1
|
Samidurai A, Olex AL, Ockaili R, Kraskauskas D, Roh SK, Kukreja RC, Das A. Integrated Analysis of lncRNA-miRNA-mRNA Regulatory Network in Rapamycin-Induced Cardioprotection against Ischemia/Reperfusion Injury in Diabetic Rabbits. Cells 2023; 12:2820. [PMID: 38132140 PMCID: PMC10742118 DOI: 10.3390/cells12242820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
The inhibition of mammalian target of rapamycin (mTOR) with rapamycin (RAPA) provides protection against myocardial ischemia/reperfusion (I/R) injury in diabetes. Since interactions between transcripts, including long non-coding RNA (lncRNA), microRNA(miRNA) and mRNA, regulate the pathophysiology of disease, we performed unbiased miRarray profiling in the heart of diabetic rabbits following I/R injury with/without RAPA treatment to identify differentially expressed (DE) miRNAs and their predicted targets of lncRNAs/mRNAs. Results showed that among the total of 806 unique miRNAs targets, 194 miRNAs were DE after I/R in diabetic rabbits. Specifically, eight miRNAs, including miR-199a-5p, miR-154-5p, miR-543-3p, miR-379-3p, miR-379-5p, miR-299-5p, miR-140-3p, and miR-497-5p, were upregulated and 10 miRNAs, including miR-1-3p, miR-1b, miR-29b-3p, miR-29c-3p, miR-30e-3p, miR-133c, miR-196c-3p, miR-322-5p, miR-499-5p, and miR-672-5p, were significantly downregulated after I/R injury. Interestingly, RAPA treatment significantly reversed these changes in miRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated the participation of miRNAs in the regulation of several signaling pathways related to I/R injury, including MAPK signaling and apoptosis. Furthermore, in diabetic hearts, the expression of lncRNAs, HOTAIR, and GAS5 were induced after I/R injury, but RAPA suppressed these lncRNAs. In contrast, MALAT1 was significantly reduced following I/R injury, with the increased expression of miR-199a-5p and suppression of its target, the anti-apoptotic protein Bcl-2. RAPA recovered MALAT1 expression with its sponging effect on miR-199-5p and restoration of Bcl-2 expression. The identification of novel targets from the transcriptome analysis in RAPA-treated diabetic hearts could potentially lead to the development of new therapeutic strategies for diabetic patients with myocardial infarction.
Collapse
Affiliation(s)
- Arun Samidurai
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Amy L. Olex
- Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Ramzi Ockaili
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Donatas Kraskauskas
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Sean K. Roh
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Rakesh C. Kukreja
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Anindita Das
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| |
Collapse
|
2
|
Dehghanzad R, Khalafiyan A, Khanahmad H. The Necessity of Using Strand-Specific cDNA for Achieving Accurate Transcriptome Analysis Result. Adv Biomed Res 2023; 12:108. [PMID: 37288031 PMCID: PMC10241614 DOI: 10.4103/abr.abr_102_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 08/04/2022] [Accepted: 08/06/2022] [Indexed: 06/09/2023] Open
Affiliation(s)
- Reyhaneh Dehghanzad
- Department of Medical Genetics, Faculty of Medical Science, Tehran University of Medical Science, Tehran, Iran
| | - Anis Khalafiyan
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| |
Collapse
|
3
|
Brancato V, Brentari I, Coscujuela Tarrero L, Furlan M, Nicassio F, Denti MA. News from around the RNA world: new avenues in RNA biology, biotechnology and therapeutics from the 2022 SIBBM meeting. Biol Open 2022; 11:277240. [PMID: 36239357 PMCID: PMC9581514 DOI: 10.1242/bio.059597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since the formalization of the Central Dogma of molecular biology, the relevance of RNA in modulating the flow of information from DNA to proteins has been clear. More recently, the discovery of a vast set of non-coding transcripts involved in crucial aspects of cellular biology has renewed the enthusiasm of the RNA community. Moreover, the remarkable impact of RNA therapies in facing the COVID19 pandemics has bolstered interest in the translational opportunities provided by this incredible molecule. For all these reasons, the Italian Society of Biophysics and Molecular Biology (SIBBM) decided to dedicate its 17th yearly meeting, held in June 2022 in Rome, to the many fascinating aspects of RNA biology. More than thirty national and international speakers covered the properties, modes of action and applications of RNA, from its role in the control of development and cell differentiation to its involvement in disease. Here, we summarize the scientific content of the conference, highlighting the take-home message of each presentation, and we stress the directions the community is currently exploring to push forward our comprehension of the RNA World 3.0.
Collapse
Affiliation(s)
- Virginia Brancato
- Center for Genomic Science IIT@SEMM, Italian Institute of Technology, Milan 20139, Italy
| | - Ilaria Brentari
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | | | - Mattia Furlan
- Center for Genomic Science IIT@SEMM, Italian Institute of Technology, Milan 20139, Italy
| | - Francesco Nicassio
- Center for Genomic Science IIT@SEMM, Italian Institute of Technology, Milan 20139, Italy
| | - Michela A Denti
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| |
Collapse
|
4
|
Yu J, Wang W, Yang J, Zhang Y, Gong X, Luo H, Cao N, Xu Z, Tian M, Yang P, Mei Q, Chen Z, Li Z, Li C, Duan X, Lyu QR, Gao C, Zhang B, Wang Y, Wu G, Zeng C. LncRNA PSR Regulates Vascular Remodeling Through Encoding a Novel Protein Arteridin. Circ Res 2022; 131:768-787. [PMID: 36134578 PMCID: PMC9588624 DOI: 10.1161/circresaha.122.321080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 09/06/2022] [Indexed: 01/26/2023]
Abstract
RATIONALE Vascular smooth muscle cells (VSMCs) phenotype switch from contractile to proliferative phenotype is a pathological hallmark in various cardiovascular diseases. Recently, a subset of long noncoding RNAs was identified to produce functional polypeptides. However, the functional impact and regulatory mechanisms of long noncoding RNAs in VSMCs phenotype switching remain to be fully elucidated. OBJECTIVES To illustrate the biological function and mechanism of a VSMC-enriched long noncoding RNA and its encoded peptide in VSMC phenotype switching and vascular remodeling. RESULTS We identified a VSMC-enriched transcript encoded by a previously uncharacterized gene, which we called phenotype switching regulator (PSR), which was markedly upregulated during vascular remodeling. Although PSR was annotated as a long noncoding RNA, we demonstrated that the lncPSR (PSR transcript) also encoded a protein, which we named arteridin. In VSMCs, both arteridin and lncPSR were necessary and sufficient to induce phenotype switching. Mechanistically, arteridin and lncPSR regulate downstream genes by directly interacting with a transcription factor YBX1 (Y-box binding protein 1) and modulating its nuclear translocation and chromatin targeting. Intriguingly, the PSR transcription was also robustly induced by arteridin. More importantly, the loss of PSR gene or arteridin protein significantly attenuated the vascular remodeling induced by carotid arterial injury. In addition, VSMC-specific inhibition of lncPSR using adeno-associated virus attenuated Ang II (angiotensin II)-induced hypertensive vascular remodeling. CONCLUSIONS PSR is a VSMC-enriched gene, and its transcript IncPSR and encoded protein (arteridin) coordinately regulate transcriptional reprogramming through a shared interacting partner, YBX1. This is a previously uncharacterized regulatory circuit in VSMC phenotype switching during vascular remodeling, with lncPSR/arteridin as potential therapeutic targets for the treatment of VSMC phenotype switching-related vascular remodeling.
