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Pereira IT, Gomes-Júnior R, Hansel-Frose A, França RSV, Liu M, Soliman HAN, Chan SSK, Dudley SC, Kyba M, Dallagiovanna B. Cardiac Development Long Non-Coding RNA ( CARDEL) Is Activated during Human Heart Development and Contributes to Cardiac Specification and Homeostasis. Cells 2024; 13:1050. [PMID: 38920678 PMCID: PMC11201801 DOI: 10.3390/cells13121050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
Successful heart development depends on the careful orchestration of a network of transcription factors and signaling pathways. In recent years, in vitro cardiac differentiation using human pluripotent stem cells (hPSCs) has been used to uncover the intricate gene-network regulation involved in the proper formation and function of the human heart. Here, we searched for uncharacterized cardiac-development genes by combining a temporal evaluation of human cardiac specification in vitro with an analysis of gene expression in fetal and adult heart tissue. We discovered that CARDEL (CARdiac DEvelopment Long non-coding RNA; LINC00890; SERTM2) expression coincides with the commitment to the cardiac lineage. CARDEL knockout hPSCs differentiated poorly into cardiac cells, and hPSC-derived cardiomyocytes showed faster beating rates after controlled overexpression of CARDEL during differentiation. Altogether, we provide physiological and molecular evidence that CARDEL expression contributes to sculpting the cardiac program during cell-fate commitment.
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Affiliation(s)
- Isabela T. Pereira
- Basic Stem Cell Biology Laboratory, Instituto Carlos Chagas-FIOCRUZ-PR, Curitiba 81350-010, PR, Brazil; (R.G.-J.); (A.H.-F.); (R.S.V.F.); (B.D.)
| | - Rubens Gomes-Júnior
- Basic Stem Cell Biology Laboratory, Instituto Carlos Chagas-FIOCRUZ-PR, Curitiba 81350-010, PR, Brazil; (R.G.-J.); (A.H.-F.); (R.S.V.F.); (B.D.)
| | - Aruana Hansel-Frose
- Basic Stem Cell Biology Laboratory, Instituto Carlos Chagas-FIOCRUZ-PR, Curitiba 81350-010, PR, Brazil; (R.G.-J.); (A.H.-F.); (R.S.V.F.); (B.D.)
| | - Rhaíza S. V. França
- Basic Stem Cell Biology Laboratory, Instituto Carlos Chagas-FIOCRUZ-PR, Curitiba 81350-010, PR, Brazil; (R.G.-J.); (A.H.-F.); (R.S.V.F.); (B.D.)
| | - Man Liu
- Department of Medicine, Division of Cardiology, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (S.C.D.J.)
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.N.S.); (S.S.K.C.); (M.K.)
| | - Hossam A. N. Soliman
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.N.S.); (S.S.K.C.); (M.K.)
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sunny S. K. Chan
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.N.S.); (S.S.K.C.); (M.K.)
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samuel C. Dudley
- Department of Medicine, Division of Cardiology, University of Minnesota, Minneapolis, MN 55455, USA; (M.L.); (S.C.D.J.)
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.N.S.); (S.S.K.C.); (M.K.)
| | - Michael Kyba
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN 55455, USA; (H.A.N.S.); (S.S.K.C.); (M.K.)
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bruno Dallagiovanna
- Basic Stem Cell Biology Laboratory, Instituto Carlos Chagas-FIOCRUZ-PR, Curitiba 81350-010, PR, Brazil; (R.G.-J.); (A.H.-F.); (R.S.V.F.); (B.D.)
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2
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Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells. CELL GENOMICS 2022; 2:100177. [PMID: 36381608 PMCID: PMC9648144 DOI: 10.1016/j.xgen.2022.100177] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human chromosomes are pervasively transcribed, but systematic understanding of coding and lncRNA genome function in cell differentiation is lacking. Using CRISPR interference (CRISPRi) in human induced pluripotent stem cells, we performed dual genome-wide screens - assessing 18,905 protein-coding and 10,678 lncRNA loci - and identified 419 coding and 201 lncRNA genes that regulate neural induction. Integrative analyses revealed distinct properties of coding and lncRNA genome function, including a 10-fold enrichment of lncRNA genes for roles in differentiation compared to proliferation. Further, we applied Perturb-seq to obtain granular insights into neural induction phenotypes. While most coding hits stalled or aborted differentiation, lncRNA hits were enriched for the genesis of diverse cellular states, including those outside the neural lineage. In addition to providing a rich resource (danlimlab.shinyapps.io/dualgenomewide) for understanding coding and lncRNA gene function in development, these results indicate that the lncRNA genome regulates lineage commitment in a manner fundamentally distinct from coding genes.
