCI rats. MRAK009713 is predicted to interact with the nociceptive P2X3 receptor by CatRAPID, a bioinformatics technology. Overexpression of MRAK009713 markedly increased expression of P2X3 in the dorsal root ganglia of the control rats, and MRAK009713 small interfering RNA significantly inhibited the P2X3 expression in the dorsal root ganglia of the CCI rats. MRAK009713 directly interacted with the P2X3 protein heterologously expressed in the human embryonic kidney (HEK) 293 cells and potentiated P2X3 receptor function. Thus, MRAK009713 is a novel positive regulator of neuropathic pain in rats through regulating the expression and function of the P2X3 receptor.
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Wang Y, Zhang J. Identification of differential expression lncRNAs in gastric cancer using transcriptome sequencing and bioinformatics analyses. Mol Med Rep 2018; 17:8189-8195. [PMID: 29693709 PMCID: PMC5983993 DOI: 10.3892/mmr.2018.8889] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 07/28/2017] [Indexed: 01/17/2023] Open
Abstract
The current study aimed to identify novel long non-coding RNAs (lncRNAs) associated with gastric cancer (GC). Transcriptome sequencing of the lncRNAs and mRNAs from GC tissues and normal adjacent tissues was performed. The data were analyzed using bioinformatics analysis, specifically analysis of differentially expressed lncRNAs and mRNA, target gene prediction and functional enrichment analysis. A total of 1,181 differentially expressed mRNA and 390 differentially expressed lncRNAs were identified. The targets of upregulated lncRNAs were significantly enriched in functions associated with collagen fibril organization, whereas the downregulated lncRNA were significantly associated with ion transmembrane transport and regulation of membrane potential. A total of 7 lncRNAs were verified by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Following RT-qPCR validation, AC016735.2, AP001626.1, RP11-400N13.3 and RP11-243M5.2 were considered to be consistent with the prediction of the bioinformatics analysis. Transcriptome sequencing and RT-qPCR experiments identified 4 lncRNAs, including AC016735.2, AP001626.1, RP11-400N13.3 and RP11-243M5.2 to have an important role in the carcinogenesis of GC.
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Affiliation(s)
- Yiyi Wang
- Department of Laboratory Medicine, Shanghai Shuguang Hospital Affiliated with Shanghai University of TCM, Shanghai 200021, P.R. China
| | - Jue Zhang
- Department of Laboratory Medicine, Shanghai Shuguang Hospital Affiliated with Shanghai University of TCM, Shanghai 200021, P.R. China
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40
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Abstract
Sleep deprivation disrupts the lives of millions of people every day and has a profound impact on the molecular biology of the brain. These effects begin as changes within a neuron, at the DNA and RNA level, and result in alterations in neuronal plasticity and dysregulation of many cognitive functions including learning and memory. The epigenome plays a critical role in regulating gene expression in the context of memory storage. In this review article, we begin by describing the effects of epigenetic alterations on the regulation of gene expression, focusing on the most common epigenetic mechanisms: (i) DNA methylation; (ii) histone modifications; and (iii) non-coding RNAs. We then discuss evidence suggesting that sleep loss impacts the epigenome and that these epigenetic alterations might mediate the changes in cognition seen following disruption of sleep. The link between sleep and the epigenome is only beginning to be elucidated, but clear evidence exists that epigenetic alterations occur following sleep deprivation. In the future, these changes to the epigenome could be utilized as biomarkers of sleep loss or as therapeutic targets for sleep-related disorders.