Collapse
Affiliation(s)
- Junyi Yu
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Wei Wang
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Jining Yang
- Research Center for Nutrition and Food Safety, Chongqing Key Laboratory of Nutrition and Food Safety, Institute of Military Preventive Medicine, The Third Military Medical University, Chongqing, P.R. China
| | - Ye Zhang
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Xue Gong
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Hao Luo
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Nian Cao
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Zaicheng Xu
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Miao Tian
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Peili Yang
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Qiao Mei
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Zhi Chen
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Zhuxin Li
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Chuanwei Li
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Xudong Duan
- Cardiovascular Research Center of Chongqing College, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Chongqing, P. R. China
| | - Qing Rex Lyu
- Cardiovascular Research Center of Chongqing College, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Chongqing, P. R. China
| | - Chen Gao
- Department of Pharmacology & Systems Physiology, University of Cincinnati College of Medicine, OH, USA
| | - Bing Zhang
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yibin Wang
- Signature Program in Cardiovascular and Metabolic Diseases, Duke-NUS School of Medicine, Singapore
| | - Gengze Wu
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
| | - Chunyu Zeng
- Department of Cardiology, Daping Hospital, The Third Military Medical University (Army Medical University), Chongqing, P.R. China
- Chongqing Key Laboratory for Hypertension Research, Chongqing Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing, P. R. China
- Cardiovascular Research Center of Chongqing College, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Chongqing, P. R. China
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, The Third Military Medical University, Chongqing, P.R. China
- Heart Center of Fujian Province, Union Hospital, Fujian Medical University, Fuzhou, P.R. China
- Department of Cardiology, Chongqing General Hospital, Chongqing, P. R. China
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, P.R. China
- Department of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing
| |
Collapse
|
5
|
Piergentili R, Basile G, Nocella C, Carnevale R, Marinelli E, Patrone R, Zaami S. Using ncRNAs as Tools in Cancer Diagnosis and Treatment-The Way towards Personalized Medicine to Improve Patients' Health. Int J Mol Sci 2022; 23:ijms23169353. [PMID: 36012617 PMCID: PMC9409241 DOI: 10.3390/ijms23169353] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 12/06/2022] Open
Abstract
Although the first discovery of a non-coding RNA (ncRNA) dates back to 1958, only in recent years has the complexity of the transcriptome started to be elucidated. However, its components are still under investigation and their identification is one of the challenges that scientists are presently facing. In addition, their function is still far from being fully understood. The non-coding portion of the genome is indeed the largest, both quantitatively and qualitatively. A large fraction of these ncRNAs have a regulatory role either in coding mRNAs or in other ncRNAs, creating an intracellular network of crossed interactions (competing endogenous RNA networks, or ceRNET) that fine-tune the gene expression in both health and disease. The alteration of the equilibrium among such interactions can be enough to cause a transition from health to disease, but the opposite is equally true, leading to the possibility of intervening based on these mechanisms to cure human conditions. In this review, we summarize the present knowledge on these mechanisms, illustrating how they can be used for disease treatment, the current challenges and pitfalls, and the roles of environmental and lifestyle-related contributing factors, in addition to the ethical, legal, and social issues arising from their (improper) use.
Collapse
Affiliation(s)
- Roberto Piergentili
- Institute of Molecular Biology and Pathology, Italian National Research Council (CNR-IBPM), 00185 Rome, Italy
| | - Giuseppe Basile
- Trauma Unit and Emergency Department, IRCCS Galeazzi Orthopedics Institute, 20161 Milan, Italy
- Head of Legal Medicine Unit, Clinical Institute San Siro, 20148 Milan, Italy
| | - Cristina Nocella
- Department of Clinical Internal, Anaesthesiological and Cardiovascular Sciences, “Sapienza” University of Rome, Viale del Policlinico, 155, 00161 Rome, Italy
| | - Roberto Carnevale
- Department of Medico-Surgical Sciences and Biotechnologies, “Sapienza” University of Rome, 04100 Latina, Italy
- Mediterranea Cardiocentro-Napoli, Via Orazio, 80122 Naples, Italy
| | - Enrico Marinelli
- Department of Medico-Surgical Sciences and Biotechnologies, “Sapienza” University of Rome, 04100 Latina, Italy
- Correspondence:
| | - Renato Patrone
- PhD ICTH, University of Federico II, HPB Department INT F. Pascale IRCCS of Naples, Via Mariano Semmola, 80131 Naples, Italy
| | - Simona Zaami
- Department of Anatomical, Histological, Forensic and Orthopedic Sciences, Section of Forensic Medicine, “Sapienza” University of Rome, 00161 Rome, Italy
| |
Collapse
|
6
|
Accolla RS. The Road to HTLV-1-Induced Leukemia by Following the Subcellular Localization of HTLV-1-Encoded HBZ Protein. Front Immunol 2022; 13:940131. [PMID: 35812456 PMCID: PMC9259882 DOI: 10.3389/fimmu.2022.940131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Human T cell leukemia virus-1 (HTLV-1) is the causative agent of a severe cancer of the lymphoid lineage that develops in 3-5% of infected individuals after many years. HTLV-1 infection may also induce a serious inflammatory pathology of the nervous system designated HTLV-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Two virus-encoded proteins, the viral transactivator Tax-1 and the HTLV-1 basic leucine-zipper factor HBZ, are strongly involved in the oncogenic process. Tax-1 is involved in initial phases of the oncogenic process. Conversely, HBZ seems to be involved in maintenance of the neoplastic state as witnessed by the generation of leukemic/lymphomatous phenotype in HBZ transgenic mice and the persistent expression of HBZ in all phases of the oncogenic process. Nevertheless, the intimate molecular and cellular mechanism mediated by the two viral proteins, particularly HBZ, in oncogenesis still remain elusive. An important step toward the complete comprehension of HBZ-associated oncogenicity is the clarification of the anatomical correlates of HBZ during the various phases of HTLV-1 infection to development of HTLV-1-associated inflammatory pathology and ultimately to the establishment of leukemia. In this review, I will summarize recent studies that have established for the first time a temporal and unidirectional expression of HBZ, beginning with an exclusive cytoplasmic localization in infected asymptomatic individuals and in HAM/TSP patients and ending to a progressive cytoplasmic-to-nuclear transition in leukemic cells. These results are framed within the present knowledge of HTLV-1 infection and the future lines of research that may shed new light on the complex mechanism of HTLV-1- mediated oncogenesis.
