751
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Coltri PP, Dos Santos MGP, da Silva GHG. Splicing and cancer: Challenges and opportunities. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1527. [PMID: 30773852 DOI: 10.1002/wrna.1527] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/14/2018] [Accepted: 01/17/2019] [Indexed: 12/11/2022]
Abstract
Cancer arises from alterations in several metabolic processes affecting proliferation, growth, replication and death of cells. A fundamental challenge in the study of cancer biology is to uncover molecular mechanisms that lead to malignant cellular transformation. Recent genomic analyses revealed that many molecular alterations observed in cancers come from modifications in the splicing process, including mutations in pre-mRNA regulatory sequences, mutations in spliceosome components, and altered ratio of specific splicing regulators. While alterations in splice site preferences might generate alternative isoforms enabling different biological functions, these might also be responsible for nonfunctional isoforms that can eventually cause dysregulation in cellular processes. Molecular characteristics of regulatory sequences and proteins might also be important prognostic tools revealing a cancer-specific splicing pattern and linking splicing control to cancer development. The connection between cancer biology and splicing regulation is of primary importance to understand the mechanisms leading to disease and also to improve development of therapeutic approaches. Splicing modulation is being explored in new anti-cancer therapies and further investigation of targeted splicing factors is critical for the success of these strategies. This article is categorized under: RNA Processing > Splicing Mechanisms RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Patricia P Coltri
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria G P Dos Santos
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Guilherme H G da Silva
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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752
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Abstract
Abdominal aortic aneurysm (AAA) is a local dilatation of the abdominal aortic vessel wall and is among the most challenging cardiovascular diseases as without urgent surgical intervention, ruptured AAA has a mortality rate of >80%. Most patients present acutely after aneurysm rupture or dissection from a previously asymptomatic condition and are managed by either surgery or endovascular repair. Patients usually are old and have other concurrent diseases and conditions, such as diabetes mellitus, obesity, and hypercholesterolemia making surgical intervention more difficult. Collectively, these issues have driven the search for alternative methods of diagnosing, monitoring, and treating AAA using therapeutics and less invasive approaches. Noncoding RNAs-short noncoding RNAs (microRNAs) and long-noncoding RNAs-are emerging as new fundamental regulators of gene expression. Researchers and clinicians are aiming at targeting these microRNAs and long noncoding RNAs and exploit their potential as clinical biomarkers and new therapeutic targets for AAAs. While the role of miRNAs in AAA is established, studies on long-noncoding RNAs are only beginning to emerge, suggesting their important yet unexplored role in vascular physiology and disease. Here, we review the role of noncoding RNAs and their target genes focusing on their role in AAA. We also discuss the animal models used for mechanistic understanding of AAA. Furthermore, we discuss the potential role of microRNAs and long noncoding RNAs as clinical biomarkers and therapeutics.
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Affiliation(s)
- Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering,
Emory University and Georgia Institute of Technology, Atlanta, GA, USA
| | - Reinier A. Boon
- Institute for Cardiovascular Regeneration, Center of
Molecular Medicine, Goethe University, Frankfurt, Germany
- Department of Physiology, Amsterdam Cardiovascular
Sciences, VU University Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The
Netherlands
- German Center of Cardiovascular Research DZHK, Frankfurt,
Germany
| | - Lars Maegdefessel
- Department of Medicine, Karolinska Institute, Stockholm,
Sweden
- Department of Vascular and Endovascular Surgery, Technical
University Munich, Munich, Germany
- German Center for Cardiovascular Research DZHK, Munich,
Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Center of
Molecular Medicine, Goethe University, Frankfurt, Germany
- German Center of Cardiovascular Research DZHK, Frankfurt,
Germany
- Corresponding authors: Hanjoong Jo, PhD, John and Jan Portman
Professor, Wallace H. Coulter Department of Biomedical Engineering, Emory
University and Georgia Institute of Technology, 1760 Haygood Drive, Atlanta, GA
30322, , Stefanie Dimmeler, PhD, Institute for
Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University
Frankfurt, Theodor Stern Kai 7, 60590, Frankfurt, Germany,
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering,
Emory University and Georgia Institute of Technology, Atlanta, GA, USA
- Division of Cardiology, Emory University, Atlanta, GA,
USA
- Corresponding authors: Hanjoong Jo, PhD, John and Jan Portman
Professor, Wallace H. Coulter Department of Biomedical Engineering, Emory
University and Georgia Institute of Technology, 1760 Haygood Drive, Atlanta, GA
30322, , Stefanie Dimmeler, PhD, Institute for
Cardiovascular Regeneration, Centre of Molecular Medicine, Goethe University
Frankfurt, Theodor Stern Kai 7, 60590, Frankfurt, Germany,
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753
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Integrated analysis of mRNAs and long noncoding RNAs in the semen from Holstein bulls with high and low sperm motility. Sci Rep 2019; 9:2092. [PMID: 30765858 PMCID: PMC6376035 DOI: 10.1038/s41598-018-38462-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/28/2018] [Indexed: 02/06/2023] Open
Abstract
Sperm motility is the main index used to assess the quality of bull semen. It may also be used to evaluate the fertility potential of bulls. Protein-coding mRNA and long noncoding RNA (lncRNA) participate in the regulation of spermatogenesis. Here, we employed strand-specific RNA sequencing to profile the semen transcriptome (mRNA and lncRNA) of six paired full-sibling Holstein bulls with divergent sperm motility and to determine the functions of mRNA and lncRNA in sperm motility. Among 20,875 protein-encoding genes detected in semen, 19 were differentially expressed between the high sperm motility group (H: H1, H2, and H3) and low sperm motility group (L: L1, L2, and L3). Of the 11,561 lncRNAs identified in sperm, 2,517 were differentially expressed between the H and L groups. We found that TCONS_00041733 lncRNA targets the node gene EFNA1 (ephrin A1), involved in male reproductive physiology. Our study provides a global mRNA and lncRNA transcriptome of bull semen, as well as novel insights into the regulation of neighboring protein coding by lncRNAs and the influence of mRNAs on sperm motility.
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754
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Barangi S, Hayes AW, Reiter R, Karimi G. The therapeutic role of long non-coding RNAs in human diseases: A focus on the recent insights into autophagy. Pharmacol Res 2019; 142:22-29. [PMID: 30742900 DOI: 10.1016/j.phrs.2019.02.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/06/2019] [Accepted: 02/07/2019] [Indexed: 12/15/2022]
Abstract
Long non-coding RNA (lncRNA) is a class of non-coding RNA with ≥200 nucleotides in length which are involved as critical regulators in various cellular processes. LncRNAs contribute to the development and progression of many human diseases. Autophagy is a key catabolic process which helps to maintain the cellular homeostasis through the decay of damaged or unwanted proteins and dysfunctional cytoplasmic organelles. The impairment of the autophagy process has been described in numerous diseases. The autophagy possess can have either a protective or a detrimental role in cells depending on its activation status and other cellular conditions. LncRNAs have been shown to have an important function in the regulation of important biological processes such as autophagy. The relationship between lncRNAs and autophagy has been shown to be involved in the progression and possibly in the prevention of many diseases. In this review, recent findings on the regulatory roles of lncRNAs in the cell autophagy pathway, as well as their relevance to different diseases such as cardiovascular disease, cerebral ischemic stroke and cancer are highlighted.
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Affiliation(s)
- Samira Barangi
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - A Wallace Hayes
- University of South Florida College of Public Health, USA; Michigan State University, East Lansing, MI, USA
| | - Russel Reiter
- University of Texas, Health Science Center at San Antonio, Department of Cellular and Structural Biology, USA
| | - Gholamreza Karimi
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Centre, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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755
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RNA-Seq profiling in peripheral blood mononuclear cells of amyotrophic lateral sclerosis patients and controls. Sci Data 2019; 6:190006. [PMID: 30720798 PMCID: PMC6362931 DOI: 10.1038/sdata.2019.6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 12/14/2018] [Indexed: 12/12/2022] Open
Abstract
Coding and long non-coding RNA (lncRNA) metabolism is now revealing its crucial role in Amyotrophic Lateral Sclerosis (ALS) pathogenesis. In this work, we present a dataset obtained via Illumina RNA-seq analysis on Peripheral Blood Mononuclear Cells (PBMCs) from sporadic and mutated ALS patients (mutations in FUS, TARDBP, SOD1 and VCP genes) and healthy controls. This dataset allows the whole-transcriptome characterization of PBMCs content, both in terms of coding and non-coding RNAs, in order to compare the disease state to the healthy controls, both for sporadic patients and for mutated patients. Our dataset is a starting point for the omni-comprehensive analysis of coding and lncRNAs, from an easy to withdraw, manage and store tissue that shows to be a suitable model for RNA profiling in ALS.
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756
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Butova R, Vychytilova-Faltejskova P, Souckova A, Sevcikova S, Hajek R. Long Non-Coding RNAs in Multiple Myeloma. Noncoding RNA 2019; 5:E13. [PMID: 30682861 PMCID: PMC6468639 DOI: 10.3390/ncrna5010013] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Multiple myeloma (MM) is the second most common hematooncological disease of malignant plasma cells in the bone marrow. While new treatment brought unprecedented increase of survival of patients, MM pathogenesis is yet to be clarified. Increasing evidence of expression of long non-coding RNA molecules (lncRNA) linked to development and progression of many tumors suggested their important role in tumorigenesis. To date, over 15,000 lncRNA molecules characterized by diversity of function and specificity of cell distribution were identified in the human genome. Due to their involvement in proliferation, apoptosis, metabolism, and differentiation, they have a key role in the biological processes and pathogenesis of many diseases, including MM. This review summarizes current knowledge of non-coding RNAs (ncRNA), especially lncRNAs, and their role in MM pathogenesis. Undeniable involvement of lncRNAs in MM development suggests their potential as biomarkers.
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Affiliation(s)
- Romana Butova
- Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
| | | | - Adela Souckova
- Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
| | - Sabina Sevcikova
- Babak Myeloma Group, Department of Pathological Physiology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
| | - Roman Hajek
- Department of Hematooncology, University Hospital Ostrava and Faculty of Medicine, University Ostrava, 70852 Ostrava, Czech Republic.
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757
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Mathias C, Zambalde EP, Rask P, Gradia DF, de Oliveira JC. Long non-coding RNAs differential expression in breast cancer subtypes: What do we know? Clin Genet 2019; 95:558-568. [PMID: 30614523 DOI: 10.1111/cge.13502] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 12/28/2018] [Accepted: 12/31/2018] [Indexed: 12/24/2022]
Abstract
Breast Cancer (BC) is the most commonly diagnosed cancer and is the leading cause of cancer deaths in women. BC is a heterogeneous disease with different clinical and genetic features. According to immunohistochemical markers, BC is subdivided into four main subtypes: luminal A, luminal B, ERBB2 positive and triple negative. Long non-coding RNAs (lncRNAs) are transcripts with more than 200 nucleotides and deregulated lncRNAs are associated with human diseases, including BC. In order to improve BC molecular classification, non-coding RNAs (ncRNAs), including lncRNAs, have been used. In this review, we focus on lncRNAs with differential expression in BC subtypes and how these RNAs may act to contribute to BC heterogeneity. We also emphasize the potential of these lncRNAs as biomarkers.