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Affiliation(s)
- Marie E Gaine
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Snehajyoti Chatterjee
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Ted Abel
- Department of Molecular Physiology and Biophysics, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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The aryl hydrocarbon receptor regulates the expression of TIPARP and its cis long non-coding RNA, TIPARP-AS1. Biochem Biophys Res Commun 2018; 495:2356-2362. [DOI: 10.1016/j.bbrc.2017.12.113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/20/2017] [Indexed: 12/11/2022]
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Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Hermoso Pulido T, Guigo R, Johnson R. LncATLAS database for subcellular localization of long noncoding RNAs. RNA (NEW YORK, N.Y.) 2017; 23:1080-1087. [PMID: 28386015 PMCID: PMC5473142 DOI: 10.1261/rna.060814.117] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/31/2017] [Indexed: 05/04/2023]
Abstract
The subcellular localization of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localization of newly discovered lncRNAs involves time-consuming and costly experimental methods. We have created "lncATLAS," a comprehensive resource of lncRNA localization in human cells based on RNA-sequencing data sets. Altogether, 6768 GENCODE-annotated lncRNAs are represented across various compartments of 15 cell lines. We introduce relative concentration index (RCI) as a useful measure of localization derived from ensemble RNA-seq measurements. LncATLAS is accessible through an intuitive and informative webserver, from which lncRNAs of interest are accessed using identifiers or names. Localization is presented across cell types and organelles, and may be compared to the distribution of all other genes. Publication-quality figures and raw data tables are automatically generated with each query, and the entire data set is also available to download. LncATLAS makes lncRNA subcellular localization data available to the widest possible number of researchers. It is available at lncatlas.crg.eu.
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Affiliation(s)
- David Mas-Ponte
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Joana Carlevaro-Fita
- Department of Clinical Research, University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
| | - Emilio Palumbo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Toni Hermoso Pulido
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Catalonia, Spain
| | - Rory Johnson
- Department of Clinical Research, University of Bern, 3008 Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital and University of Bern, 3010 Bern, Switzerland
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Chen SW, Zhu J, Ma J, Zhang JL, Zuo S, Chen GW, Wang X, Pan YS, Liu YC, Wang PY. Overexpression of long non-coding RNA H19 is associated with unfavorable prognosis in patients with colorectal cancer and increased proliferation and migration in colon cancer cells. Oncol Lett 2017; 14:2446-2452. [PMID: 28781681 DOI: 10.3892/ol.2017.6390] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/21/2017] [Indexed: 01/07/2023] Open
Abstract
Long non-coding RNA-imprinted maternally expressed transcript (non-protein coding) (H19) has been previously identified to be involved in the development of a number of types of cancer. However, the function of H19 in the pathogenesis of colorectal cancer remains unclear. The expression level of H19 in colorectal tumor tissues, and the association between H19 expression and clinicopathological variables and prognosis was investigated in the present study. In addition, the effect of H19 overexpression on viability, migration and epithelial-mesenchymal transition (EMT) of colon cancer cells was investigated in HCT-116 and SW-480 cells. The results of the present study suggest that overexpression of H19 is associated with decreased recurrence-free survival and overall survival rates in patients with colorectal cancer, and increased viability and migration in colon cancer cells. The induction of the EMT process may be an underlying molecular mechanism associated with the H19-induced increased metastasis potential of colon cancer cells.
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Affiliation(s)
- Shan-Wen Chen
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Jing Zhu
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Ju Ma
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Jun-Ling Zhang
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Shuai Zuo
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Guo-Wei Chen
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Xin Wang
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Yi-Sheng Pan
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Yu-Cun Liu
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
| | - Peng-Yuan Wang
- Division of General Surgery, Peking University First Hospital, Peking University, Beijing 100034, P.R. China
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H19 Overexpression Induces Resistance to 1,25(OH)2D3 by Targeting VDR Through miR-675-5p in Colon Cancer Cells. Neoplasia 2017; 19:226-236. [PMID: 28189050 PMCID: PMC5300698 DOI: 10.1016/j.neo.2016.10.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 02/07/2023] Open
Abstract
The long noncoding (lnc) RNA H19 was involved in the tumorigenesis of many types of cancer. However, the role of H19 in the tumorigenesis of colon cancer has not been fully illustrated. Recent studies suggested a potential relationship between H19 and vitamin D receptor (VDR) signaling. Considering the pivotal role of VDR signaling in the colon epithelium both physiologically and pathologically, the correlation between H19 and VDR signaling may have an important role in the development of colon cancer. In this study, the correlation between H19 and vitamin D receptor (VDR) signaling and the underlying mechanisms in colon cancer were investigated both in vitro and in vivo. The results suggested that VDR signaling was able to inhibit the expression of H19 through regulating C-Myc/Mad-1 network. H19, on the other hand, was able to inhibit the expression of VDR through micro RNA 675-5p (miR-675-5p). Furthermore, H19 overexpression induced resistance to the treatment with 1,25(OH)2D3 both in vitro and in vivo. Together, these results suggested that H19 overexpression might be one of the mechanisms underlying the development of resistance to the treatment with 1,25(OH)2D3 in the advanced stage of colon cancer.