Collapse
|
7
|
Wang X, Parodi L, Hawkins SM. Translational Applications of Linear and Circular Long Noncoding RNAs in Endometriosis. Int J Mol Sci 2021; 22:10626. [PMID: 34638965 PMCID: PMC8508676 DOI: 10.3390/ijms221910626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 12/12/2022] Open
Abstract
Endometriosis is a chronic gynecologic disease that negatively affects the quality of life of many women. Unfortunately, endometriosis does not have a cure. The current medical treatments involve hormonal manipulation with unwanted side effects and high recurrence rates after stopping the medication. Sadly, a definitive diagnosis for endometriosis requires invasive surgical procedures, with the risk of complications, additional surgeries in the future, and a high rate of recurrence. Both improved therapies and noninvasive diagnostic tests are needed. The unique molecular features of endometriosis have been studied at the coding gene level. While the molecular components of endometriosis at the small RNA level have been studied extensively, other noncoding RNAs, such as long intergenic noncoding RNAs and the more recently discovered subset of long noncoding RNAs called circular RNAs, have been studied more limitedly. This review describes the molecular formation of long noncoding and the unique circumstances of the formation of circular long noncoding RNAs, their expression and function in endometriosis, and promising preclinical studies. Continued translational research on long noncoding RNAs, including the more stable circular long noncoding RNAs, may lead to improved therapeutic and diagnostic opportunities.
Collapse
Affiliation(s)
- Xiyin Wang
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN 55905, USA
| | - Luca Parodi
- Obstetrics and Gynecology Department, Istituto Clinico Sant’Anna, 25127 Brescia, Italy;
| | - Shannon M. Hawkins
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| |
Collapse
|
8
|
Ye Z, Ke H, Chen S, Cruz-Cano R, He X, Zhang J, Dorgan J, Milton DK, Ma T. Biomarker Categorization in Transcriptomic Meta-Analysis by Concordant Patterns With Application to Pan-Cancer Studies. Front Genet 2021; 12:651546. [PMID: 34276766 PMCID: PMC8283696 DOI: 10.3389/fgene.2021.651546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/28/2021] [Indexed: 01/21/2023] Open
Abstract
With the increasing availability and dropping cost of high-throughput technology in recent years, many-omics datasets have accumulated in the public domain. Combining multiple transcriptomic studies on related hypothesis via meta-analysis can improve statistical power and reproducibility over single studies. For differential expression (DE) analysis, biomarker categorization by DE pattern across studies is a natural but critical task following biomarker detection to help explain between study heterogeneity and classify biomarkers into categories with potentially related functionality. In this paper, we propose a novel meta-analysis method to categorize biomarkers by simultaneously considering the concordant pattern and the biological and statistical significance across studies. Biomarkers with the same DE pattern can be analyzed together in downstream pathway enrichment analysis. In the presence of different types of transcripts (e.g., mRNA, miRNA, and lncRNA, etc.), integrative analysis including miRNA/lncRNA target enrichment analysis and miRNA-mRNA and lncRNA-mRNA causal regulatory network analysis can be conducted jointly on all the transcripts of the same category. We applied our method to two Pan-cancer transcriptomic study examples with single or multiple types of transcripts available. Targeted downstream analysis identified categories of biomarkers with unique functionality and regulatory relationships that motivate new hypothesis in Pan-cancer analysis.
Collapse
Affiliation(s)
- Zhenyao Ye
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, College Park, MD, United States
| | - Hongjie Ke
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, College Park, MD, United States
| | - Shuo Chen
- Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Raul Cruz-Cano
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, College Park, MD, United States
| | - Xin He
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, College Park, MD, United States
| | - Jing Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, College Park, MD, United States
| | - Joanne Dorgan
- Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, United States
| | - Donald K Milton
- Maryland Institute for Applied Environmental Health, School of Public Health, University of Maryland, College Park, College Park, MD, United States
| | - Tianzhou Ma
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, College Park, MD, United States
| |
Collapse
|
9
|
Chowdhary A, Satagopam V, Schneider R. Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer. Front Genet 2021; 12:649619. [PMID: 34276764 PMCID: PMC8281131 DOI: 10.3389/fgene.2021.649619] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/20/2021] [Indexed: 01/09/2023] Open
Abstract
Long non-coding RNAs are diverse class of non-coding RNA molecules >200 base pairs of length having various functions like gene regulation, dosage compensation, epigenetic regulation. Dysregulation and genomic variations of several lncRNAs have been implicated in several diseases. Their tissue and developmental specific expression are contributing factors for them to be viable indicators of physiological states of the cells. Here we present an comprehensive review the molecular mechanisms and functions, state of the art experimental and computational pipelines and challenges involved in the identification and functional annotation of lncRNAs and their prospects as biomarkers. We also illustrate the application of co-expression networks on the TCGA-LIHC dataset for putative functional predictions of lncRNAs having a therapeutic potential in Hepatocellular carcinoma (HCC).
Collapse
Affiliation(s)
- Anshika Chowdhary
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Venkata Satagopam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Reinhard Schneider
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| |
Collapse
|
10
|
Monti M, Guiducci G, Paone A, Rinaldo S, Giardina G, Liberati FR, Cutruzzolá F, Tartaglia GG. Modelling of SHMT1 riboregulation predicts dynamic changes of serine and glycine levels across cellular compartments. Comput Struct Biotechnol J 2021; 19:3034-3041. [PMID: 34136101 PMCID: PMC8175283 DOI: 10.1016/j.csbj.2021.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/04/2021] [Accepted: 05/09/2021] [Indexed: 01/15/2023] Open
Abstract
Human serine hydroxymethyltransferase (SHMT) regulates the serine-glycine one carbon metabolism and plays a role in cancer metabolic reprogramming. Two SHMT isozymes are acting in the cell: SHMT1 encoding the cytoplasmic isozyme, and SHMT2 encoding the mitochondrial one. Here we present a molecular model built on experimental data reporting the interaction between SHMT1 protein and SHMT2 mRNA, recently discovered in lung cancer cells. Using a stochastic dynamic model, we show that RNA moieties dynamically regulate serine and glycine concentration, shaping the system behaviour. For the first time we observe an active functional role of the RNA in the regulation of the serine-glycine metabolism and availability, which unravels a complex layer of regulation that cancer cells exploit to fine tune amino acids availability according to their metabolic needs. The quantitative model, complemented by an experimental validation in the lung adenocarcinoma cell line H1299, exploits RNA molecules as metabolic switches of the SHMT1 activity. Our results pave the way for the development of RNA-based molecules able to unbalance serine metabolism in cancer cells.