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Affiliation(s)
- Carolina Mathias
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
| | - Erika P Zambalde
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
| | - Philip Rask
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Daniela F Gradia
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
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758
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Li D, Tolleson WH, Yu D, Chen S, Guo L, Xiao W, Tong W, Ning B. Regulation of cytochrome P450 expression by microRNAs and long noncoding RNAs: Epigenetic mechanisms in environmental toxicology and carcinogenesis. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2019; 37:180-214. [PMID: 31305208 PMCID: PMC6737535 DOI: 10.1080/10590501.2019.1639481] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Environmental exposures to hazardous chemicals are associated with a variety of human diseases and disorders, including cancers. Phase I metabolic activation and detoxification reactions catalyzed by cytochrome P450 enzymes (CYPs) affect the toxicities of many xenobiotic compounds. Proper regulation of CYP expression influences their biological effects. Noncoding RNAs (ncRNAs) are involved in regulating CYP expression, and ncRNA expression is regulated in response to environmental chemicals. The mechanistic interactions between ncRNAs and CYPs associated with the toxicity and carcinogenicity of environmental chemicals are described in this review, focusing on microRNA-dependent CYP regulation. The role of long noncoding RNAs in regulating CYP expression is also presented and new avenues of research concerning this regulatory mechanism are described.
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Affiliation(s)
- Dongying Li
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - William H Tolleson
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Dianke Yu
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Si Chen
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Lei Guo
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Wenming Xiao
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Weida Tong
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Baitang Ning
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
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759
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Tschumper RC, Shanafelt TD, Kay NE, Jelinek DF. Role of long non-coding RNAs in disease progression of early stage unmutated chronic lymphocytic leukemia. Oncotarget 2019; 10:60-75. [PMID: 30713603 PMCID: PMC6343752 DOI: 10.18632/oncotarget.26538] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 12/12/2018] [Indexed: 12/15/2022] Open
Abstract
Predicting disease progression in chronic lymphocytic leukemia (CLL) remains challenging particularly in patients with Rai Stage 0/I disease that have an unmutated immunoglobulin heavy chain variable region (UM IGHV). Even though patients with UM IGHV have a poor prognosis and generally require earlier treatment, not all UM IGHV patients experience more rapid disease progression with some remaining treatment free for many years. This observation suggests biologic characteristics other than known prognostic factors influence disease progression. Alterations in long non-coding RNA (lncRNA) expression levels have been implicated in diagnosis and prognosis of various cancers, however, their role in disease progression of early Rai stage UM CLL is unknown. Here we use microarray analysis to compare lncRNA and mRNA profiles of Rai 0/I UM IGHV patients who progressed in <2 years relative to patients who had not progressed for >5 years. Over 1,300 lncRNAs and 940 mRNAs were differentially expressed (fold change ≥ 2.0; p-value ≤ 0.05). Of interest, the differentially expressed lncRNAs T204050, NR_002947, and uc.436+, have known associated genes that have been linked to CLL. Thus, our study reveals differentially expressed lncRNAs in progressive early stage CLL requiring therapy versus indolent early Rai stage UM CLL. These lncRNAs have the potential to impact relevant biological processes and pathways that influence clinical outcome in CLL.
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Affiliation(s)
| | - Tait D Shanafelt
- Department of Hematology/Oncology, Stanford University, Stanford, CA, USA
| | - Neil E Kay
- Department of Internal Medicine, Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Diane F Jelinek
- Department of Immunology, Mayo Clinic, Scottsdale, AZ, USA.,Department of Internal Medicine, Division of Hematology, Mayo Clinic, Rochester, MN, USA
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760
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Bocci F, Jolly MK, Levine H, Onuchic JN. Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks. Methods Mol Biol 2019; 1912:341-366. [PMID: 30635901 DOI: 10.1007/978-1-4939-8982-9_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RNA is mostly known for its role in protein synthesis, where it encodes information for protein sequence in its messenger RNA (mRNA) form (translation). Yet, RNA molecules regulate several cellular processes other than translation. Here, we present an overview of several mathematical models that help understanding and characterizing the role of noncoding RNA molecules (ncRNAs) in regulating gene expression and protein synthesis. First, we discuss relatively simple models where ncRNAs can modulate protein synthesis via targeting a mRNA. Then, we consider the case of feedback interactions between ncRNAs and their target proteins, and discuss several biological applications where these feedback architectures modulate a cellular phenotype and control the levels of intrinsic and extrinsic noise. Building from these simple circuit motifs, we examine feed-forward circuit motifs involving ncRNAs that generate precise spatial and temporal patterns of protein expression. Further, we investigate the competition between ncRNAs and other endogenous RNA molecules and show that the cross talk between coding and noncoding RNAs can form large genetic circuits that involve up to hundreds of chemical species. Finally, we discuss the role of ncRNAs in modulating cell-cell signaling pathways and therefore the dynamics of spatiotemporal pattern formation in a tissue.
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Affiliation(s)
- Federico Bocci
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Department of Chemistry, Rice University, Houston, TX, USA
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. .,Department of Chemistry, Rice University, Houston, TX, USA. .,Department of Bioengineering, Rice University, Houston, TX, USA. .,Department of Physics and Astronomy, Rice University, Houston, TX, USA.
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. .,Department of Chemistry, Rice University, Houston, TX, USA. .,Department of Physics and Astronomy, Rice University, Houston, TX, USA. .,Department of Biosciences, Rice University, Houston, TX, USA.
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761
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Tiwari P, Gupta S, Kumar A, Sharma M, Sundararajan VS, Kothari SL, Mathur SK, Medicherla KM, Suravajhala P, Malik B. Characterizing and Functional Assignment of Noncoding RNAs. ENCYCLOPEDIA OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 2019:47-59. [DOI: 10.1016/b978-0-12-809633-8.20077-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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762
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Wang C, Zhang Q, Hu Y, Zhu J, Yang J. Emerging role of long non-coding RNA MALAT1 in predicting clinical outcomes of patients with digestive system malignancies: A meta-analysis. Oncol Lett 2018; 17:2159-2170. [PMID: 30719108 PMCID: PMC6350192 DOI: 10.3892/ol.2018.9875] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 11/28/2018] [Indexed: 12/16/2022] Open
Abstract
Digestive system malignancies are the most common cancer types worldwide and exhibit an extremely low overall 5-year survival rate. Therefore, clinically applicable biomarkers for predicting clinical outcome are urgently required. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is abnormally expressed in several cancer types. However, to the best of our knowledge, the association between MALAT1 expression and the prognosis of digestive system malignancies remains unknown. Therefore, the current study performed a meta-analysis to comprehensively summarize the association between MALAT1 expression and digestive system malignancies. A total of 1,157 Asian patients from 12 eligible studies [eight studies that investigated overall survival (OS), two studies that investigated disease-free survival and two studies that investigated both indicators] were analyzed. The present results identified a significant association between MALAT1 abundance and poor OS in patients with digestive system malignancies, with a pooled hazard ratio (HR) of 1.62 [95% confidence interval (CI), 1.35–1.88; P<0.001]. The tumor type, region, sample size and analysis type did not alter the predictive value of MALAT1 as an independent factor for survival. Furthermore, MALAT1 overexpression was an unfavorable prognostic factor for the overall survival of patients with esophageal carcinoma, pancreatic cancer, hepatocellular carcinoma and gastric cancer, with HRs of 1.89 (95% CI, 1.29–2.49), 1.76 (95% CI, 0.89–2.63), 1.46 (95% CI, 0.76–2.17) and 1.41 (95% CI, 1.04–1.78), respectively. In particular, increased MALAT1 expression levels were significantly associated with decreased OS in patients with colorectal cancer (HR, 3.04; 95% CI, 1.77–4.31). In conclusion, lncRNA MALAT1 may be a potential prognostic factor for digestive system malignancies in Asian populations.
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Affiliation(s)
- Chao Wang
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Qiaoling Zhang
- Department of Clinical Medicine and Rehabilitation, Jiangsu College of Nursing, Huai'an, Jiangsu 223005, P.R. China
| | - Yuhuan Hu
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Jianshen Zhu
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China
| | - Jinyou Yang
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, P.R. China.,Department of Clinical Medicine and Rehabilitation, Jiangsu College of Nursing, Huai'an, Jiangsu 223005, P.R. China
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763
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Sattarifard H, Hashemi M, Hassanzarei S, Basiri A, Narouie B, Ghavami S. Long non-coding RNA POLR2E gene polymorphisms increased the risk of prostate cancer in a sample of the Iranian population. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 38:1-11. [PMID: 30587086 DOI: 10.1080/15257770.2017.1391394] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The current study aimed to examine the impact of POLR2E rs1046040 and rs3787016 polymorphisms on prostate cancer (PCa) risk in a sample of southeast Iranian population. The present case-control study was performed on 178 patients with PCa and 180 benign prostatic hyperplasia (BPH). Genotyping of the variants was done by mismatch PCR-RFLP. The findings showed that the rs3787016 C > T variant significantly increased the risk of PCa in codominant (OR = 1.84, 95% CI = 1.12-3.03, P = 0.018, CT vs CC), dominant (OR = 1.88, 95% CI = 1.63-3.05, P = 0.011, CT + TT vas CC) and allele (OR = 1.77, 95% CI = 1.52-2.72, P = 0.010, T vs C) inheritance model. Regarding rs1046040 C > T polymorphism, the findings revealed that the CT genotype significantly increased the risk of PCa compared to the CC genotype (OR = 1.60, 95% CI = 1.03-2.49, P = 0.043). Furthermore, rs3787016 CT/rs1046040 CC as well as rs3787016 CT/rs1046040 CT increased the risk of PCa compared to the CC/CC genotype (p = 0.029 and p = 0.014, respectively). Haplotype analysis proposed that rs3787016 T/rs1046040 C significantly increased the risk of PCa compared to C/C (p = 0.037). No significant association was observed between POLR2E variants and clinicopathological characteristics of PCa patients. In conclusion, the findings propose that POLR2E variants may be a risk factor for susceptibility to PCa in a sample of Iranian population.