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3
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Yokoi S, Nakagawa S. UPA-Seq-Based Search Method for Functional lncRNA Candidates. Methods Mol Biol 2022; 2509:269-278. [PMID: 35796969 DOI: 10.1007/978-1-0716-2380-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Long noncoding RNAs (lncRNAs) constitute a large fraction of the transcriptome in mammals, and recent studies have revealed important functions of lncRNAs in a variety of biological processes. However, the fraction of lncRNAs that have been functionally validated is small, and only sequence and expression information are available for most lncRNAs. Here, we describe the procedures for UV-phenol aqueous-phase RNA sequencing (UPA-seq), a method for searching for functional lncRNA candidates among whole genomes based on the assumption that functional lncRNAs exert their functions through associations with proteins.
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Affiliation(s)
- Saori Yokoi
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
- Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
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4
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CRISPR/Cas9-mediated gene editing on Sox2ot promoter leads to its truncated expression and does not influence neural tube closure and embryonic development in mice. Biochem Biophys Res Commun 2021; 573:107-111. [PMID: 34403806 DOI: 10.1016/j.bbrc.2021.08.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/09/2021] [Indexed: 11/21/2022]
Abstract
Sox2 overlapping transcript (Sox2ot) is a long non-coding RNA (lncRNA), which harbors one of the major regulators of pluripotency, the Sox2 gene, in its intronic region. Sox2ot is primarily expressed in the developing neuroepithelium. However, its role in neural tube closure and embryonic development remains unclear. To investigate if Sox2ot is required for neural tube closure and embryonic development, Sox2ot promoter was deleted by CRISPR-Cas9 genome editing technology to prevent Sox2ot gene expression in mice. We designed 9 guide RNAs to specifically target the Sox2ot promoter and 3 gRNAs induced gene editing on the promoter of the Sox2ot gene in cells transfected with Cas9 mRNA and gRNAs. Then, these gRNAs and Cas9 mRNA were injected into mouse zygotes and implanted into pseudopregnant mice. A Sox2ot promoter-deleted mouse line was identified with complete deletion of promoter as well as deletion of exon 1 and exon 2. Sox2ot transcript was truncated with a lack of exon 1 and exon 2 in Sox2ot promoter-deleted mice. Furthermore, neural tube closure and embryonic development were checked at E9.5, E10.5, E14.5, E17.5 and after-birth (P2) and we did not find any failure of neural tube closure and aberrant embryonic development in Sox2ot promoter-deleted mice. Thus, our study demonstrated that CRISPR-Cas9 gene editing in Sox2ot promoter leads to its truncated expression and does not influence neural tube closure and embryonic development.
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5
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ArcRNAs and the formation of nuclear bodies. Mamm Genome 2021; 33:382-401. [PMID: 34085114 DOI: 10.1007/s00335-021-09881-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/25/2021] [Indexed: 01/13/2023]
Abstract
Long noncoding RNAs (lncRNAs) have long been collectively and passively defined as transcripts that do not encode proteins. However, extensive functional studies performed over the last decade have enabled the classification of lncRNAs into multiple categories according to their functions and/or molecular properties. Architectual RNAs (arcRNAs) are a group of lncRNAs that serve as architectural components of submicron-scale cellular bodies or nonmembranous organelles, which are composed of specific sets of proteins and nucleic acids involved in particular molecular processes. In this review, we focus on arcRNAs that function in the nucleus, which provide a structural basis for the formation of nuclear bodies, nonmembranous organelles in the cell nucleus. We will summarize the current list of arcRNAs and proteins associated with classic and more recently discovered nuclear bodies and discuss general rules that govern the formation of nuclear bodies, emphasizing weak multivalent interactions mediated by innately flexible biomolecules.