Collapse
Affiliation(s)
- Michele Monti
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- RNA System Biology Lab, Centre for Human Technologies, Istituto Italiano di Tecnologia (IIT), Enrico Melen 83, 16152 Genova, Italy
| | - Giulia Guiducci
- Department of Biochemical Sciences “A.Rossi Fanelli”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences “A.Rossi Fanelli”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences “A.Rossi Fanelli”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences “A.Rossi Fanelli”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| | - Francesca Romana Liberati
- Department of Biochemical Sciences “A.Rossi Fanelli”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| | - Francesca Cutruzzolá
- Department of Biochemical Sciences “A.Rossi Fanelli”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- RNA System Biology Lab, Centre for Human Technologies, Istituto Italiano di Tecnologia (IIT), Enrico Melen 83, 16152 Genova, Italy
- ICREA, Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
- Department of Biology and Biotechnology “C. Darwin”, Sapienza University of Rome, P-le A.Moro 5, 00185 Rome, Italy
| |
Collapse
|
11
|
Human retroviral antisense mRNAs are retained in the nuclei of infected cells for viral persistence. Proc Natl Acad Sci U S A 2021; 118:2014783118. [PMID: 33875584 DOI: 10.1073/pnas.2014783118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Human retroviruses, including human T cell leukemia virus type 1 (HTLV-1) and HIV type 1 (HIV-1), encode an antisense gene in the negative strand of the provirus. Besides coding for proteins, the messenger RNAs (mRNAs) of retroviral antisense genes have also been found to regulate transcription directly. Thus, it has been proposed that retroviruses likely localize their antisense mRNAs to the nucleus in order to regulate nuclear events; however, this opposes the coding function of retroviral antisense mRNAs that requires a cytoplasmic localization for protein translation. Here, we provide direct evidence that retroviral antisense mRNAs are localized predominantly in the nuclei of infected cells. The retroviral 3' LTR induces inefficient polyadenylation and nuclear retention of antisense mRNA. We further reveal that retroviral antisense RNAs retained in the nucleus associate with chromatin and have transcriptional regulatory function. While HTLV-1 antisense mRNA is recruited to the promoter of C-C chemokine receptor type 4 (CCR4) and enhances transcription from it to support the proliferation of HTLV-1-infected cells, HIV-1 antisense mRNA is recruited to the viral LTR and inhibits sense mRNA expression to maintain the latency of HIV-1 infection. In summary, retroviral antisense mRNAs are retained in nucleus, act like long noncoding RNAs instead of mRNAs, and contribute to viral persistence.
Collapse
|
12
|
Plasek LM, Valadkhan S. lncRNAs in T lymphocytes: RNA regulation at the heart of the immune response. Am J Physiol Cell Physiol 2021; 320:C415-C427. [PMID: 33296288 PMCID: PMC8294623 DOI: 10.1152/ajpcell.00069.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genome-wide analyses in the last decade have uncovered the presence of a large number of long non-protein-coding transcripts that show highly tissue- and state-specific expression patterns. High-throughput sequencing analyses in diverse subsets of immune cells have revealed a complex and dynamic expression pattern for these long noncoding RNAs (lncRNAs) that correlate with the functional states of immune cells. Although the vast majority of lncRNAs expressed in immune cells remain unstudied, functional studies performed on a small subset have indicated that their state-specific expressions pattern frequently has a regulatory impact on the function of immune cells. In vivo and in vitro studies have pointed to the involvement of lncRNAs in a wide variety of cellular processes, including both the innate and adaptive immune response through mechanisms ranging from epigenetic and transcriptional regulation to sequestration of functional molecules in subcellular compartments. This review will focus mainly on the role of lncRNAs in CD4+ and CD8+ T cells, which play pivotal roles in adaptive immunity. Recent studies have pointed to key physiological functions for lncRNAs during several developmental and functional stages of the life cycle of lymphocytes. Although lncRNAs play important physiological roles in lymphocytic response to antigenic stimulation, differentiation into effector cells, and secretion of cytokines, their dysregulated expression can promote or sustain pathological states such as autoimmunity, chronic inflammation, cancer, and viremia. This, together with their highly cell type-specific expression patterns, makes lncRNAs ideal therapeutic targets and underscores the need for additional studies into the role of these understudied transcripts in adaptive immune response.
Collapse
|
13
|
Martin AM, Cassirer EF, Waits LP, Plowright RK, Cross PC, Andrews KR. Genomic association with pathogen carriage in bighorn sheep ( Ovis canadensis). Ecol Evol 2021; 11:2488-2502. [PMID: 33767816 PMCID: PMC7981200 DOI: 10.1002/ece3.7159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/03/2022] Open
Abstract
Genetic composition can influence host susceptibility to, and transmission of, pathogens, with potential population-level consequences. In bighorn sheep (Ovis canadensis), pneumonia epidemics caused by Mycoplasma ovipneumoniae have been associated with severe population declines and limited recovery across North America. Adult survivors either clear the infection or act as carriers that continually shed M. ovipneumoniae and expose their susceptible offspring, resulting in high rates of lamb mortality for years following the outbreak event. Here, we investigated the influence of genomic composition on persistent carriage of M. ovipneumoniae in a well-studied bighorn sheep herd in the Wallowa Mountains of Oregon, USA. Using 10,605 SNPs generated using RADseq technology for 25 female bighorn sheep, we assessed genomic diversity metrics and employed family-based genome-wide association methodologies to understand variant association and genetic architecture underlying chronic carriage. We observed no differences among genome-wide diversity metrics (heterozygosity and allelic richness) between groups. However, we identified two variant loci of interest and seven associated candidate genes, which may influence carriage status. Further, we found that the SNP panel explained ~55% of the phenotypic variance (SNP-based heritability) for M. ovipneumoniae carriage, though there was considerable uncertainty in these estimates. While small sample sizes limit conclusions drawn here, our study represents one of the first to assess the genomic factors influencing chronic carriage of a pathogen in a wild population and lays a foundation for understanding genomic influence on pathogen persistence in bighorn sheep and other wildlife populations. Future research should incorporate additional individuals as well as distinct herds to further explore the genomic basis of chronic carriage.
Collapse
Affiliation(s)
- Alynn M. Martin
- United States Geological SurveyNorthern Rocky Mountain Science CenterBozemanMTUSA
| | | | | | - Raina K. Plowright
- Department of Microbiology and ImmunologyMontana State UniversityBozemanMTUSA
| | - Paul C. Cross
- United States Geological SurveyNorthern Rocky Mountain Science CenterBozemanMTUSA
| | - Kimberly R. Andrews
- Institute for Bioinformatics and Evolutionary Studies (IBEST)University of IdahoMoscowIDUSA
| |
Collapse
|
14
|
Huang Y, Wang J, Zhao Y, Wang H, Liu T, Li Y, Cui T, Li W, Feng Y, Luo J, Gong J, Ning L, Zhang Y, Wang D, Zhang Y. cncRNAdb: a manually curated resource of experimentally supported RNAs with both protein-coding and noncoding function. Nucleic Acids Res 2021; 49:D65-D70. [PMID: 33010163 PMCID: PMC7778915 DOI: 10.1093/nar/gkaa791] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/30/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022] Open
Abstract
RNA endowed with both protein-coding and noncoding functions is referred to as 'dual-function RNA', 'binary functional RNA (bifunctional RNA)' or 'cncRNA (coding and noncoding RNA)'. Recently, an increasing number of cncRNAs have been identified, including both translated ncRNAs (ncRNAs with coding functions) and untranslated mRNAs (mRNAs with noncoding functions). However, an appropriate database for storing and organizing cncRNAs is still lacking. Here, we developed cncRNAdb, a manually curated database of experimentally supported cncRNAs, which aims to provide a resource for efficient manipulation, browsing and analysis of cncRNAs. The current version of cncRNAdb documents about 2600 manually curated entries of cncRNA functions with experimental evidence, involving more than 2,000 RNAs (including over 1300 translated ncRNAs and over 600 untranslated mRNAs) across over 20 species. In summary, we believe that cncRNAdb will help elucidate the functions and mechanisms of cncRNAs and develop new prediction methods. The database is available at http://www.rna-society.org/cncrnadb/.