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Affiliation(s)
- Hedieh Sattarifard
- a Cellular and Molecular Research Center , Zahedan University of Medical Sciences , Zahedan , Iran.,b Department of Clinical Biochemistry, School of Medicine , Zahedan University of Medical Sciences , Zahedan , Iran
| | - Mohammad Hashemi
- a Cellular and Molecular Research Center , Zahedan University of Medical Sciences , Zahedan , Iran.,b Department of Clinical Biochemistry, School of Medicine , Zahedan University of Medical Sciences , Zahedan , Iran
| | - Shekoufeh Hassanzarei
- b Department of Clinical Biochemistry, School of Medicine , Zahedan University of Medical Sciences , Zahedan , Iran
| | - Abbas Basiri
- c Department of Urology, Urology and Nephrology Research Center, Shahid Labbafinejad Medical Center , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Behzad Narouie
- c Department of Urology, Urology and Nephrology Research Center, Shahid Labbafinejad Medical Center , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Saeid Ghavami
- d Department of Human Anatomy and Cell Science, Faculty of Health Sciences, College of Medicine , University of Manitoba , Winnipeg , Canada.,e Health Policy Research Center , Shiraz University of Medical Sciences , Shiraz , Iran
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764
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Abdeahad H, Avan A, Pashirzad M, Khazaei M, Soleimanpour S, Ferns GA, Fiuji H, Ryzhikov M, Bahrami A, Hassanian SM. The prognostic potential of long noncoding RNA HOTAIR expression in human digestive system carcinomas: A meta-analysis. J Cell Physiol 2018; 234:10926-10933. [PMID: 30569489 DOI: 10.1002/jcp.27918] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 10/24/2018] [Indexed: 01/17/2023]
Abstract
Homeobox transcript antisense intergenic RNA (HOTAIR), one of the well-known long noncoding RNAs (lncRNAs), plays an important role in initiation and development of various tumors. Elevated level of HOTAIR is associated with metastatic behavior of primary tumor and poor outcome in several cancers. Therefore, we conducted a meta-analysis to clearly measure the prognostic impact of HOTAIR in patients with digestive system carcinomas. Fourteen studies including 2,666 patients with five different type of digestive system cancers were selected to be entered in meta-analysis. Finding demonstrated that HOTAIR overexpression could predict unfavorable outcome in digestive system carcinomas (hazard ratio [HR] = 2.4, 95% confidence interval [CI]: 2.0-2.9; p < 0.001; fixed-effect model). In stratified analysis, increased level of HOTAIR predicted poor overall survival in gastric cancer (HR = 2.1, 95% CI: 1.6-2.9; p < 0.001), colorectal cancer (HR = 4.1, 95% CI: 1.6-10.2; p = 0.002), esophageal squamous cell carcinoma (HR = 2.3, 95% CI: 1.7-3.0; p < 0.001), and hepatocellular carcinoma (HR = 3.4, 95% CI: 1.9-6.1; p < 0.001). Our meta-analysis results clearly support the prognostic value of HOTAIR to predict unfavorable prognostic outcomes in diverse digestive system carcinomas.
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Affiliation(s)
- Hossein Abdeahad
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Modern Sciences and Technologies, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehran Pashirzad
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Physiology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saman Soleimanpour
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Division of Medical Education, Brighton & Sussex Medical School, Brighton, UK
| | - Hamid Fiuji
- Department of Biochemistry, Payame-Noor University, Mashhad, Iran
| | - Mikhail Ryzhikov
- Division of Pulmonary and Critical Care Medicine, Washington University, School of Medicine, Saint Louis, Missouri
| | - Afsane Bahrami
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Seyed Mahdi Hassanian
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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765
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Arumugam B, Vishal M, Shreya S, Malavika D, Rajpriya V, He Z, Partridge NC, Selvamurugan N. Parathyroid hormone-stimulation of Runx2 during osteoblast differentiation via the regulation of lnc-SUPT3H-1:16 (RUNX2-AS1:32) and miR-6797-5p. Biochimie 2018; 158:43-52. [PMID: 30562548 DOI: 10.1016/j.biochi.2018.12.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022]
Abstract
Parathyroid hormone (PTH) acts as a regulator of calcium homeostasis and bone remodeling. Runx2, an essential transcription factor in bone, is required for osteoblast differentiation. Noncoding RNAs such as long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) play crucial roles in regulating gene expression in osteoblasts. In this study, we investigated the effects of PTH on osteoblast differentiation via Runx2, lncRNA, and miRNA expression in human bone marrow stromal cells (hBMSCs) and human osteoblastic cells (MG63). PTH-treatment of hBMSCs for 24 h, 7 days, and 14 days stimulated Runx2 mRNA expression. Using bioinformatics tools, we identified 17 lncRNAs originating from human Runx2 gene. Among these, lnc-SUPT3H-1:16 (RUNX2-AS1:32) expression was highly up-regulated by the 7 d PTH-treatment in hBMSCs. We also identified miR-6797-5p as the putative target of lnc-SUPT3H-1:16 and Runx2 using bioinformatics tools. PTH-treatment increased the expression of miR-6797-5p in hBMSCs, and overexpression of miR-6797-5p decreased osteoblast differentiation in MG63 cells, suggesting a role for lnc-SUPT3H-1:16 as sponge molecule. A luciferase gene reporter assay identified direct targeting of miR-6797-5p with lnc-SUPT3H-1:16 and 3'UTR Runx2 in MG63 cells. Thus, PTH stimulated the expression of lnc-SUPT3H-1:16, miR-6797-5p and Runx2, and due to the sponging mechanism of lnc- SUPT3H-1:16 towards miR-6797-5p, Runx2 was protected, resulting in the promotion of osteoblast differentiation.
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Affiliation(s)
- B Arumugam
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - M Vishal
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - S Shreya
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - D Malavika
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - V Rajpriya
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India
| | - Z He
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York University, NY, USA
| | - N C Partridge
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York University, NY, USA
| | - N Selvamurugan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, India.
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766
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Su H, Xu X, Yan C, Shi Y, Hu Y, Dong L, Ying S, Ying K, Zhang R. LncRNA H19 promotes the proliferation of pulmonary artery smooth muscle cells through AT 1R via sponging let-7b in monocrotaline-induced pulmonary arterial hypertension. Respir Res 2018; 19:254. [PMID: 30547791 PMCID: PMC6295077 DOI: 10.1186/s12931-018-0956-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/29/2018] [Indexed: 02/21/2023] Open
Abstract
BACKGROUND Pulmonary arterial hypertension (PAH) is related to inflammation, and the lncRNA H19 is associated with inflammation. However, whether PDGF-BB-H19-let-7b-AT1R axis contributes to the pathogenesis of PAH has not been thoroughly elucidated to date. This study investigated the role of H19 in PAH and its related mechanism. METHODS In the present study, SD rats, C57/BL6 mice and H19-/- mice were injected with monocrotaline (MCT) to establish a PAH model. H19 was detected in the cytokine-stimulated pulmonary arterial smooth muscle cells (PASMCs), serum and lungs of rats/mice. H19 overexpression and knockdown experiments were also conducted. A dual luciferase reporter assay was used to explore whether let-7b is a sponge miRNA of H19, and AT1R is a novel target of let-7b. A CCK-8 assay and flow cytometry were used to analyse cell proliferation. RESULTS The results showed that H19 was highly expressed in the serum and lungs of MCT-induced rats/mice, and H19 was upregulated by PDGF-BB in vitro. H19 upregulated AT1R expression via sponging miRNA let-7b following PDGF-BB stimulation. AT1R is a novel target of let-7b. Moreover, the overexpression of H19 and AT1R could facilitate PASMCs proliferation in vitro. H19 knockout protected mice from pulmonary artery remodeling and PAH following MCT treatment. CONCLUSION Our study showed that H19 is highly expressed in MCT-induced rodent lungs and upregulated by PDGF-BB. The H19-let-7b-AT1R axis contributed to the pathogenesis of PAH by stimulating PASMCs proliferation. The H19 knockout had a protective role in the development of PAH. H19 may be a potential tar-get for the treatment of PAH.
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Affiliation(s)
- Hua Su
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Xiaoling Xu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Chao Yan
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Yangfeng Shi
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Yanjie Hu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Liangliang Dong
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Songmin Ying
- Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Zhejiang, Hangzhou China
| | - Kejing Ying
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
| | - Ruifeng Zhang
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, No. 3 Qingchun Road East, Zhejiang, Hangzhou China
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767
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Viruses and long non-coding RNAs: implicating an evolutionary conserved region. Virusdisease 2018; 29:478-485. [PMID: 30539050 DOI: 10.1007/s13337-018-0486-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/03/2018] [Indexed: 12/23/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a class of cellular transcripts, which are involved in various biological processes. There is conflicting data regarding to the origin of these non-coding molecules and lncRNAs are thought to be the origin of viral genome. Here we sought to find the homology between human lncRNAs and viruses. For this purpose, the lncRNAdb database was searched for human lncRNAs. The lncRNAs' sequences were aligned with virus taxa using NCBI's BLAST tool. The phylogenic study was performed with maximum-likelihood based algorithm. The database contains 152 human lncRNAs. As a result, 63 (41.44%) of the lncRNAs have homologies with viruses. Of which, 50 (79.36%) have homology with Stealth virus. Other viruses with homology to lncRNAs were nuclear integrating DNA/RNA viruses. Moreover, 35 of 64 (23.03%) of cancer-associated lncRNAs have sequence homology with the same viruses. In phylogenetic analyses, lncRNAs with no homology to viruses were found to be the ancestor of those with homology to viruses and cancer-irrelevant lncRNAs were found to be the ancestor of cancer-related transcripts. In conclusion, lncRNAs could be the origin of nuclear integrating viruses and the nuclear integrating viruses may evolved from the non-coding regions. The results imply the role of lncRNAs with homology to viruses in human cancers.
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768
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Yang Q, Jia L, Li X, Guo R, Huang Y, Zheng Y, Li W. Long Noncoding RNAs: New Players in the Osteogenic Differentiation of Bone Marrow- and Adipose-Derived Mesenchymal Stem Cells. Stem Cell Rev Rep 2018; 14:297-308. [PMID: 29464508 DOI: 10.1007/s12015-018-9801-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mesenchymal stem cells (MSCs) are an important population of multipotent stem cells that differentiate into multiple lineages and display great potential in bone regeneration and repair. Although the role of protein-coding genes in the osteogenic differentiation of MSCs has been extensively studied, the functions of noncoding RNAs in the osteogenic differentiation of MSCs are unclear. The recent application of next-generation sequencing to MSC transcriptomes has revealed that long noncoding RNAs (lncRNAs) are associated with the osteogenic differentiation of MSCs. LncRNAs are a class of non-coding transcripts of more than 200 nucleotides in length. Noncoding RNAs are thought to play a key role in osteoblast differentiation through various regulatory mechanisms including chromatin modification, transcription factor binding, competent endogenous mechanism, and other post-transcriptional mechanisms. Here, we review the roles of lncRNAs in the osteogenic differentiation of bone marrow- and adipose-derived stem cells and provide a theoretical foundation for future research.
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Affiliation(s)
- Qiaolin Yang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Lingfei Jia
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, 100081, People's Republic of China
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, 100081, People's Republic of China
| | - Xiaobei Li
- Department of Orthodontics, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Runzhi Guo
- Department of Orthodontics, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Yiping Huang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China
| | - Yunfei Zheng
- Department of Orthodontics, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China.
| | - Weiran Li
- Department of Orthodontics, Peking University School and Hospital of Stomatology, 22 Zhongguancun Avenue South, Haidian District, Beijing, 100081, People's Republic of China.