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Karlsson O, Rodosthenous RS, Jara C, Brennan KJ, Wright RO, Baccarelli AA, Wright RJ. Detection of long non-coding RNAs in human breastmilk extracellular vesicles: Implications for early child development. Epigenetics 2016; 11:721-729. [PMID: 27494402 DOI: 10.1080/15592294.2016.1216285] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Breastmilk has many documented beneficial effects on the developing human infant, but the components of breastmilk that influence these developmental pathways have not been fully elucidated. Increasing evidence suggests that non-coding RNAs encapsulated in extracellular vesicles (EVs) represent an important mechanism of communication between the mother and child. Long non-coding RNAs (lncRNAs) are of particular interest given their key role in gene expression and development. However, it is not known whether breastmilk EVs contain lncRNAs. We used qRT-PCR to determine whether EVs isolated from human breastmilk contain lncRNAs previously reported to be important for developmental processes. We detected 55 of the 87 screened lncRNAs in EVs from the 30 analyzed breastmilk samples, and CRNDE, DANCR, GAS5, SRA1 and ZFAS1 were detected in >90% of the samples. GAS5, SNHG8 and ZFAS1 levels were highly correlated (Spearman's rho > 0.9; P < 0.0001), which may indicate that the loading of these lncRNAs into breastmilk EVs is regulated by the same pathways. The detected lncRNAs are important epigenetic regulators involved in processes such as immune cell regulation and metabolism. They may target a repertoire of recipient cells in offspring and could be essential for child development and health. Further experimental and epidemiological studies are warranted to determine the impact of breastmilk EV-encapsulated lnRNAs in mother to child signaling.
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Affiliation(s)
- Oskar Karlsson
- a Center for Molecular Medicine , Department of Clinical Neuroscience , Karolinska Institute , Stockholm , Sweden.,b Department of Environmental Health , Harvard T.H. Chan School of Public Health , Boston , MA , USA
| | | | - Calvin Jara
- c Department of Preventive Medicine , Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | - Kasey J Brennan
- b Department of Environmental Health , Harvard T.H. Chan School of Public Health , Boston , MA , USA
| | - Robert O Wright
- c Department of Preventive Medicine , Icahn School of Medicine at Mount Sinai , New York , NY , USA.,d Kravis Children's Hospital , Department of Pediatrics , Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | - Andrea A Baccarelli
- b Department of Environmental Health , Harvard T.H. Chan School of Public Health , Boston , MA , USA
| | - Rosalind J Wright
- c Department of Preventive Medicine , Icahn School of Medicine at Mount Sinai , New York , NY , USA.,d Kravis Children's Hospital , Department of Pediatrics , Icahn School of Medicine at Mount Sinai , New York , NY , USA
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Effect of Long Noncoding RNA H19 Overexpression on Intestinal Barrier Function and Its Potential Role in the Pathogenesis of Ulcerative Colitis. Inflamm Bowel Dis 2016; 22:2582-2592. [PMID: 27661667 DOI: 10.1097/mib.0000000000000932] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Recently, long noncoding RNA (lncRNA) H19 has been reported to be related with VDR signaling and the development of inflammatory diseases including osteoarthritis. The aim of this study was to investigate the correlation between the expression level of H19 and VDR in ulcerative colitis (UC) tissues and to investigate the effect of H19 overexpression on intestinal epithelial barrier function. METHODS The expression level of H19, miR-675-5p, and VDR in UC tissues and paired normal tissues collected from 12 patients with UC was investigated by quantitative real-time polymerase chain reaction. Caco-2 monolayers were used to test the