Collapse
MESH Headings
- 3' Untranslated Regions
- 5' Untranslated Regions
- Animals
- Databases, Nucleic Acid/organization & administration
- Drosophila melanogaster/genetics
- Humans
- Mice
- MicroRNAs/classification
- MicroRNAs/genetics
- Pan troglodytes/genetics
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Messenger/classification
- RNA, Messenger/genetics
- RNA, Ribosomal/classification
- RNA, Ribosomal/genetics
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Transfer/classification
- RNA, Transfer/genetics
- Software
- Zebrafish/genetics
Collapse
Affiliation(s)
- Yan Huang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| | - Jing Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yue Zhao
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou 310053, China
| | - Huafeng Wang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| | - Tianyuan Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuhe Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Weiyi Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yige Feng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaxin Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaqi Gong
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lin Ning
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yong Zhang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| | - Dong Wang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yang Zhang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China
| |
Collapse
|
15
|
Adil MS, Khulood D, Somanath PR. Targeting Akt-associated microRNAs for cancer therapeutics. Biochem Pharmacol 2020; 189:114384. [PMID: 33347867 DOI: 10.1016/j.bcp.2020.114384] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/19/2022]
Abstract
The uncontrolled growth and spread of abnormal cells because of activating protooncogenes and/or inactivating tumor suppressor genes are the hallmarks of cancer. The PI3K/Akt signaling is one of the most frequently activated pathways in cancer cells responsible for the regulation of cell survival and proliferation in stress and hypoxic conditions during oncogenesis. Non-coding RNAs are a large family of RNAs that are not involved in protein-coding, and microRNAs (miRNAs) are a sub-set of non-coding RNAs with a single strand of 18-25 nucleotides. miRNAs are extensively involved in the post-transcriptional regulation of gene expression and play an extensive role in the regulatory mechanisms including cell differentiation, proliferation, apoptosis, and tumorigenesis. The impact of cancer on mRNA stability and translation efficiency is extensive and therefore, cancerous tissues exhibit drastic alterations in the expression of miRNAs. miRNAs can be modulated by utilizing techniques such as miRNA mimics, miRNA antagonists, or CRISPR/Cas9. In addition to their capacity as potential targets in cancer therapy, they can be used as reliable biomarkers to diagnose the disease at the earliest stage. Recent evidence indicates that microRNA-mediated gene regulation intersects with the Akt pathway, forming an Akt-microRNA regulatory network. miRNAs and Akt in this network operate together to exert their cellular tasks. In the current review, we discuss the Akt-associated miRNAs in several cancers, their molecular regulation, and how this newly emerging knowledge may contribute greatly to revolutionize cancer therapy.
Collapse
Affiliation(s)
- Mir S Adil
- Clinical and Experimental Therapeutics, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, United States
| | - Daulat Khulood
- Clinical and Experimental Therapeutics, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, United States
| | - Payaningal R Somanath
- Clinical and Experimental Therapeutics, University of Georgia and Charlie Norwood VA Medical Center, Augusta, GA, United States.
| |
Collapse
|
16
|
Ofoeyeno N, Ekpenyong E, Braconi C. Pathogenetic Role and Clinical Implications of Regulatory RNAs in Biliary Tract Cancer. Cancers (Basel) 2020; 13:E12. [PMID: 33375055 PMCID: PMC7792779 DOI: 10.3390/cancers13010012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 02/07/2023] Open
Abstract
Biliary tract cancer (BTC) is characterised by poor prognosis and low overall survival in patients. This is generally due to minimal understanding of its pathogenesis, late diagnosis and limited therapeutics in preventing or treating BTC patients. Non-coding RNA (ncRNA) are small RNAs (mRNA) that are not translated to proteins. ncRNAs were considered to be of no importance in the genome, but recent studies have shown they play essential roles in biology and oncology such as transcriptional repression and degradation, thus regulating mRNA transcriptomes. This has led to investigations into the role of ncRNAs in the pathogenesis of BTC, and their clinical implications. In this review, the mechanisms of action of ncRNA are discussed and the role of microRNAs in BTC is summarised. The scope of this review will be limited to miRNA as they have been shown to play the most significant roles in BTC progression. There is huge potential in miRNA-based biomarkers and therapeutics in BTC, but more studies, research and technological advancements are required before it can be translated into clinical practice for patients.
Collapse
Affiliation(s)
- Nduka Ofoeyeno
- The Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK;
| | | | - Chiara Braconi
- The Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK;
- Beatson West of Scotland Cancer Centre, Glasgow G12 Y0N, UK
| |
Collapse
|
17
|
Bogard B, Francastel C, Hubé F. Multiple information carried by RNAs: total eclipse or a light at the end of the tunnel? RNA Biol 2020; 17:1707-1720. [PMID: 32559119 PMCID: PMC7714488 DOI: 10.1080/15476286.2020.1783868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/06/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022] Open
Abstract
The findings that an RNA is not necessarily either coding or non-coding, or that a precursor RNA can produce different types of mature RNAs, whether coding or non-coding, long or short, have challenged the dichotomous view of the RNA world almost 15 years ago. Since then, and despite an increasing number of studies, the diversity of information that can be conveyed by RNAs is rarely searched for, and when it is known, it remains largely overlooked in further functional studies. Here, we provide an update with prominent examples of multiple functions that are carried by the same RNA or are produced by the same precursor RNA, to emphasize their biological relevance in most living organisms. An important consequence is that the overall function of their locus of origin results from the balance between various RNA species with distinct functions and fates. The consideration of the molecular basis of this multiplicity of information is obviously crucial for downstream functional studies when the targeted functional molecule is often not the one that is believed.
Collapse
Affiliation(s)
- Baptiste Bogard
- Université De Paris, Epigenetics and Cell Fate, CNRS, Paris, France
| | | | - Florent Hubé
- Université De Paris, Epigenetics and Cell Fate, CNRS, Paris, France
| |
Collapse
|
18
|
Li J, Zhang X, Liu C. The computational approaches of lncRNA identification based on coding potential: Status quo and challenges. Comput Struct Biotechnol J 2020; 18:3666-3677. [PMID: 33304463 PMCID: PMC7710504 DOI: 10.1016/j.csbj.2020.11.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) make up a large proportion of transcriptome in eukaryotes, and have been revealed with many regulatory functions in various biological processes. When studying lncRNAs, the first step is to accurately and specifically distinguish them from the colossal transcriptome data with complicated composition, which contains mRNAs, lncRNAs, small RNAs and their primary transcripts. In the face of such a huge and progressively expanding transcriptome data, the in-silico approaches provide a practicable scheme for effectively and rapidly filtering out lncRNA targets, using machine learning and probability statistics. In this review, we mainly discussed the characteristics of algorithms and features on currently developed approaches. We also outlined the traits of some state-of-the-art tools for ease of operation. Finally, we pointed out the underlying challenges in lncRNA identification with the advent of new experimental data.