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769
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Fattore L, Mancini R, Ascierto PA, Ciliberto G. The potential of BRAF-associated non-coding RNA as a therapeutic target in melanoma. Expert Opin Ther Targets 2018; 23:53-68. [PMID: 30507327 DOI: 10.1080/14728222.2019.1554057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The advent of targeted therapies and immune checkpoints inhibitors has enhanced the treatment of metastatic melanomas. Despite striking improvements of patients' survival, drug resistance continues to limit the efficacy of such treatments. Genetic and nongenetic/adaptive mechanisms of resistance could be involved; in the latter mechanism, noncoding RNAs (ncRNAs) are emerging as key players. Areas covered: This article outlines the current knowledge of ncRNA involvement in BRAF-mutant melanomas and the development of resistance to targeted/immunotherapies. We also discuss how ncRNAs can be exploited for the development of therapeutic and diagnostic approaches. Expert opinion: ncRNAs can be envisaged as powerful diagnostics and therapeutics. Despite progress in our knowledge about their deregulation in cancer, it is still difficult to derive universal and robust ncRNAs unique signatures of malignancy for diagnostic purposes, which need validation in large cohort of patients. Also, ncRNA specific targeting to melanoma cells in vivo requires the development of improved systemic delivery tools. In this regard, the development of stable nanodelivery particles seems to offer renewed hope for success in the clinic.
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Affiliation(s)
- Luigi Fattore
- a IRCCS , Regina Elena National Cancer Institute , Rome , Italy
| | - Rita Mancini
- b Department of Molecular and Clinical Medicine , University of Roma "Sapienza" , Rome , Italy
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770
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Liu Y, Qi B, Xie J, Wu X, Ling Y, Cao X, Kong F, Xin J, Jiang X, Wu Q, Wang W, Li Q, Zhang S, Wu F, Zhang D, Wang R, Zhang X, Li W. Filtered reproductive long non-coding RNAs by genome-wide analyses of goat ovary at different estrus periods. BMC Genomics 2018; 19:866. [PMID: 30509164 PMCID: PMC6278114 DOI: 10.1186/s12864-018-5268-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 11/19/2018] [Indexed: 11/15/2022] Open
Abstract
Background The goat is an important farm animal. Reproduction is an important process of goat farming. The ovary is the most important reproductive organ for goats. In recent years, an increasing number of long non-coding RNAs (lncRNAs) have been implicated in the regulation of mammal reproduction. However, there are few studies on the function of lncRNAs in reproduction, particularly lncRNAs in the ovary. Results The sequencing of goat ovaries generated 1,122,014,112 clean reads, and 4926 lncRNAs and 1454 TUCPs (transcripts of uncertain coding potential) were identified for further analysis by using the coding potential analysis software, CNCI, CPC and Pfam-sca. There were 115 /22 differential lncRNAs /TUCPs transcripts between the ovaries of the luteal phase and the follicular phase. We predicted the related genes of lncRNA /TUCP based on co-expression and co-localization methods. In total, 2584 /904 genes were predicted by co-expression, and 326/73 genes were predicted by co-localization. The functions of these genes were further analyzed with GO and KEGG analysis. The results showed that lncRNAs /TUCPs, which are highly expressed in goat ovaries in the luteal phase, are mainly associated with the synthesis of progesterone, and we filtered the lncRNAs /TUCPs, such as XR_001918177.1 and TUCP_001362, which may regulate the synthesis of progesterone; lncRNAs /TUCPs, which are highly expressed in goat ovaries in the follicular phase, are mainly associated with oogenesis and the maturation of oocytes, and we filtered the lncRNAs /TUCPs that may regulate the oogenesis and maturation of oocyte, such as XR_001917388.1 and TUCP_000849. Conclusion The present study provided the genome expression profile of lncRNAs /TUCPs in goat ovaries at different estrus periods and filtered the potential lncRNAs /TUCPs associated with goat reproduction. These results are helpful to further study the molecular mechanisms of goat reproduction. Electronic supplementary material The online version of this article (10.1186/s12864-018-5268-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yong Liu
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Bing Qi
- School of Life Sciences, Taishan Medical University, Taian, 271016, Shandong, China
| | - Juan Xie
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Xiaoqing Wu
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Yinghui Ling
- Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China
| | - Xinyan Cao
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, No.4899 Juye Street, Jingyue District, Changchun, 130112, China
| | - Feng Kong
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Jing Xin
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Xin Jiang
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Qiaoqin Wu
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Wenying Wang
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Qingmei Li
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Shengnan Zhang
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Fengrui Wu
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Di Zhang
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Rong Wang
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China
| | - Xiaorong Zhang
- School of Life Sciences, Taishan Medical University, Taian, 271016, Shandong, China
| | - Wenyong Li
- Key Laboratory of Embryo Development, Reproductive Regulation of Anhui Province, Fuyang Normal University, Fuyang, 236041, Anhui, China.
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771
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Fanelli GN, Gasparini P, Coati I, Cui R, Pakula H, Chowdhury B, Valeri N, Loupakis F, Kupcinskas J, Cappellesso R, Fassan M. LONG-NONCODING RNAs in gastroesophageal cancers. Noncoding RNA Res 2018; 3:195-212. [PMID: 30533569 PMCID: PMC6257886 DOI: 10.1016/j.ncrna.2018.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/26/2018] [Accepted: 10/26/2018] [Indexed: 02/07/2023] Open
Abstract
Despite continuing improvements in multimodal therapies, gastro-esophageal malignances remain widely prevalent in the population and is characterized by poor overall and disease-free survival rates. Due to the lack of understanding about the pathogenesis and absence of reliable markers, gastro-esophageal cancers are associated with delayed diagnosis. The increasing understanding about cancer's molecular landscape in the recent years, offers the possibility of identifying 'targetable' molecular events and in particular facilitates novel treatment strategies and development of biomarkers for early stage diagnosis. At least 98% of our genome is actively transcribed into non-coding RNAs encompassing long non-coding RNAs (lncRNAs) constituted of transcripts longer than 200 nucleotides with no protein-coding capacity. Many studies have demonstrated that lncRNAs are functional genomic elements playing pivotal roles in main oncogenic processes. LncRNA can act at multiple levels developing a complex molecular network that can modulate directly or indirectly the expression of genes involved in tumorigenesis. In this review, we focus on lncRNAs as emerging players in gastro-esophageal carcinogenesis and critically assess their potential as reliable noninvasive biomarkers and in next generation targeted therapies.
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Affiliation(s)
- Giuseppe Nicolò Fanelli
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, PD, Italy
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pierluigi Gasparini
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Irene Coati
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, PD, Italy
| | - Ri Cui
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hubert Pakula
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Basudev Chowdhury
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Fotios Loupakis
- Oncology Unit, Istituto Oncologico Veneto, IOV-IRCCS, Padua, PD, Italy
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rocco Cappellesso
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, PD, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology & Cytopathology Unit, University of Padua, Padua, PD, Italy
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772
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Genomic transcriptional response to 20-hydroxyecdysone in the fat body of silkworm, Bombyx mori. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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773
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Yang X, Wu Y, Zhang B, Ni B. Noncoding RNAs in multiple sclerosis. Clin Epigenetics 2018; 10:149. [PMID: 30497529 PMCID: PMC6267072 DOI: 10.1186/s13148-018-0586-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022] Open
Abstract
Multiple sclerosis (MS), a chronic inflammatory demyelinating disease of the central nervous system, is characterized by axonal degeneration and gliosis. Although the causes of MS remain unknown, gene dysregulation in the central nervous system has been associated with the disease pathogenesis. As such, the various regulators of gene expression may be contributing factors. The noncoding (nc) RNAs have piqued the interest of MS researchers due to their known functions in human physiology and various pathological processes, despite being generally characterized as transcripts without apparent protein-coding capacity. Accumulating evidence has indicated that ncRNAs participate in the regulation of MS by acting as epigenetic factors, especially the long (l) ncRNAs and the micro (mi) RNAs, and they are now recognized as key regulatory molecules in MS. In this review, we summarize the most current studies on the contribution of ncRNAs in MS pathogenic processes and discuss their potential applications in the diagnosis and treatment of MS.
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Affiliation(s)
- Xuan Yang
- Department of Immunology, Medical College of Qingdao University, 308 Ningxia Road, Shinan District, Qingdao, 266003, China.,Department of Pathophysiology, Third Military Medical University, 30 Gaotanyan St., Shapingba District, Chongqing, 400038, China
| | - Yuzhang Wu
- Institute of Immunology of PLA, Third Military Medical University, 30 Gaotanyan St., Shapingba District, Chongqing, 400038, China
| | - Bei Zhang
- Department of Immunology, Medical College of Qingdao University, 308 Ningxia Road, Shinan District, Qingdao, 266003, China.
| | - Bing Ni
- Department of Pathophysiology, Third Military Medical University, 30 Gaotanyan St., Shapingba District, Chongqing, 400038, China.
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774
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An H, Williams NG, Shelkovnikova TA. NEAT1 and paraspeckles in neurodegenerative diseases: A missing lnc found? Noncoding RNA Res 2018; 3:243-252. [PMID: 30533572 PMCID: PMC6257911 DOI: 10.1016/j.ncrna.2018.11.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/13/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative diseases are among the most common causes of disability worldwide. Although neurodegenerative diseases are heterogeneous in both their clinical features and the underlying physiology, they are all characterised by progressive loss of specific neuronal populations. Recent experimental evidence suggests that long non-coding RNAs (lncRNAs) play important roles in the CNS in health and disease. Nuclear Paraspeckle Assembly Transcript 1 (NEAT1) is an abundant, ubiquitously expressed lncRNA, which forms a scaffold for a specific RNA granule in the nucleus, or nuclear body, the paraspeckle. Paraspeckles act as molecular hubs for cellular processes commonly affected by neurodegeneration. Transcriptomic analyses of the diseased human tissue have revealed altered NEAT1 levels in the CNS in major neurodegenerative disorders as well as in some disease models. Although it is clear that changes in NEAT1 expression (and in some cases, paraspeckle assembly) accompany neuronal damage, our understanding of NEAT1 contribution to the disease pathogenesis is still rudimentary. In this review, we have summarised the available knowledge on NEAT1 involvement in the molecular processes linked to neurodegeneration and on NEAT1 dysregulation in this type of disease, with a special focus on amyotrophic lateral sclerosis. The goal of this review is to attract the attention of researchers in the field of neurodegeneration to NEAT1 and paraspeckles.
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Affiliation(s)
- Haiyan An
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Non G Williams
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
| | - Tatyana A Shelkovnikova
- Medicines Discovery Institute, School of Biosciences, Cardiff University, Park Place, Cardiff, CF10 3AT, United Kingdom
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775
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Musavi Shenas MH, Eghbal-Fard S, Mehrisofiani V, Abd Yazdani N, Rahbar Farzam O, Marofi F, Yousefi M. MicroRNAs and signaling networks involved in epithelial-mesenchymal transition. J Cell Physiol 2018; 234:5775-5785. [PMID: 30417364 DOI: 10.1002/jcp.27489] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 09/06/2018] [Indexed: 12/17/2022]
Abstract
Epithelial-mesenchymal transition (EMT) is a phenomenon in which epithelial cells lose their cell-to-cell connection and are detached from the base membrane. EMT is fundamental for many biological processes such as embryonic development and neurogenesis. It also plays a significant role in cancer progression and metastasis. EMT regulation occurs through a sophisticated network of transcription regulations that include many signaling pathways. The exact mechanism of cancer gene regulation has not been understood yet. However, it is interesting to study the role of microRNAs and epigenetics mechanism in the cancer development. In this review, the transcription regulation of EMT and the analysis of possible overlap between microRNAs and their targets which are involved in the cancer development are scrutinized.