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6
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Chen H, Shan G. The physiological function of long-noncoding RNAs. Noncoding RNA Res 2020; 5:178-184. [PMID: 32959025 PMCID: PMC7494506 DOI: 10.1016/j.ncrna.2020.09.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
The physiological processes of cells and organisms are regulated by various biological macromolecules, including long-noncoding RNAs (lncRNAs), which cannot be translated into protein and are different from small-noncoding RNAs on their length. In animals, lncRNAs are involved in development, metabolism, reproduction, aging and other life events by cis or trans effects. For many functional lncRNAs, there is growing evidence that they play different roles on cellular level and organismal level. On the other hand, many annotated lncRNAs are not essential and could be transcription noises. In this minireview, we investigate the physiological function of lncRNAs in cells and focus on their functions and functional mechanisms on the organismal level. The studies on lncRNAs using different classic animal models such as worms and flies are summarized and discussed in this article.
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Affiliation(s)
- He Chen
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, 230027, China
| | - Ge Shan
- CAS Key Laboratory of Innate Immunity and Chronic Disease, CAS Center for Excellence in Molecular Cell Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui Province, 230027, China
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7
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Gast M, Rauch BH, Haghikia A, Nakagawa S, Haas J, Stroux A, Schmidt D, Schumann P, Weiss S, Jensen L, Kratzer A, Kraenkel N, Müller C, Börnigen D, Hirose T, Blankenberg S, Escher F, Kühl AA, Kuss AW, Meder B, Landmesser U, Zeller T, Poller W. Long noncoding RNA NEAT1 modulates immune cell functions and is suppressed in early onset myocardial infarction patients. Cardiovasc Res 2020; 115:1886-1906. [PMID: 30924864 DOI: 10.1093/cvr/cvz085] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 02/15/2019] [Accepted: 03/27/2019] [Indexed: 12/16/2022] Open
Abstract
AIMS Inflammation is a key driver of atherosclerosis and myocardial infarction (MI), and beyond proteins and microRNAs (miRs), long noncoding RNAs (lncRNAs) have been implicated in inflammation control. To obtain further information on the possible role of lncRNAs in the context of atherosclerosis, we obtained comprehensive transcriptome maps of circulating immune cells (peripheral blood mononuclear cells, PBMCs) of early onset MI patients. One lncRNA significantly suppressed in post-MI patients was further investigated in a murine knockout model. METHODS AND RESULTS Individual RNA-sequencing (RNA-seq) was conducted on PBMCs from 28 post-MI patients with a history of MI at age ≤50 years and stable disease ≥3 months before study participation, and from 31 healthy individuals without manifest cardiovascular disease or family history of MI as controls. RNA-seq revealed deregulated protein-coding transcripts and lncRNAs in post-MI PBMCs, among which nuclear enriched abundant transcript (NEAT1) was the most highly expressed lncRNA, and the only one significantly suppressed in patients. Multivariate statistical analysis of validation cohorts of 106 post-MI patients and 85 controls indicated that the PBMC NEAT1 levels were influenced (P = 0.001) by post-MI status independent of statin intake, left ventricular ejection fraction, low-density lipoprotein or high-density lipoprotein cholesterol, or age. We investigated NEAT1-/- mice as a model of NEAT1 deficiency to evaluate if NEAT1 depletion may directly and causally alter immune regulation. RNA-seq of NEAT1-/- splenocytes identified disturbed expression and regulation of chemokines/receptors, innate immunity genes, tumour necrosis factor (TNF) and caspases, and increased production of reactive oxygen species (ROS) under baseline conditions. NEAT1-/- spleen displayed anomalous Treg and TH cell differentiation. NEAT1-/- bone marrow-derived macrophages (BMDMs) displayed altered transcriptomes with disturbed chemokine/chemokine receptor expression, increased baseline phagocytosis (P < 0.0001), and attenuated proliferation (P = 0.0013). NEAT1-/- BMDMs responded to LPS with increased (P < 0.0001) ROS production and disturbed phagocytic activity (P = 0.0318). Monocyte-macrophage differentiation was deregulated in NEAT1-/- bone marrow and blood. NEAT1-/- mice displayed aortic wall CD68+ cell infiltration, and there was evidence of myocardial inflammation which could lead to severe and potentially life-threatening structural damage in some of these animals. CONCLUSION The study indicates distinctive alterations of lncRNA expression in post-MI patient PBMCs. Regarding the monocyte-enriched NEAT1 suppressed in post-MI patients, the data from NEAT1-/- mice identify NEAT1 as a novel lncRNA-type immunoregulator affecting monocyte-macrophage functions and T cell differentiation. NEAT1 is part of a molecular circuit also involving several chemokines and interleukins persistently deregulated post-MI. Individual profiling of this circuit may contribute to identify high-risk patients likely to benefit from immunomodulatory therapies. It also appears reasonable to look for new therapeutic targets within this circuit.