Collapse
Affiliation(s)
- Jing Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Xuan Zhang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
| |
Collapse
|
19
|
Bensaoud C, Martins LA, Aounallah H, Hackenberg M, Kotsyfakis M. Emerging roles of non-coding RNAs in vector-borne infections. J Cell Sci 2020; 134:134/5/jcs246744. [PMID: 33154170 DOI: 10.1242/jcs.246744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are nucleotide sequences that are known to assume regulatory roles previously thought to be reserved for proteins. Their functions include the regulation of protein activity and localization and the organization of subcellular structures. Sequencing studies have now identified thousands of ncRNAs encoded within the prokaryotic and eukaryotic genomes, leading to advances in several fields including parasitology. ncRNAs play major roles in several aspects of vector-host-pathogen interactions. Arthropod vector ncRNAs are secreted through extracellular vesicles into vertebrate hosts to counteract host defense systems and ensure arthropod survival. Conversely, hosts can use specific ncRNAs as one of several strategies to overcome arthropod vector invasion. In addition, pathogens transmitted through vector saliva into vertebrate hosts also possess ncRNAs thought to contribute to their pathogenicity. Recent studies have addressed ncRNAs in vectors or vertebrate hosts, with relatively few studies investigating the role of ncRNAs derived from pathogens and their involvement in establishing infections, especially in the context of vector-borne diseases. This Review summarizes recent data focusing on pathogen-derived ncRNAs and their role in modulating the cellular responses that favor pathogen survival in the vertebrate host and the arthropod vector, as well as host ncRNAs that interact with vector-borne pathogens.
Collapse
Affiliation(s)
- Chaima Bensaoud
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, Ceske Budejovice (Budweis), Czechia
| | - Larissa Almeida Martins
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, Ceske Budejovice (Budweis), Czechia
| | - Hajer Aounallah
- Université de Tunis El Manar, Institut Pasteur de Tunis, LR11IPT03, Service d'entomologie médicale, 1002, Tunis, Tunisie.,Innovation and Development Laboratory, Innovation and Development Center, Instituto Butantan, São Paulo 05503-900, Brazil
| | - Michael Hackenberg
- Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071, Granada, Spain.,Lab. de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento s/n, Granada 18100, Spain
| | - Michail Kotsyfakis
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005, Ceske Budejovice (Budweis), Czechia
| |
Collapse
|
20
|
Chantsalnyam T, Lim DY, Tayara H, Chong KT. ncRDeep: Non-coding RNA classification with convolutional neural network. Comput Biol Chem 2020; 88:107364. [DOI: 10.1016/j.compbiolchem.2020.107364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/04/2020] [Accepted: 08/18/2020] [Indexed: 12/21/2022]
|
21
|
Sun Q, Song YJ, Prasanth KV. One locus with two roles: microRNA-independent functions of microRNA-host-gene locus-encoded long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1625. [PMID: 32945142 PMCID: PMC7965793 DOI: 10.1002/wrna.1625] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/22/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022]
Abstract
Long noncoding RNAs (lncRNAs) are RNA transcripts longer than 200 nucleotides that do not code for proteins. LncRNAs play crucial regulatory roles in several biological processes via diverse mechanisms and their aberrant expression is associated with various diseases. LncRNA genes are further subcategorized based on their relative organization in the genome. MicroRNA (miRNA)-host-gene-derived lncRNAs (lnc-MIRHGs) refer to lncRNAs whose genes also harbor miRNAs. There exists crosstalk between the processing of lnc-MIRHGs and the biogenesis of the encoded miRNAs. Although the functions of the encoded miRNAs are usually well understood, whether those lnc-MIRHGs play independent functions are not fully elucidated. Here, we review our current understanding of lnc-MIRHGs, including their biogenesis, function, and mechanism of action, with a focus on discussing the miRNA-independent functions of lnc-MIRHGs, including their involvement in cancer. Our current understanding of lnc-MIRHGs strongly indicates that this class of lncRNAs could play important roles in basic cellular events as well as in diseases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
Collapse
Affiliation(s)
- Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - You Jin Song
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
22
|
Mobasheri T, Rayzan E, Shabani M, Hosseini M, Mahmoodi Chalbatani G, Rezaei N. Neuroblastoma-targeted nanoparticles and novel nanotechnology-based treatment methods. J Cell Physiol 2020; 236:1751-1775. [PMID: 32735058 DOI: 10.1002/jcp.29979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 07/11/2020] [Accepted: 07/16/2020] [Indexed: 12/17/2022]
Abstract
Neuroblastoma is a complicated pediatric tumor, originating from the neural crest, which is the most prevalent in adrenal glands, but may rarely be seen in some other tissues as well. Studies are focused on developing new strategies through novel chemo- and immuno-therapeutic drug targets. Different types of oncogenes such as MYCN, tumor suppressor genes such as p53, and some structural genes such as vascular endothelial growth factor are considered as targets for neuroblastoma therapy. The individual expression patterns in NB cells make them appropriate for this purpose. The combined effect of nano-drug delivery systems and specific drug targets will result in lower systemic side effects, prolonged therapeutic effects, and improvements in the pharmacokinetic properties of the drugs. Some of these novel drug delivery systems with a focus on liposomes as carriers are also discussed. In this review, genes and protein products that are beneficial as drug targets in the treatment of neuroblastoma have been discussed.
Collapse
Affiliation(s)
- Taranom Mobasheri
- International Hematology/Oncology of Pediatrics Experts (IHOPE), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Elham Rayzan
- International Hematology/Oncology of Pediatrics Experts (IHOPE), Universal Scientific Education and Research Network (USERN), Tehran, Iran.,Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsima Shabani
- Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,International Hematology/Oncology of Pediatrics Experts (IHOPE), Universal Scientific Education and Research Network (USERN), Baltimore, Maryland
| | - Mina Hosseini
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Nima Rezaei
- Research Center for Immunodeficiencies (RCID), Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| |
Collapse
|
23
|
Yang X, Bam M, Becker W, Nagarkatti PS, Nagarkatti M. Long Noncoding RNA AW112010 Promotes the Differentiation of Inflammatory T Cells by Suppressing IL-10 Expression through Histone Demethylation. THE JOURNAL OF IMMUNOLOGY 2020; 205:987-993. [PMID: 32690657 DOI: 10.4049/jimmunol.2000330] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022]
Abstract
Long noncoding RNAs (lncRNAs) have been demonstrated to play important regulatory roles in gene expression, from histone modification to protein stability. However, the functions of most identified lncRNAs are not known. In this study, we investigated the role of an lncRNA called AW112010. The expression of AW112010 was significantly increased in CD4+ T cells from C57BL/6J mice activated in vivo with myelin oligodendrocyte glycoprotein, Staphylococcal enterotoxin B, or in vitro with anti-CD3 anti-CD28 mAbs, thereby demonstrating that activation of T cells leads to induction of AW112010. In contrast, anti-inflammatory cannabinoids such as cannabidiol or δ-9-tetrahydrocannabinol decreased the expression of AW112010 in T cells. Interestingly, the expression of AW112010 was high in in vitro-polarized Th1 and Th17 cells but low in Th2 cells, suggesting that this lncRNA may regulate inflammation. To identify genes that might be regulated by AW112010, we used chromatin isolation by RNA purification, followed by sequencing. This approach demonstrated that AW112010 regulated the transcription of IL-10. Additionally, the level of IL-10 in activated T cells was low when the expression of AW112010 was increased. Use of small interfering RNA to knock down AW112010 expression in activated T cells led to increased IL-10 expression and a decrease in the expression of IFN-γ. Further studies showed that AW112010 interacted with histone demethylase KDM5A, which led to decreased H3K4 methylation in IL-10 gene locus. Together, these studies demonstrate that lncRNA AW112010 promotes the differentiation of inflammatory T cells by suppressing IL-10 expression through histone demethylation.