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Affiliation(s)
| | - Shadi Eghbal-Fard
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahid Mehrisofiani
- Aging Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nima Abd Yazdani
- Aging Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Omid Rahbar Farzam
- Aging Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Faroogh Marofi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Aging Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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776
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Gudenas BL, Wang L. Prediction of LncRNA Subcellular Localization with Deep Learning from Sequence Features. Sci Rep 2018; 8:16385. [PMID: 30401954 PMCID: PMC6219567 DOI: 10.1038/s41598-018-34708-w] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/19/2018] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs are involved in biological processes throughout the cell including the nucleus, chromatin and cytosol. However, most lncRNAs remain unannotated and functional annotation of lncRNAs is difficult due to their low conservation and their tissue and developmentally specific expression. LncRNA subcellular localization is highly informative regarding its biological function, although it is difficult to discover because few prediction methods currently exist. While protein subcellular localization prediction is a well-established research field, lncRNA localization prediction is a novel research problem. We developed DeepLncRNA, a deep learning algorithm which predicts lncRNA subcellular localization directly from lncRNA transcript sequences. We analyzed 93 strand-specific RNA-seq samples of nuclear and cytosolic fractions from multiple cell types to identify differentially localized lncRNAs. We then extracted sequence-based features from the lncRNAs to construct our DeepLncRNA model, which achieved an accuracy of 72.4%, sensitivity of 83%, specificity of 62.4% and area under the receiver operating characteristic curve of 0.787. Our results suggest that primary sequence motifs are a major driving force in the subcellular localization of lncRNAs.
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Affiliation(s)
- Brian L Gudenas
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Liangjiang Wang
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA.
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777
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Noviello TMR, Di Liddo A, Ventola GM, Spagnuolo A, D’Aniello S, Ceccarelli M, Cerulo L. Detection of long non-coding RNA homology, a comparative study on alignment and alignment-free metrics. BMC Bioinformatics 2018; 19:407. [PMID: 30400819 PMCID: PMC6220562 DOI: 10.1186/s12859-018-2441-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/19/2018] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) represent a novel class of non-coding RNAs having a crucial role in many biological processes. The identification of long non-coding homologs among different species is essential to investigate such roles in model organisms as homologous genes tend to retain similar molecular and biological functions. Alignment-based metrics are able to effectively capture the conservation of transcribed coding sequences and then the homology of protein coding genes. However, unlike protein coding genes the poor sequence conservation of long non-coding genes makes the identification of their homologs a challenging task. RESULTS In this study we compare alignment-based and alignment-free string similarity metrics and look at promoter regions as a possible source of conserved information. We show that promoter regions encode relevant information for the conservation of long non-coding genes across species and that such information is better captured by alignment-free metrics. We perform a genome wide test of this hypothesis in human, mouse, and zebrafish. CONCLUSIONS The obtained results persuaded us to postulate the new hypothesis that, unlike protein coding genes, long non-coding genes tend to preserve their regulatory machinery rather than their transcribed sequence. All datasets, scripts, and the prediction tools adopted in this study are available at https://github.com/bioinformatics-sannio/lncrna-homologs .
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Affiliation(s)
- Teresa M. R. Noviello
- Dep. of Science and Technology, University of Sannio, via Port’Arsa, 11, Benevento, 82100 Italy
- BioGeM, Institute of Genetic Research “Gaetano Salvatore”, Camporeale, Ariano Irpino (AV), 83031 Italy
| | - Antonella Di Liddo
- Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Straße 13, Frankfurt am Main, 60438 Germany
| | | | - Antonietta Spagnuolo
- Dep. of Biology and Evolution of Marine Organisms, Stazione Zoologica “A. Dohrn”, Villa Comunale, Napoli, 80121 Italy
| | - Salvatore D’Aniello
- Dep. of Biology and Evolution of Marine Organisms, Stazione Zoologica “A. Dohrn”, Villa Comunale, Napoli, 80121 Italy
| | - Michele Ceccarelli
- Dep. of Science and Technology, University of Sannio, via Port’Arsa, 11, Benevento, 82100 Italy
- BioGeM, Institute of Genetic Research “Gaetano Salvatore”, Camporeale, Ariano Irpino (AV), 83031 Italy
| | - Luigi Cerulo
- Dep. of Science and Technology, University of Sannio, via Port’Arsa, 11, Benevento, 82100 Italy
- BioGeM, Institute of Genetic Research “Gaetano Salvatore”, Camporeale, Ariano Irpino (AV), 83031 Italy
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778
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Liu H, Lu Y, Wang J, Hu J, Wuyun T. Genome-wide screening of long non-coding RNAs involved in rubber biosynthesis in Eucommia ulmoides. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1070-1082. [PMID: 29944209 DOI: 10.1111/jipb.12693] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/25/2018] [Indexed: 06/08/2023]
Abstract
Increasing evidence indicates that long non-coding RNAs (lncRNAs) play pivotal roles in regulatory networks controlling plant and animal gene expression. However, lncRNA roles in regulating rubber biosynthesis in Eucommia ulmoides, an emerging source of natural rubber (Eu-rubber), are currently unknown. Here, we report on RNA deep-sequencing of E. ulmoides fruits at two developmental stages. Based on application of a stringent pipeline, 29,103 lncRNAs and 9,048 transcripts of uncertain coding potential (TUCPs) were identified. Two differentially expressed (DE) TUCPs appear to simultaneously regulate 12 protein-coding genes involved in Eu-rubber biosynthesis (GIEBs), as well as 95 DE genes. Functional categorization of these 95 DE genes indicated their involvement in subcellular microstructures and cellular processes, such as cell wall, cell division, and growth. These DE genes may participate in the differentiation and development of laticifers, where Eu-rubber is synthesized. A model is proposed in which "commanders" (DE TUCPs) direct the "builders" (DE genes) to construct a "storehouse" of materials needed for Eu-rubber synthesis, and the "workers" (GIEBs) to synthesize Eu-rubber. These findings provide insights into both cis- and trans-polyisoprene biosynthesis in plants, laying the foundation for additional studies of this crucial process.
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Affiliation(s)
- Huimin Liu
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China
| | - Yan Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Juan Wang
- Chemistry department, University of Missouri-Columbia, Columbia MO 65201, USA
| | - Jingjing Hu
- Inertia Shanghai Biotechnology Co., Ltd., Shanghai 200335, China
| | - Tana Wuyun
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China
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779
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Non-Coding RNAs and Hepatitis C Virus-Induced Hepatocellular Carcinoma. Viruses 2018; 10:v10110591. [PMID: 30380697 PMCID: PMC6265700 DOI: 10.3390/v10110591] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 10/27/2018] [Accepted: 10/29/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) infection is a worldwide health problem and is one of the main causes of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma (HCC). Despite recent improvements, effective treatments for HCC are still missing and new tools for early detection are needed. Non-coding RNAs (ncRNAs) have emerged as important regulators of gene expression and key players in human carcinogenesis, including HCC. Aberrant expression of ncRNAs is associated with HCC metastasis, invasion, dissemination, and recurrence. This review will focus on the recent advances in ncRNA expression profiles, their dysregulation in HCV-related HCC, and the clinical perspective of ncRNA signatures for the early detection of HCC.
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780
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Panoutsopoulou K, Avgeris M, Scorilas A. miRNA and long non-coding RNA: molecular function and clinical value in breast and ovarian cancers. Expert Rev Mol Diagn 2018; 18:963-979. [DOI: 10.1080/14737159.2018.1538794] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Konstantina Panoutsopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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781
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Chen B, Li Y, He Y, Xue C, Xu F. The emerging roles of long non-coding RNA in gallbladder cancer tumorigenesis. Cancer Biomark 2018; 22:359-366. [PMID: 29758925 DOI: 10.3233/cbm-170979] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Accumulating evidence suggests that long non-coding RNAs (lncRNAs) have important regulatory functions in gallbladder cancer (GBC) tumorigenesis and can serve as potential novel markers and/or targets for GBC. In this review, we critically discuss the emerging alteration of lncRNAs in GBC, the lncRNAs induced epigenetic regulation, the interaction of lncRNAs with microRNAs and lncRNAs effects on tumor-related signaling pathways. Additionally, contributions of lncRNAs in epithelial-mesenchymal transition process and energy metabolism reprogramming in GBC are also addressed. This may pave new ways towards the determination of GBC pathogenesis and lead to the development of new preventive and therapeutic strategies for GBC.
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Affiliation(s)
- Bing Chen
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China.,Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Ya Li
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China.,Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Yuting He
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Chen Xue
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
| | - Feng Xu
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, Henan, China
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782
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Long non-coding RNA LY86-AS1 and HCG27_201 expression in type 2 diabetes mellitus. Mol Biol Rep 2018; 45:2601-2608. [DOI: 10.1007/s11033-018-4429-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 10/05/2018] [Indexed: 12/13/2022]
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783
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Pan B, Zhao M, Xu L. Long noncoding RNA gastric cancer-associated transcript 3 plays oncogenic roles in glioma through sponging miR-3127-5p. J Cell Physiol 2018; 234:8825-8833. [PMID: 30317610 DOI: 10.1002/jcp.27542] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/13/2018] [Indexed: 02/02/2023]
Abstract
Evidence is emerging that long noncoding RNAs (lncRNAs) play vital roles in tumorigenesis. LncRNA gastric cancer-associated transcript 3 (GACAT3) is reported to participate in the development of breast cancer, colorectal cancer, nonsmall cell lung cancer, and gastric cancer. However, whether it is implicated in glioma has not been elucidated. Here, we found that GACAT3 level was aberrantly elevated in glioma tissues and cell lines. Higher GACAT3 expression predicted lower survival rate. Knockdown of GACAT3 suppressed the proliferation, colony formation, migration, and invasion but promoting apoptosis in glioma cells. Next, we determined that GACAT3 contributes to glioma progression through inhibiting microRNA (miR)-3127-5p. Subsequently, ELAVL1 was identified as a direct target of miR-3127-5p by bioinformatics analysis and luciferase reporter assay. Moreover, we confirmed that GACAT3 promoted ELAVL1 expression through sponging miR-3127-5p, leading to glioma progression. Taken together, our study elucidated that GACAT3/miR-3127-5p/ELAVL1 signaling regulates glioma development and might be a promising therapeutic target.
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Affiliation(s)
- Bailin Pan
- Department of Neurosurgery, Zhuji People's Hospital of Zhejiang Province, Zhuji Affiliated Hospital of Wenzhou Medical University, Zhuji, China
| | - Ming Zhao
- Department of Neurosurgery, Zhuji People's Hospital of Zhejiang Province, Zhuji Affiliated Hospital of Wenzhou Medical University, Zhuji, China
| | - Longbiao Xu
- Department of Neurosurgery, Zhuji People's Hospital of Zhejiang Province, Zhuji Affiliated Hospital of Wenzhou Medical University, Zhuji, China
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784
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Karlik E, Gozukirmizi N. Expression analysis of lncRNA AK370814 involved in the barley vitamin B6 salvage pathway under salinity. Mol Biol Rep 2018; 45:1597-1609. [PMID: 30298351 DOI: 10.1007/s11033-018-4289-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/30/2018] [Indexed: 01/17/2023]
Abstract
Long non-coding RNAs (lncRNAs), which are longer than > 200 nt, perform various functions in a variety of important biological processes. The aim of this study is the investigation of relative expression levels of AK372815 putative pyridoxal reductase (PLR) gene and sense lncRNA AK370814 on four barley genotypes (Hasat, Beysehir 99, Konevi 98 and Tarm 92) in response to 150 mM salinity application during 3 days post-germination. Seeds were placed randomly in petri dishes containing (a) only H2O (control), (b) 150 mM NaCl, for 72 h. RNA isolation was carried out using TriPure® reagent from 150 mM salt-treated root and shoot samples. Relative expression levels of AK372815 PLR and sense lncRNA AK370814 were determined by qPCR. Results demonstrated that salinity affected the expression levels of both AK372815 PLR gene and sense lncRNA AK370814 during germination. Although expression levels of AK372815 PLR tended to be down-regulated under salinity, expression levels of sense lncRNA AK370814 were up-regulated. Another goal of this study is improvement of alternative approach to NGS technologies for determination of relative expression levels of sense lncRNAs under particular circumstances. This is the first report that demonstrates a relationship between lncRNA and vitamin B6 salvage pathway.