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Affiliation(s)
- Martina Gast
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany
| | - Bernhard H Rauch
- Institute for Pharmacology, Universitätsmedizin Greifswald, Felix-Hausdorff-Strasse 3, Greifswald, Germany.,German Center for Cardiovascular Research (DZHK), Site Greifswald, Felix-Hausdorff-Strasse 3, Greifswald
| | - Arash Haghikia
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany.,RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan.,Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 jo, Nishi 6-chome, Kita-ku, Sapporo, Japan
| | - Jan Haas
- Department of Cardiology, Institute for Cardiomyopathies, University Hospital Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Site Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
| | - Andrea Stroux
- Institute for Biometry and Clinical Epidemiology, Hindenburgdamm 30, Berlin, Germany
| | - David Schmidt
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany
| | - Paul Schumann
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genome Research, University of Greifswald, Felix-Hausdorff-Strasse 8, Greifswald, Germany
| | - Lars Jensen
- Interfaculty Institute for Genetics and Functional Genome Research, University of Greifswald, Felix-Hausdorff-Strasse 8, Greifswald, Germany
| | - Adelheid Kratzer
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany
| | - Nicolle Kraenkel
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany
| | - Christian Müller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, Martinistrasse 52, Hamburg, Germany
| | - Daniela Börnigen
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, Martinistrasse 52, Hamburg, Germany
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Stefan Blankenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, Martinistrasse 52, Hamburg, Germany
| | - Felicitas Escher
- German Center for Cardiovascular Research (DZHK), Site Berlin, Hindenburgdamm 30, Berlin, Germany.,Institute of Cardiac Diagnostics and Therapy (IKDT), Hindenburgdamm 30, Berlin, Germany.,Department of Cardiology CVK, Hindenburgdamm 30, Berlin, Germany
| | - Anja A Kühl
- iPATH.Berlin-Core Unit Immunopathology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas W Kuss
- Interfaculty Institute for Genetics and Functional Genome Research, University of Greifswald, Felix-Hausdorff-Strasse 8, Greifswald, Germany
| | - Benjamin Meder
- Department of Cardiology, Institute for Cardiomyopathies, University Hospital Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Site Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany.,Department of Genetics, Genome Technology Center, Stanford University Medical School, Stanford, CA, USA
| | - Ulf Landmesser
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Site Berlin, Hindenburgdamm 30, Berlin, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Strasse 2, Berlin, Germany
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, Martinistrasse 52, Hamburg, Germany
| | - Wolfgang Poller
- Department of Cardiology, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11, Hindenburgdamm 30, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Site Berlin, Hindenburgdamm 30, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Hindenburgdamm 30, Berlin, Germany
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8
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Macrophage Long Non-Coding RNAs in Pathogenesis of Cardiovascular Disease. Noncoding RNA 2020; 6:ncrna6030028. [PMID: 32664594 PMCID: PMC7549353 DOI: 10.3390/ncrna6030028] [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: 06/29/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022] Open
Abstract
Chronic inflammation is inextricably linked to cardiovascular disease (CVD). Macrophages themselves play important roles in atherosclerosis, as well as acute and chronic heart failure. Although the role of macrophages in CVD pathophysiology is well-recognized, little is known regarding the precise mechanisms influencing their function in these contexts. Long non-coding RNAs (lncRNAs) have emerged as significant regulators of macrophage function; as such, there is rising interest in understanding how these nucleic acids influence macrophage signaling, cell fate decisions, and activity in health and disease. In this review, we summarize current knowledge regarding lncRNAs in directing various aspects of macrophage function in CVD. These include foam cell formation, Toll-like receptor (TLR) and NF-kβ signaling, and macrophage phenotype switching. This review will provide a comprehensive understanding concerning previous, ongoing, and future studies of lncRNAs in macrophage functions and their importance in CVD.