Collapse
Affiliation(s)
- Xiaoming Yang
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC 29209
| | - Marpe Bam
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC 29209
| | - William Becker
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC 29209
| | - Prakash S Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC 29209
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC 29209
| |
Collapse
|
24
|
Salvatori B, Biscarini S, Morlando M. Non-coding RNAs in Nervous System Development and Disease. Front Cell Dev Biol 2020; 8:273. [PMID: 32435641 PMCID: PMC7218086 DOI: 10.3389/fcell.2020.00273] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
The rapid advance of RNA sequencing technologies contributed to a deep understanding of transcriptome composition and has allowed the discovery of a large number of non-coding RNAs (ncRNAs). The ability of these RNA molecules to be engaged in intricate and dynamic interactions with proteins and nucleic acids led to a great expansion of gene expression regulation mechanisms. By this matter, ncRNAs contribute to the increase in regulatory complexity that becomes highly specific between tissues and cell types. Among the ncRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are especially abundant in nervous system and have been shown to be implicated in its development, plasticity and aging as well as in neurological disorders. This review provides an overview of how these two diverse classes of ncRNAs control cellular processes during nervous system development, physiology, and disease conditions with particular emphasis on neurodegenerative disorders. The use of ncRNAs as biomarkers, tools, or targets for therapeutic intervention in neurodegeneration are also discussed.
Collapse
Affiliation(s)
- Beatrice Salvatori
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Silvia Biscarini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Mariangela Morlando
- Department of Pharmaceutical Sciences, "Department of Excellence 2018-2022", University of Perugia, Perugia, Italy
| |
Collapse
|
25
|
Expression of non-coding RNAs in hematological malignancies. Eur J Pharmacol 2020; 875:172976. [DOI: 10.1016/j.ejphar.2020.172976] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/18/2020] [Accepted: 01/29/2020] [Indexed: 12/22/2022]
|
26
|
Casimiro-Soriguer CS, Rubio A, Jimenez J, Pérez-Pulido AJ. Ancient evolutionary signals of protein-coding sequences allow the discovery of new genes in the Drosophila melanogaster genome. BMC Genomics 2020; 21:210. [PMID: 32138644 PMCID: PMC7059364 DOI: 10.1186/s12864-020-6632-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/28/2020] [Indexed: 12/20/2022] Open
Abstract
Background The current growth in DNA sequencing techniques makes of genome annotation a crucial task in the genomic era. Traditional gene finders focus on protein-coding sequences, but they are far from being exhaustive. The number of this kind of genes continuously increases due to new experimental data and development of improved bioinformatics algorithms. Results In this context, AnABlast represents a novel in silico strategy, based on the accumulation of short evolutionary signals identified by protein sequence alignments of low score. This strategy potentially highlights protein-coding regions in genomic sequences regardless of traditional homology or translation signatures. Here, we analyze the evolutionary information that the accumulation of these short signals encloses. Using the Drosophila melanogaster genome, we stablish optimal parameters for the accurate gene prediction with AnABlast and show that this new strategy significantly contributes to add genes, exons and pseudogenes regions, yet to be discovered in both already annotated and new genomes. Conclusions AnABlast can be freely used to analyze genomic regions of whole genomes where it contributes to complete the previous annotation.
Collapse
Affiliation(s)
- Carlos S Casimiro-Soriguer
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Alejandro Rubio
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Juan Jimenez
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Antonio J Pérez-Pulido
- Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA). Facultad de Ciencias Experimentales (Área de Genética), Universidad Pablo de Olavide, 41013, Sevilla, Spain.
| |
Collapse
|
27
|
Long non-coding RNAs in immune regulation and their potential as therapeutic targets. Int Immunopharmacol 2020; 81:106279. [PMID: 32058929 DOI: 10.1016/j.intimp.2020.106279] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 12/18/2022]
Abstract
Long non-coding RNAs (lncRNAs) are potent regulators of immune cell development and function. Their implication in multiple immune-mediated disorders highlights lncRNAs as exciting biomarkers and potential drug targets. Recent technological innovations in oligo-based therapeutics, development of RNA-targeting small molecules, and CRISPR-based approaches, position RNA as the next therapeutic frontier. Here, we review the latest advances made toward understanding the role of lncRNAs in human immunological disorders and further discuss RNA-targeting approaches that could be potentially exploited to manipulate lncRNA function as a clinical intervention.
Collapse
|
28
|
Carvalho Barbosa C, Calhoun SH, Wieden HJ. Non-coding RNAs: what are we missing? Biochem Cell Biol 2020; 98:23-30. [DOI: 10.1139/bcb-2019-0037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Over the past two decades, the importance of small non-coding RNAs (sncRNAs) as regulatory molecules has become apparent in all three domains of life (archaea, bacteria, eukaryotes). In fact, sncRNAs play an important role in the control of gene expression at both the transcriptional and the post-transcriptional level, with crucial roles in fine-tuning cell responses during internal and external stress. Multiple pathways for sncRNA biogenesis and diverse mechanisms of regulation have been reported, and although biogenesis and mechanisms of sncRNAs in prokaryotes and eukaryotes are different, remarkable similarities exist. Here, we briefly review and compare the major sncRNA classes that act post-transcriptionally, and focus on recent discoveries regarding the ribosome as a target of regulation and the conservation of these mechanisms between prokaryotes and eukaryotes.
Collapse
Affiliation(s)
- Cristina Carvalho Barbosa
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Sydnee H. Calhoun
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| |
Collapse
|
29
|
Long non-coding RNA LINC00504 regulates the Warburg effect in ovarian cancer through inhibition of miR-1244. Mol Cell Biochem 2019; 464:39-50. [PMID: 31691157 DOI: 10.1007/s11010-019-03647-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/25/2019] [Indexed: 12/24/2022]
Abstract
Ovarian cancer (OC) is the most lethal gynecologic malignancy and long non-coding RNAs (lncRNAs) have been acknowledged as important regulators in human OC. This study aimed to investigate the function and underlying mechanisms of LINC00504 in OC. The expression levels of LINC00504 in human OC tissues and cell lines were investigated by qRT-PCR analysis. The OC cell proliferation, and apoptosis were evaluated by MTT assay, colony-formation assay, Caspase-3 activity assay, and nucleosome ELISA assay, respectively. The metabolic shift in OC cells was examined by aerobic glycolysis analysis. Dual-luciferase activity reporter assay and mRNA-miRNA pull-down assay were conducted to validate the interaction between LINC00504 and miR-1244. LINC00504 was upregulated in OC cell lines and specimens. Knockdown of LINC00504 inhibited cell proliferation, enhanced apoptosis, decreased glycolysis-related gene (PKM2, HK2, and PDK1) expression, and altered aerobic glycolysis in OC cells and vice versa. LINC00504 downregulated miR-1244 expression levels by acting as an endogenous sponge of miR-1244. Inhibition of miR-1244 diminished the effects of LINC00504 on OC cells. Our study shows that LINC00504 promotes OC cell progression and stimulates aerobic glycolysis by interacting with miR-1244, which indicates that LINC00504 might act as a promising therapeutic target for OC treatment.