effect of H19 and miR-675-5p overexpression on the intestinal epithelial barrier function and the status of tight junction proteins and VDR. Luciferase assay was used to validate the target site of miR-675-5p in the 3'UTR of VDR mRNA. RESULTS The expression of H19 was found to be negatively correlated with the expression of VDR in UC tissues (r = 0.5369, P < 0.05). The expression of miR-675-5p was also found to be negatively correlated with the expression of VDR in UC tissues (r = 0.5233, P < 0.01). H19 overexpression increased Caco-2 monolayer permeability and decreased the expression of tight junction proteins and VDR, which was significantly attenuated by cotransfection with miR-675-5p inhibitors. The 3'UTR of VDR mRNA was validated to be one of the direct targets of miR-675-5p. CONCLUSIONS This study reveals the destructive effect of H19 overexpression on intestinal epithelial barrier function and suggests a potential role of H19 in the development of UC. In addition, H19 overexpression may be one of the mechanisms underlying the decreased expression of VDR in UC tissues and the interaction between H19 and VDR signaling may provide potential therapeutic targets for UC.
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Abstract
An individual's risk of developing a common disease typically depends on an interaction of genetic and environmental factors. Epigenetic research is uncovering novel ways through which environmental factors such as diet, air pollution, and chemical exposure can affect our genes. DNA methylation and histone modifications are the most commonly studied epigenetic mechanisms. The role of long non-coding RNAs (lncRNAs) in epigenetic processes has been more recently highlighted. LncRNAs are defined as transcribed RNA molecules greater than 200 nucleotides in length with little or no protein-coding capability. While few functional lncRNAs have been well characterized to date, they have been demonstrated to control gene regulation at every level, including transcriptional gene silencing via regulation of the chromatin structure and DNA methylation. This review aims to provide a general overview of lncRNA function with a focus on their role as key regulators of health and disease and as biomarkers of environmental exposure.
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Affiliation(s)
- Oskar Karlsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institutet, 171 76, Stockholm, Sweden.
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
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48
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The roles of non-coding RNAs in Parkinson's disease. Mol Biol Rep 2016; 43:1193-1204. [PMID: 27492082 DOI: 10.1007/s11033-016-4054-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/01/2016] [Indexed: 12/19/2022]
Abstract
Parkinson's disease (PD) is considered as a high prevalence neurodegenerative disorders worldwide. Pathologically, the demise of dopamine-producing cells, in large part due to an abnormal accumulation of the α-synuclein in the substantia nigra, is one of the main causes of the disease. Up until now, many de novo investigations have been conducted to disclose the mechanisms underlying in PD. Among them, impacts of non-coding RNAs (ncRNAs) on the pathogenesis and/or progression of PD need to be highlighted. microRNAs (miRNAs) and long ncRNAs (lncRNAs) are more noteworthy in this context. miRNAs are small ncRNAs (with 18-25 nucleotide in length) that control the expression of multiple genes at post-transcriptional level, while lncRNAs have longer size (over 200 nucleotides) and are involved in some key biological processes through various mechanisms. Involvement of miRNAs has been well documented in the development of PD, particularly gene expression. Hence, in this current review, we will discuss the impacts of miRNAs in regulation of the expression of PD-related genes and the role of lncRNAs in the pathogenesis of PD.