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Affiliation(s)
- Elif Karlik
- Department of Biotechnology, Istanbul University, 34134, Vezneciler, Istanbul, Turkey.
| | - Nermin Gozukirmizi
- Department of Molecular Biology and Genetics, Istanbul University, 34134, Vezneciler, Istanbul, Turkey.,Department of Molecular Biology and Genetics, İstinye University, 34010, Zeytinburnu, İstanbul, Turkey
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785
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Li BJ, Jiang DL, Meng ZN, Zhang Y, Zhu ZX, Lin HR, Xia JH. Genome-wide identification and differentially expression analysis of lncRNAs in tilapia. BMC Genomics 2018; 19:729. [PMID: 30286721 PMCID: PMC6172845 DOI: 10.1186/s12864-018-5115-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/25/2018] [Indexed: 12/28/2022] Open
Abstract
Background Long noncoding RNAs (LncRNAs) play important roles in fundamental biological processes. However, knowledge about the genome-wide distribution and stress-related expression of lncRNAs in tilapia is still limited. Results Genome-wide identification of lncRNAs in the tilapia genome was carried out in this study using bioinformatics tools. 103 RNAseq datasets that generated in our laboratory or collected from NCBI database were analyzed. In total, 72,276 high-confidence lncRNAs were identified. The averaged positive correlation coefficient (r_mean = 0.286) between overlapped lncRNA and mRNA pairs showed significant differences with the values for all lncRNA-mRNA pairs (r_mean = 0.176, z statistics = − 2.45, p value = 0.00071) and mRNA-mRNA pairs (r_mean = 0.186, z statistics = − 2.23, p value = 0.0129). Weighted correlation network analysis of the lncRNA and mRNA datasets from 12 tissues identified 21 modules and many interesting mRNA genes that clustered with lncRNAs. Overrepresentation test indicated that these mRNAs enriched in many biological processes, such as meiosis (p = 0.00164), DNA replication (p = 0.00246), metabolic process (p = 0.000838) and in molecular function, e.g., helicase activity (p = 0.000102) and catalytic activity (p = 0.0000612). Differential expression (DE) analysis identified 99 stress-related lncRNA genes and 1955 tissue-specific DE lncRNA genes. MiRNA-lncRNA interaction analysis detected 72,267 lncRNAs containing motifs with sequence complementary to 458 miRNAs. Conclusions This study provides an invaluable resource for further studies on molecular bases of lncRNAs in tilapia genomes. Further function analysis of the lncRNAs will help to elucidate their roles in regulating stress-related adaptation in tilapia. Electronic supplementary material The online version of this article (10.1186/s12864-018-5115-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dan Li Jiang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zi Ning Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yong Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Zong Xian Zhu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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786
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Zhu E, Zhang J, Li Y, Yuan H, Zhou J, Wang B. Long noncoding RNA Plnc1 controls adipocyte differentiation by regulating peroxisome proliferator-activated receptor γ. FASEB J 2018; 33:2396-2408. [PMID: 30277818 DOI: 10.1096/fj.201800739rrr] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Detailed understanding of molecular mechanisms controlling adipogenesis is of great importance to identify new targets for treating obesity. Emerging evidence suggests that long noncoding RNAs (lncRNAs) may play a pivotal role in adipogenesis. Here, we have identified a novel lncRNA, Plnc1, which is transcribed from a position ∼25,000 bp upstream of the peroxisome proliferator-activated receptor γ2 ( PPAR-γ2) gene. Plnc1 is abundantly expressed in adipose tissue, and obese mice have higher Plnc1 expression in adipose tissue than nonobese mice. Plnc1 was induced in established adipogenic lines ST2, 3T3-L1, and C3H10T1/2 as well as in bone marrow stromal cells (BMSCs) after adipogenic treatment. Plnc1 knockdown blocked differentiation of ST2 cells and BMSCs into mature adipocytes, along with the reduction of PPAR-γ, CCAAT/enhancer binding protein-α, and adipocyte protein 2. Conversely, overexpression of Plnc1 promoted ST2 cells and BMSCs to fully differentiate. Mechanism studies revealed that Plnc1 could reduce the methylation level of CpG region in the PPAR-γ2 promoter and enhance the transcriptional activity of the promoter and thereby increase PPAR-γ2 transcription. Our study suggests that Plnc1 promotes adipogenic differentiation through controlling the key adipogenic transcription factor PPAR-γ and highlights the potential of Plnc1 as a target for new therapies to control metabolic disorders like obesity.-Zhu, E., Zhang, J., Li, Y., Yuan, H., Zhou, J., Wang, B. Long noncoding RNA Plnc1 controls adipocyte differentiation by regulating peroxisome proliferator-activated receptor γ.
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Affiliation(s)
- Endong Zhu
- Key Laboratory of Hormones and Development, Ministry of Health, Tianjin Metabolic Diseases Hospital, Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Metabolic Diseases, Tianjin Metabolic Diseases Hospital and Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Juanjuan Zhang
- Key Laboratory of Hormones and Development, Ministry of Health, Tianjin Metabolic Diseases Hospital, Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Metabolic Diseases, Tianjin Metabolic Diseases Hospital and Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Yachong Li
- Department of Endodontics, Stomatological Hospital, Tianjin Medical University, Tianjin, China
| | - Hairui Yuan
- Key Laboratory of Hormones and Development, Ministry of Health, Tianjin Metabolic Diseases Hospital, Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Metabolic Diseases, Tianjin Metabolic Diseases Hospital and Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Jie Zhou
- Key Laboratory of Hormones and Development, Ministry of Health, Tianjin Metabolic Diseases Hospital, Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Metabolic Diseases, Tianjin Metabolic Diseases Hospital and Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
| | - Baoli Wang
- Key Laboratory of Hormones and Development, Ministry of Health, Tianjin Metabolic Diseases Hospital, Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China.,Tianjin Key Laboratory of Metabolic Diseases, Tianjin Metabolic Diseases Hospital and Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, China
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787
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Scherrer K. Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review. Exp Cell Res 2018; 373:1-33. [PMID: 30266658 DOI: 10.1016/j.yexcr.2018.09.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 12/15/2022]
Abstract
The main purpose of this review is to recall for investigators - and in particular students -, some of the early data and concepts in molecular genetics and biology that are rarely cited in the current literature and are thus invariably overlooked. There is a growing tendency among editors and reviewers to consider that only data produced in the last 10-20 years or so are pertinent. However this is not the case. In exact science, sound data and lucid interpretation never become obsolete, and even if forgotten, will resurface sooner or later. In the field of gene expression, covered in the present review, recent post-genomic data have indeed confirmed many of the earlier results and concepts developed in the mid-seventies, well before the start of the recombinant DNA revolution. Human brains and even the most powerful computers, have difficulty in handling and making sense of the overwhelming flow of data generated by recent high-throughput technologies. This was easier when low throughput, more integrative methods based on biochemistry and microscopy dominated biological research. Nowadays, the need for organising concepts is ever more important, otherwise the mass of available data can generate only "building ruins" - the bricks without an architect. Concepts such as pervasive transcription of genomes, large genomic domains, full domain transcripts (FDTs) up to 100 kb long, the prevalence of post-transcriptional events in regulating eukaryotic gene expression, and the 3D-genome architecture, were all developed and discussed before 1990, and are only now coming back into vogue. Thus, to review the impact of earlier concepts on later developments in the field, I will confront former and current data and ideas, including a discussion of old and new methods. Whenever useful, I shall first briefly report post-genomic developments before addressing former results and interpretations. Equally important, some of the terms often used sloppily in scientific discussions will be clearly defined. As a basis for the ensuing discussion, some of the issues and facts related to eukaryotic gene expression will first be introduced. In chapter 2 the evolution in perception of biology over the last 60 years and the impact of the recombinant DNA revolution will be considered. Then, in chapter 3 data and theory concerning the genome, gene expression and genetics will be reviewed. The experimental and theoretical definition of the gene will be discussed before considering the 3 different types of genetic information - the "Triad" - and the importance of post-transcriptional regulation of gene expression in the light of the recent finding that 90% of genomic DNA seems to be transcribed. Some previous attempts to provide a conceptual framework for these observations will be recalled, in particular the "Cascade Regulation Hypothesis" (CRH) developed in 1967-85, and the "Gene and Genon" concept proposed in 2007. A knowledge of the size of primary transcripts is of prime importance, both for experimental and theoretical reasons, since these molecules represent the primary units of the "RNA genome" on which most of the post-transcriptional regulation of gene expression occurs. In chapter 4, I will first discuss some current post-genomic topics before summarising the discovery of the high Mr-RNA transcripts, and the investigation of their processing spanning the last 50 years. Since even today, a consensus concerning the real form of primary transcripts in eukaryotic cells has not yet been reached, I will refer to the viral and specialized cellular models which helped early on to understand the mechanisms of RNA processing and differential splicing which operate in cells and tissues. As a well-studied example of expression and regulation of a specific cellular gene in relation to differentiation and pathology, I will discuss the early and recent work on expression of the globin genes in nucleated avian erythroblasts. An important concept is that the primary transcript not only embodies protein-coding information and regulation of its expression, but also the 3D-structure of the genomic DNA from which it was derived. The wealth of recent post-genomic data published in this field emphasises the importance of a fundamental principle of genome organisation and expression that has been overlooked for years even though it was already discussed in the 1970-80ties. These issues are addressed in chapter 5 which focuses on the involvement of the nuclear matrix and nuclear architecture in DNA and RNA biology. This section will make reference to the Unified Matrix Hypothesis (UMH), which was the first molecular model of the 3D organisation of DNA and RNA. The chapter on the "RNA-genome and peripheral memories" discusses experimental data on the ribonucleoprotein complexes containing pre-mRNA (pre-mRNPs) and mRNA (mRNPs) which are organised in nuclear and cytoplasmic spaces respectively. Finally, "Outlook " will enumerate currently unresolved questions in the field, and will propose some ideas that may encourage further investigation, and comprehension of available experimental data still in need of interpretation. In chapter 8, some propositions and paradigms basic to the authors own analysis are discussed. "In conclusion" the raison d'être of this review is recalled and positioned within the overall framework of scientific endeavour.