Collapse
|
30
|
Géranton SM. Does epigenetic 'memory' of early-life stress predispose to chronic pain in later life? A potential role for the stress regulator FKBP5. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190283. [PMID: 31544613 DOI: 10.1098/rstb.2019.0283] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Animal behaviours are affected not only by inherited genes but also by environmental experiences. For example, in both rats and humans, stressful early-life events such as being reared by an inattentive mother can leave a lasting trace and affect later stress response in adult life. This is owing to a chemical trace left on the chromatin attributed to so-called epigenetic mechanisms. Such an epigenetic trace often has consequences, sometimes long-lasting, on the functioning of our genes, thereby allowing individuals to rapidly adapt to a new environment. One gene under such epigenetic control is FKBP5, the gene that encodes the protein FKPB51, a crucial regulator of the stress axis and a significant driver of chronic pain states. In this article, we will discuss the possibility that exposure to stress could drive the susceptibly to chronic pain via epigenetic modifications of genes within the stress axis such as FKBP5. The possibility that such modifications, and therefore, the susceptibility to chronic pain, could be transmitted across generations in mammals and whether such mechanisms may be evolutionarily conserved across phyla will also be debated. This article is part of the Theo Murphy meeting issue 'Evolution of mechanisms and behaviour important for pain'.
Collapse
Affiliation(s)
- S M Géranton
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| |
Collapse
|
31
|
Li J, Liu C. Coding or Noncoding, the Converging Concepts of RNAs. Front Genet 2019; 10:496. [PMID: 31178900 PMCID: PMC6538810 DOI: 10.3389/fgene.2019.00496] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/06/2019] [Indexed: 12/18/2022] Open
Abstract
Technological advances over the past decade have unraveled the remarkable complexity of RNA. The identification of small peptides encoded by long non-coding RNAs (lncRNAs) as well as regulatory functions mediated by non-coding regions of mRNAs have further complicated our understanding of the multifaceted functions of RNA. In this review, we summarize current evidence pointing to dual roles of RNA molecules defined by their coding and non-coding potentials. We also discuss how the emerging roles of RNA transform our understanding of gene expression and evolution.
Collapse
Affiliation(s)
- Jing Li
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resource and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, China
| |
Collapse
|
32
|
The Function of Non-Coding RNAs in Lung Cancer Tumorigenesis. Cancers (Basel) 2019; 11:cancers11050605. [PMID: 31052265 PMCID: PMC6563001 DOI: 10.3390/cancers11050605] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/18/2019] [Accepted: 04/25/2019] [Indexed: 01/08/2023] Open
Abstract
Lung cancer is the most prevalent and deadliest cancer worldwide. A significant part of lung cancer studies is dedicated to the expression alterations of non-coding RNAs. The non-coding RNAs are transcripts that cannot be translated into proteins. While the study of microRNAs and siRNAs in lung cancer received a lot of attention over the last decade, highly efficient therapeutic option or the diagnostic methods based on non-coding RNAs are still lacking. Because of this, it is of utmost importance to direct future research on lung cancer towards analyzing other RNA types for which the currently available data indicates that are essential at modulating lung tumorigenesis. Through our review of studies on this subject, we identify the following non-coding RNAs as tumor suppressors: ts-46, ts-47, ts-101, ts-53, ts-3676, ts-4521 (tRNA fragments), SNORD116-26, HBII-420, SNORD15A, SNORA42 (snoRNAs), piRNA-like-163, piR-35127, the piR-46545 (piRNAs), CHIAP2, LOC100420907, RPL13AP17 (pseudogenes), and uc.454 (T-UCR). We also found non-coding RNAs with tumor-promoting function: tRF-Leu-CAG, tRNA-Leu, tRNA-Val (tRNA fragments), circ-RAD23B, circRNA 100146, circPVT1, circFGFR3, circ_0004015, circPUM1, circFLI1, circABCB10, circHIPK3 (circRNAs), SNORA42, SNORA3, SNORD46, SNORA21, SNORD28, SNORA47, SNORD66, SNORA68, SNORA78 (snoRNAs), piR-65, piR-34871, piR-52200, piR651 (piRNAs), hY4 5’ fragments (YRNAs), FAM83A-AS1, WRAP53, NKX2-1-AS1 (NATs), DUXAP8, SFTA1P (pseudogene transcripts), uc.338, uc.339 (T-UCRs), and hTERC.
Collapse
|
33
|
Lejars M, Kobayashi A, Hajnsdorf E. Physiological roles of antisense RNAs in prokaryotes. Biochimie 2019; 164:3-16. [PMID: 30995539 DOI: 10.1016/j.biochi.2019.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/12/2019] [Indexed: 12/16/2022]
Abstract
Prokaryotes encounter constant and often brutal modifications to their environment. In order to survive, they need to maintain fitness, which includes adapting their protein expression patterns. Many factors control gene expression but this review focuses on just one, namely antisense RNAs (asRNAs), a class of non-coding RNAs (ncRNAs) characterized by their location in cis and their perfect complementarity with their targets. asRNAs were considered for a long time to be trivial and only to be found on mobile genetic elements. However, recent advances in methodology have revealed that their abundance and potential activities have been underestimated. This review aims to illustrate the role of asRNA in various physiologically crucial functions in both archaea and bacteria, which can be regrouped in three categories: cell maintenance, horizontal gene transfer and virulence. A literature survey of asRNAs demonstrates the difficulties to characterize and assign a role to asRNAs. With the aim of facilitating this task, we describe recent technological advances that could be of interest to identify new asRNAs and to discover their function.
Collapse
Affiliation(s)
- Maxence Lejars
- CNRS UMR8261, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
| | - Asaki Kobayashi
- SABNP, INSERM U1204, Université d'Evry Val-d'Essonne, Bâtiment Maupertuis, Rue du Père Jarlan, 91000, Évry Cedex, France.
| | - Eliane Hajnsdorf
- CNRS UMR8261, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
| |
Collapse
|
34
|
Valadkhan S, Plasek LM. Long Non-Coding RNA-Mediated Regulation of the Interferon Response: A New Perspective on a Familiar Theme. Pathog Immun 2018. [PMID: 30135954 PMCID: PMC6101671 DOI: 10.20411/pai.v3i1.252] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The interferon (IFN) response is a critical and ubiquitous component of the innate immune response to pathogens. Detailed studies in the last decades have elucidated the function of a large number of proteins that mediate the complex signaling pathways and gene expression programs involved in the interferon response. The recent discovery of the long non-coding RNAs (lncRNAs) as a new category of cellular effectors has led to studies aiming to understand the role of these transcripts in the IFN response. Several high throughput studies have shown that a large number of lncRNAs are differentially expressed following IFN stimulation and/or viral infections. In-depth study of a very small fraction of the identified lncRNAs has revealed critical roles for this class of transcripts in the regulation of multiple steps of the IFN response, and pointed to the presence of an extensive RNA-mediated regulatory network during the antiviral response. As the vast majority of the identified potential regulatory lncRNAs remain unstudied, it is highly likely that future studies will reveal a completely new perspective on the regulation of the IFN response, with lncRNA- and protein-mediated regulatory networks coordinating the duration, magnitude, and character of this aspect of the innate immune response. In addition to providing a more complete picture of the IFN response, these studies will likely identify new therapeutic targets that in the long term may impact the therapeutic options available against microbial infections and diseases of the immune system.
Collapse
Affiliation(s)
- Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Leah M Plasek
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio
| |
Collapse
|