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49
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Cheng Z, Guo J, Chen L, Luo N, Yang W, Qu X. A long noncoding RNA AB073614 promotes tumorigenesis and predicts poor prognosis in ovarian cancer. Oncotarget 2016; 6:25381-9. [PMID: 26299803 PMCID: PMC4694838 DOI: 10.18632/oncotarget.4541] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/17/2015] [Indexed: 12/28/2022] Open
Abstract
Long noncoding RNA (lncRNA) profiles in ovarian cancer (OC) remain largely unknown. In the present study, we screened AB073614 as a new candidate lncRNA which promotes development of OC, in two independent datasets (GSE18521 and GSE38666) from the Gene Expression Omnibus (GEO). The level of AB073614 was then detected in 75 paired OC tissues and adjacent normal tissues by qRT-PCR. Results showed that AB073614 expression was significantly up-regulated in 85.3% (64/75) cancerous tissues compared with normal counterparts (P < 0.01). Further, the 5-year overall survival (OS) in OC patients with high expression of AB073614 was inferior to that with low expression (17.2 months vs 30.0 months, P = 0.0025). To investigate the functional role of AB073614, AB073614 siRNA was transfected into OC cell lines. Knockdown of AB073614 expression significantly inhibited cell proliferation and invasion, resulted in cell arrest in G1 phase of cell cycle and a dramatic increase of apoptosis, both in HO-8910 and OVCAR3 cells. In vivo experiment also revealed that knockdown AB073614 inhibited OVCAR3 cells proliferation. Finally, western blot assays indicated that lncRNA AB073614 may exert its function by targeting ERK1/2 and AKT-mediated signaling pathway. In conclusion, our study suggests that lncRNA AB073614 acts as a functional oncogene in OC development.
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Affiliation(s)
- Zhongping Cheng
- Department of Obstetrics and Gynecology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, PR China.,Institute of Gynecological Minimally Invasive Medicine, Tongji University School of Medicine, Shanghai, PR China
| | - Jing Guo
- Department of Obstetrics and Gynecology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, PR China.,Institute of Gynecological Minimally Invasive Medicine, Tongji University School of Medicine, Shanghai, PR China
| | - Li Chen
- Department of Obstetrics and Gynecology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, PR China.,Institute of Gynecological Minimally Invasive Medicine, Tongji University School of Medicine, Shanghai, PR China
| | - Ning Luo
- Department of Obstetrics and Gynecology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, PR China.,Institute of Gynecological Minimally Invasive Medicine, Tongji University School of Medicine, Shanghai, PR China
| | - Weihong Yang
- Department of Obstetrics and Gynecology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, PR China.,Institute of Gynecological Minimally Invasive Medicine, Tongji University School of Medicine, Shanghai, PR China
| | - Xiaoyan Qu
- Department of Obstetrics and Gynecology, Yangpu Hospital, Tongji University School of Medicine, Shanghai, PR China.,Institute of Gynecological Minimally Invasive Medicine, Tongji University School of Medicine, Shanghai, PR China
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Abstract
Neuroblastoma is a disease that affects infants and despite intense multimodal therapy, high-risk patients have low survival rates (<50%). In recent years long noncoding RNAs (lncRNAs) have become the cutting edge of cancer research with inroads made in understanding their roles in multiple cancer types, including prostate and breast cancers. The roles of lncRNAs in neuroblastoma have just begun to be elucidated. This review summarises where we are with regards to lncRNAs in neuroblastoma. The known mechanistic roles of lncRNAs during neuroblastoma pathogenesis are discussed, as well as the relationship between lncRNA expression and the differentiation capacity of neuroblastoma cells. We speculate about the use of some of these lncRNAs, such as those mapping to the 6p22 hotspot, as biomarkers for neuroblastoma prognosis and treatment. This novel way of thinking about both neuroblastoma and lncRNAs brings a new perspective to the prognosis and treatment of high-risk patients.
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