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Affiliation(s)
- Klaus Scherrer
- Institute Jacques Monod, CNRS, University Paris Diderot, Paris, France.
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788
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Su M, Xiao Y, Ma J, Cao D, Zhou Y, Wang H, Liao Q, Wang W. Long non-coding RNAs in esophageal cancer: molecular mechanisms, functions, and potential applications. J Hematol Oncol 2018; 11:118. [PMID: 30223861 PMCID: PMC6142629 DOI: 10.1186/s13045-018-0663-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022] Open
Abstract
Esophageal cancer (EC) is the sixth leading cause of cancer-related death worldwide. The lack of early diagnostic biomarkers and effective prognostic indicators for metastasis and recurrence has resulted in the poor prognosis of EC. In addition, the underlying molecular mechanisms of EC development have yet to be elucidated. Accumulating evidence has demonstrated that lncRNAs play a vital role in the pathological progression of EC. LncRNAs may regulate gene expression through the recruitment of histone-modifying complexes to the chromatin and through interactions with RNAs or proteins. Recent evidence has demonstrated that the dysregulation of lncRNAs plays important roles in the proliferation, metastasis, invasion, angiogenesis, apoptosis, chemoradiotherapy resistance, and stemness of EC, which suggests potential clinical implications. In this review, we highlight the emerging roles and regulatory mechanisms of lncRNAs in the context of EC and discuss their potential clinical applications as diagnostic and prognostic biomarkers.
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Affiliation(s)
- Min Su
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, People's Republic of China. .,Department of the Central Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, People's Republic of China.
| | - Yuhang Xiao
- Department of Pharmacy, Xiangya Hospital of Xiangya School of Medicine, Central South University, Changsha, 410001, Hunan, People's Republic of China
| | - Junliang Ma
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Deliang Cao
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Yong Zhou
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Hui Wang
- Department of Thoracic Radiotherapy, Key laboratory of Translational Radiation Oncology, Department of Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Qianjin Liao
- Department of the Central Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, People's Republic of China.
| | - Wenxiang Wang
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, People's Republic of China.
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789
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LINC00657 played oncogenic roles in esophageal squamous cell carcinoma by targeting miR-615-3p and JunB. Biomed Pharmacother 2018; 108:316-324. [PMID: 30227324 DOI: 10.1016/j.biopha.2018.09.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 09/02/2018] [Accepted: 09/03/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The prognosis of esophageal squamous cell carcinoma (ESCC) is relatively poor due to the absence of efficient treatment. In this manuscript, we have investigated the specific roles and molecular mechanisms of LINC00657 to order to identify novel therapeutic targets for ESCC. METHOD The LINC00657 expression in ESCC tissues and cell lines were evaluated by quantitative real-time PCR. The expression of LINC00657 in ESCC cells was regulated by lentivirus transfection. Online bioinformatics analysis tools were used to predict the potential targets of LINC00657 and miR-615-3p. TCGA database was used to analyze the prognosis of ESCC patients. Transwell, wound healing assay and MTT were performed to investigate the ESCC cells' biological functions. JunB expression was evaluated by Western blot. RESULT LINC00657 was moderately increased in ESCC both in vivo and in vitro and up regulated by irradiation. LINC00657 knockdown could inhibit the migration and proliferation of ESCC cells. And downregulation of LINC00657 significantly enhanced the radio-sensitivity. Moreover, LINC00657 could act as a ceRNA to increase the expression of JunB by binding to miR-615-3p. Meanwhile, overexpression of miR-615-3p resulted in anti-tumor effects and led to the down-regulation of JunB. Survival analysis from TCGA indicated that ESCC patients with higher JunB expression had significant poorer prognosis. CONCLUSION LINC00657 might be involved in regulating ESCC's response to radiation; and it functioned as an oncogene in ESCC by targeting miR-615-3p and JunB, providing novel potential therapeutic targets.
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790
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Yu H, Rong L. Emerging role of long non-coding RNA in the development of gastric cancer. World J Gastrointest Oncol 2018; 10:260-270. [PMID: 30254721 PMCID: PMC6147769 DOI: 10.4251/wjgo.v10.i9.260] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/14/2018] [Accepted: 06/27/2018] [Indexed: 02/05/2023] Open
Abstract
Gastric cancer is a common, worldwide malignancy and has a poor prognosis due to late diagnosis. Long non-coding RNAs (lncRNAs) are a significant subtype of RNA molecules with a length longer than 200 nucleotides (nt) that rarely encode proteins. In recent decades, deregulation of lncRNAs has been shown to be involved in tumorigenesis and tumor progression in various human carcinomas, including gastric cancer. Accumulating evidence has shown that some lncRNAs may function as diagnostic biomarkers or therapeutic targets for gastric cancer. Thus, exploring the specific functions of lncRNAs will help both gain a better understanding of the pathogenesis and develop novel treatments for gastric cancer. In this review, we highlight the expression and functional roles of lncRNAs in gastric cancer, and analyze the potential applications of lncRNAs as diagnostic markers and therapeutic targets.
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Affiliation(s)
- Hang Yu
- Department of Endoscopic Center, Peking University First Hospital, Beijing 100034, China
| | - Long Rong
- Department of Endoscopic Center, Peking University First Hospital, Beijing 100034, China
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791
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Wang Z, Ren B, Huang J, Yin R, Jiang F, Zhang Q. LncRNA DUXAP10 modulates cell proliferation in esophageal squamous cell carcinoma through epigenetically silencing p21. Cancer Biol Ther 2018; 19:998-1005. [PMID: 30215547 DOI: 10.1080/15384047.2018.1470723] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Esophageal Squamous Cell Carcinoma (ESCC) belongs to malignant tumor of human digestive system. It has greatly threatened human health both mentally and physically. Long non-coding RNAs have been discovered to be special molecular regulators in various cancers, including ESCC. LncRNA DUXAP10 is a newfound RNA, which is able to improve the progression of cancers 1-3 . In this study, DUXAP10 was certified to be upregulated in ESCC tissues and cells. Besides, it was positively correlated with short survival time. Moreover, down-expression of DUXAP10 contributed to decreased cell proliferation and metastasis. Silenced DUXAP10 led to increased apoptosis rate and stagnation of cell cycle. Results of mechanism experiments suggested that DUXAP10 motivated ESCC progression through recruiting enhancer of zeste homolog 2 (EZH2) to the promoter of p21. Our findings suggested that the pseudogene-derived from lncRNA DUXAP10 drove the biological progression of ESCC. DUXAP10 was likely to be a potential therapeutic target for ESCC.
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Affiliation(s)
- Zhongqiu Wang
- a Department of Thoracic Surgery , Jiangsu Cancer Hospital, Institute Affiliated to Nanjing Medical University, Cancer Institute of Jiangsu Province. No.42 , Baiziting Road, Xuanwu District, 210009, Nanjing , Jiangsu Province , PR China
| | - Binhui Ren
- a Department of Thoracic Surgery , Jiangsu Cancer Hospital, Institute Affiliated to Nanjing Medical University, Cancer Institute of Jiangsu Province. No.42 , Baiziting Road, Xuanwu District, 210009, Nanjing , Jiangsu Province , PR China
| | - Jianfeng Huang
- a Department of Thoracic Surgery , Jiangsu Cancer Hospital, Institute Affiliated to Nanjing Medical University, Cancer Institute of Jiangsu Province. No.42 , Baiziting Road, Xuanwu District, 210009, Nanjing , Jiangsu Province , PR China
| | - Rong Yin
- a Department of Thoracic Surgery , Jiangsu Cancer Hospital, Institute Affiliated to Nanjing Medical University, Cancer Institute of Jiangsu Province. No.42 , Baiziting Road, Xuanwu District, 210009, Nanjing , Jiangsu Province , PR China
| | - Feng Jiang
- a Department of Thoracic Surgery , Jiangsu Cancer Hospital, Institute Affiliated to Nanjing Medical University, Cancer Institute of Jiangsu Province. No.42 , Baiziting Road, Xuanwu District, 210009, Nanjing , Jiangsu Province , PR China
| | - Qin Zhang
- a Department of Thoracic Surgery , Jiangsu Cancer Hospital, Institute Affiliated to Nanjing Medical University, Cancer Institute of Jiangsu Province. No.42 , Baiziting Road, Xuanwu District, 210009, Nanjing , Jiangsu Province , PR China
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792
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Balas MM, Johnson AM. Exploring the mechanisms behind long noncoding RNAs and cancer. Noncoding RNA Res 2018; 3:108-117. [PMID: 30175284 PMCID: PMC6114262 DOI: 10.1016/j.ncrna.2018.03.001] [Citation(s) in RCA: 211] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 03/23/2018] [Indexed: 02/06/2023] Open
Abstract
Over the past decade, long noncoding RNAs (lncRNAs) have been identified as significant players in gene regulation. They are often differentially expressed and widely-associated with a majority of cancer types. The aberrant expression of these transcripts has been linked to tumorigenesis, metastasis, cancer stage progression and patient survival. Despite their apparent link to cancer, it has been challenging to gain a mechanistic understanding of how they contribute to cancer, partially due the difficulty in discriminating functional RNAs from other noncoding transcription events. However, there are several well-studied lncRNAs where specific mechanisms have been more clearly defined, leading to new discoveries into how these RNAs function. One major observation that has come to light is the context-dependence of lncRNA mechanisms, where they often have unique function in specific cell types and environment. Here, we review the molecular mechanisms of lncRNAs with a focus on cancer pathways, illustrating a few informative examples. Together, this type of detailed insight will lead to a greater understanding of the potential for the application of lncRNAs as targets of cancer therapies and diagnostics.
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Affiliation(s)
- Maggie M. Balas
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus 12801 East 17th Ave., Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus 12801 East 17th Ave., Aurora, CO, United States
- RNA Bioscience Initiative, University of Colorado Denver Anschutz Medical Campus 12801 East 17th Ave., Aurora, CO, United States
| | - Aaron M. Johnson
- Molecular Biology Program, University of Colorado Denver Anschutz Medical Campus 12801 East 17th Ave., Aurora, CO, United States
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus 12801 East 17th Ave., Aurora, CO, United States
- RNA Bioscience Initiative, University of Colorado Denver Anschutz Medical Campus 12801 East 17th Ave., Aurora, CO, United States
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793
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Hermans-Beijnsberger S, van Bilsen M, Schroen B. Long non-coding RNAs in the failing heart and vasculature. Noncoding RNA Res 2018; 3:118-130. [PMID: 30175285 PMCID: PMC6114261 DOI: 10.1016/j.ncrna.2018.04.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 04/09/2018] [Accepted: 04/09/2018] [Indexed: 02/06/2023] Open
Abstract
Following completion of the human genome, it became evident that the majority of our DNA is transcribed into non-coding RNAs (ncRNAs) instead of protein-coding messenger RNA. Deciphering the function of these ncRNAs, including both small- and long ncRNAs (lncRNAs), is an emerging field of research. LncRNAs have been associated with many disorders and a number have been identified as key regulators in the development and progression of disease, including cardiovascular disease (CVD). CVD causes millions of deaths worldwide, annually. Risk factors include coronary artery disease, high blood pressure and ageing. In this review, we will focus on the roles of lncRNAs in the cellular and molecular processes that underlie the development of CVD: cardiomyocyte hypertrophy, fibrosis, inflammation, vascular disease and ageing. Finally, we discuss the biomarker and therapeutic potential of lncRNAs.
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Affiliation(s)
- Steffie Hermans-Beijnsberger
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
| | - Marc van Bilsen
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
- Department of Physiology, CARIM School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
| | - Blanche Schroen
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, 6200 MD, Maastricht, The Netherlands
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794
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Wang Y, Ye W, Wang Y. Genome-wide identification of long non-coding RNAs suggests a potential association with effector gene transcription in Phytophthora sojae. MOLECULAR PLANT PATHOLOGY 2018; 19:2177-2186. [PMID: 29665235 PMCID: PMC6638102 DOI: 10.1111/mpp.12692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/14/2018] [Accepted: 04/12/2018] [Indexed: 05/08/2023]
Abstract
Numerous long non-coding RNAs (lncRNAs) identified and characterized in mammals, plants and fungi have been found to play critical regulatory roles in biological processes. However, little is known about the role of lncRNAs in oomycete plant pathogens, which cause devastating damage to the economy and ecosystems. We used strand-specific RNA sequencing (RNA-seq) to generate a computational pipeline to identify lncRNAs in Phytophthora sojae, a model oomycete plant pathogen. In total, 940 lncRNAs with 1010 isoforms were identified from RNA-seq data obtained from four representative stages of P. sojae. The lncRNAs had shorter transcript lengths, longer exon lengths, fewer numbers of exons, lower GC content and higher minimum free energy values compared with protein-coding genes. lncRNAs in P. sojae exhibited low sequence conservation amongst oomycetes and P. sojae isolates. Transcriptional data indicated that P. sojae lncRNAs tended to be transcribed in a stage-specific manner; representative lncRNAs were validated by semi-quantitative reverse transcription-polymerase chain reaction. Phytophthora sojae lncRNAs were concentrated in gene-sparse regions, and lncRNAs were associated with secreted protein and effector coding genes. The neighbouring genes of lncRNAs encoded various effector family members, and RNA-seq data revealed a correlation between the transcription level of lncRNAs and their neighbouring genes. Our results provide the first comprehensive identification of lncRNAs in oomycetes and suggest a potential association between lncRNAs and effector genes.
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Affiliation(s)
- Yang Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsu 210095China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjingJiangsu 210095China
| | - Wenwu Ye
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsu 210095China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjingJiangsu 210095China
| | - Yuanchao Wang
- Department of Plant PathologyNanjing Agricultural UniversityNanjingJiangsu 210095China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of EducationNanjingJiangsu 210095China
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795
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Abstract
Epidemiological studies in humans and animal models (including ruminants and horses) have highlighted the critical role of nutrition on developmental programming. Indeed, it has been demonstrated that the nutritional environment during the periconceptional period and foetal development can altered the postnatal performance of the resultant offspring. This nutritional programming can be exerted by maternal and paternal lineages and can affect offspring beyond the F1 generation. Alterations in epigenetic mechanisms have been proposed as the causative link behind the programming trajectories observed in the offspring. Although a clear cause-effect relationship between epigenetic modifications during early development and later offspring phenotype has not been demonstrated in livestock species, strong associations have been reported for some epigenetic marks (e.g. messenger RNA) that are worth exploring as possible predictors of future offspring phenotype. In this review, we shortly describe the main epigenetic mechanisms studied so far in mammals (i.e. mainly in the mouse) thought to be associated with developmental programming, and discuss the few studies available in mammalian herbivores (e.g. cattle) showing the effect of nutrition on epigenetic marks and the associated phenotype. Clearly, there is a need to develop research on nutritional strategies capable of modulating the epigenetic machinery with positive influence on the phenotype of livestock herbivores. This type of research is needed to alleviate the challenges currently faced by the livestock industry (e.g. impaired fertility of high-yielding dairy cows). This in turn will have a positive influence on animal welfare and productivity of livestock enterprises.
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796
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Lin Y, Leng Q, Zhan M, Jiang F. A Plasma Long Noncoding RNA Signature for Early Detection of Lung Cancer. Transl Oncol 2018; 11:1225-1231. [PMID: 30098474 PMCID: PMC6089091 DOI: 10.1016/j.tranon.2018.07.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/19/2018] [Accepted: 07/24/2018] [Indexed: 01/14/2023] Open
Abstract
The early detection of lung cancer is a major clinical challenge. Long noncoding RNAs (lncRNAs) have important functions in tumorigenesis. Plasma lncRNAs directly released from primary tumors or the circulating cancer cells might provide cell-free cancer biomarkers. The objective of this study was to investigate whether the lncRNAs could be used as plasma biomarkers for early-stage lung cancer. By using droplet digital polymerase chain reaction, we determined the diagnostic performance of 26 lung cancer–associated lncRNAs in plasma of a development cohort of 63 lung cancer patients and 33 cancer-free individuals, and a validation cohort of 39 lung cancer patients and 28 controls. In the development cohort, 7 of the 26 lncRNAs were reliably measured in plasma. Two (SNHG1 and RMRP) displayed a considerably high plasma level in lung cancer patients vs. cancer-free controls (all P < .001). Combined use of the plasma lncRNAs as a biomarker signature produced 84.13% sensitivity and 87.88% specificity for diagnosis of lung cancer, independent of stage and histological type of lung tumor, and patients' age and sex (all P > .05). The diagnostic value of the plasma lncRNA signature for lung cancer early detection was confirmed in the validation cohort. The plasma lncRNA signature may provide a potential blood-based assay for diagnosing lung cancer at the early stage. Nevertheless, a prospective study is warranted to validate its clinical value.
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Affiliation(s)
- Yanli Lin
- Department of Cell Engineering, Beijing Institute of Biotechnology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China; Department of Pathology, University of Maryland School of Medicine, 10 S. Pine St. Baltimore, MD 21201, USA
| | - Qixin Leng
- Department of Cell Engineering, Beijing Institute of Biotechnology, No. 20 Dongdajie Street, Fengtai District, Beijing 100071, China
| | - Min Zhan
- Departments of Epidemiology & Public Health, University of Maryland School of Medicine, 660 W. Redwood St. Baltimore, MD 21201, USA
| | - Feng Jiang
- Department of Pathology, University of Maryland School of Medicine, 10 S. Pine St. Baltimore, MD 21201, USA.
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797
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Huang H, Sun J, Sun Y, Wang C, Gao S, Li W, Hu JF. Long noncoding RNAs and their epigenetic function in hematological diseases. Hematol Oncol 2018; 37:15-21. [PMID: 30052285 DOI: 10.1002/hon.2534] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022]
Abstract
Recent discoveries demonstrate the importance of long noncoding RNA (lncRNA) in the regulation of multiple major processes impacting development, differentiation, and metastasis of hematological diseases through epigenetic mechanisms. In contrast to genetic changes, epigenetic modification does not modify genes but is frequently reversible, thus providing opportunities for targeted treatment using specific inhibitors. In this review, we will summarize the function and epigenetic mechanism of lncRNA in malignant hematologic diseases.
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Affiliation(s)
- Hanying Huang
- Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jingnan Sun
- Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, California
| | - Yunpeng Sun
- Cardiovascular Surgery Department, First Hospital of Jilin University, Changchun, Jilin, China
| | - Cong Wang
- Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, California
| | - Sujun Gao
- Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Li
- Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China
| | - Ji-Fan Hu
- Cancer Center, First Hospital of Jilin University, Changchun, Jilin, China.,Stanford University Medical School, Palo Alto Veterans Institute for Research, Palo Alto, California
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798
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Cao D, Gu C, Ye D, Dai B, Zhu Y. PCA3 rs544190G>A and prostate cancer risk in an eastern Chinese population. Int Braz J Urol 2018; 44:500-505. [PMID: 29412547 PMCID: PMC5996780 DOI: 10.1590/s1677-5538.ibju.2017.0146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 11/22/2017] [Indexed: 11/28/2022] Open
Abstract
Background: The association of prostate cancer antigen 3 (PCA3) polymorphism (SNP, rs544190G>A) with metastatic prostate cancer in European descent has been reported. Our aim of the current study was to re-validate the effect of PCA3 polymorphism on prostate cancer risk in an Eastern Chinese population and then estimate possible genetic discrepancies among population. Materials and Methods: Taqman assay was employed to determine genotype of SNP rs544190 in 1015 ethnic Han Chinese patients with prostate cancer and 1032 cancer-free controls. Simultaneously, odds ratios (OR) and 95% confidence intervals (95%CI) for risk relationship were calculated by logistic regression models. Results: The statistically significant relationship between PCA3 rs544190G>A and higher prostate cancer risk was not found. Stratification analysis revealed that there was no remarkable association of rs544190 variant AG/AA genotype with prostate cancer risk in every subgroup, except for patients with Gleason score ≤7(3+4). Conclusion: Although the results demonstrated that SNP rs544190 was not involved in prostate cancer risk in Eastern Chinese descent, unlike in European population, these might have clinical implications on prostate cancer heterogeneity around the World. To validate these findings, well-designed studies with different ethnic populations are warranted.
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Affiliation(s)
- Dalong Cao
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chengyuan Gu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bo Dai
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yao Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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799
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Deciphering the Far-Reaching Functions of Non-coding RNA in Colorectal Cancer. CURRENT COLORECTAL CANCER REPORTS 2018. [DOI: 10.1007/s11888-018-0408-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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800
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Abdalla BA, Chen J, Nie Q, Zhang X. Genomic Insights Into the Multiple Factors Controlling Abdominal Fat Deposition in a Chicken Model. Front Genet 2018; 9:262. [PMID: 30073018 PMCID: PMC6060281 DOI: 10.3389/fgene.2018.00262] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/28/2018] [Indexed: 12/12/2022] Open
Abstract
Genetic selection for an increased growth rate in meat-type chickens has been accompanied by excessive fat accumulation particularly in abdominal cavity. These progressed to indirect and often unhealthy effects on meat quality properties and increased feed cost. Advances in genomics technology over recent years have led to the surprising discoveries that the genome is more complex than previously thought. Studies have identified multiple-genetic factors associated with abdominal fat deposition. Meanwhile, the obesity epidemic has focused attention on adipose tissue and the development of adipocytes. The aim of this review is to summarize the current understanding of genetic/epigenetic factors associated with abdominal fat deposition, or as it relates to the proliferation and differentiation of preadipocytes in chicken. The results discussed here have been identified by different genomic approaches, such as QTL-based studies, the candidate gene approach, epistatic interaction, copy number variation, single-nucleotide polymorphism screening, selection signature analysis, genome-wide association studies, RNA sequencing, and bisulfite sequencing. The studies mentioned in this review have described multiple-genetic factors involved in an abdominal fat deposition. Therefore, it is inevitable to further study the multiple-genetic factors in-depth to develop novel molecular markers or potential targets, which will provide promising applications for reducing abdominal fat deposition in meat-type chicken.
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Affiliation(s)
- Bahareldin A. Abdalla
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- National-Local Joint Engineering Research Center for Livestock Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Jie Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- National-Local Joint Engineering Research Center for Livestock Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- National-Local Joint Engineering Research Center for Livestock Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- National-Local Joint Engineering Research Center for Livestock Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
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