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9
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Ganesh S, Horvat F, Drutovic D, Efenberkova M, Pinkas D, Jindrova A, Pasulka J, Iyyappan R, Malik R, Susor A, Vlahovicek K, Solc P, Svoboda P. The most abundant maternal lncRNA Sirena1 acts post-transcriptionally and impacts mitochondrial distribution. Nucleic Acids Res 2020; 48:3211-3227. [PMID: 31956907 PMCID: PMC7102984 DOI: 10.1093/nar/gkz1239] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 12/10/2019] [Accepted: 01/02/2020] [Indexed: 12/13/2022] Open
Abstract
Tens of thousands of rapidly evolving long non-coding RNA (lncRNA) genes have been identified, but functions were assigned to relatively few of them. The lncRNA contribution to the mouse oocyte physiology remains unknown. We report the evolutionary history and functional analysis of Sirena1, the most expressed lncRNA and the 10th most abundant poly(A) transcript in mouse oocytes. Sirena1 appeared in the common ancestor of mouse and rat and became engaged in two different post-transcriptional regulations. First, antisense oriented Elob pseudogene insertion into Sirena1 exon 1 is a source of small RNAs targeting Elob mRNA via RNA interference. Second, Sirena1 evolved functional cytoplasmic polyadenylation elements, an unexpected feature borrowed from translation control of specific maternal mRNAs. Sirena1 knock-out does not affect fertility, but causes minor dysregulation of the maternal transcriptome. This includes increased levels of Elob and mitochondrial mRNAs. Mitochondria in Sirena1−/− oocytes disperse from the perinuclear compartment, but do not change in number or ultrastructure. Taken together, Sirena1 contributes to RNA interference and mitochondrial aggregation in mouse oocytes. Sirena1 exemplifies how lncRNAs stochastically engage or even repurpose molecular mechanisms during evolution. Simultaneously, Sirena1 expression levels and unique functional features contrast with the lack of functional importance assessed under laboratory conditions.
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Affiliation(s)
- Sravya Ganesh
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Filip Horvat
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Croatia
| | - David Drutovic
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Michaela Efenberkova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Dominik Pinkas
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Anna Jindrova
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Josef Pasulka
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Rajan Iyyappan
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Radek Malik
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Andrej Susor
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Kristian Vlahovicek
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Croatia
| | - Petr Solc
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Petr Svoboda
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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10
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Gast M, Rauch BH, Nakagawa S, Haghikia A, Jasina A, Haas J, Nath N, Jensen L, Stroux A, Böhm A, Friebel J, Rauch U, Skurk C, Blankenberg S, Zeller T, Prasanth KV, Meder B, Kuss A, Landmesser U, Poller W. Immune system-mediated atherosclerosis caused by deficiency of long non-coding RNA MALAT1 in ApoE-/-mice. Cardiovasc Res 2020; 115:302-314. [PMID: 30101304 DOI: 10.1093/cvr/cvy202] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 08/03/2018] [Indexed: 02/07/2023] Open
Abstract
Aims The immune system is considered a key driver of atherosclerosis, and beyond proteins and microRNAs (miRs), long non-coding RNAs (lncRNAs) are implicated in immune control. We previously described that lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is involved in cardiac innate immunity in a myocarditis model. Here, we investigated the impact of MALAT1 deficiency upon atherosclerosis development. Methods and results Heterozygous MALAT1-deficient ApoE-/- mice displayed massive immune system dysregulation and atherosclerosis within 2 months even when kept on normal diet. Aortic plaque area (P < 0.05) and aortic root plaque size (P < 0.001) were increased in MALAT1-deficient vs. MALAT1-wildtype ApoE-/- mice. Serum levels of interferon-γ (IFN-γ), tumour necrosis factor (TNF), and interleukin 6 (IL6) were elevated (P < 0.001) in MALAT1-deficient animals. MALAT1-deficient bone marrow-derived macrophages showed enhanced expression of TNF (P = 0.001) and inducible NO synthase (NOS2) (P = 0.002), suppressed MMP9 (P < 0.001), and impaired phagocytic activity (P < 0.001) upon lipopolysaccharide stimulation. RNA-sequencing revealed grossly altered transcriptomes of MALAT1-deficient splenocytes already at baseline, with massive induction of IFN- γ, TNF, NOS2, and granzyme B; CC and CXC chemokines and CCR8; and innate immunity genes interferon-induced protein with tetratricopeptide repeats (IFIT)1/3, interferon-induced transmembrane protein (IFITM)1/3, ISG15. Multiple miRs were up to 45-fold upregulated. Further, selective ablation of the cytosolic part of the MALAT1 system only, the enzymatically MALAT1-derived mascRNA, resulted in massive induction of TNF (P = 0.004) and IL6 (P = 0.028) in macrophages. Northern analysis of post-myocardial infarction patient vs. control peripheral blood mononuclear cells showed reduced (P = 0.005) mascRNA in the patients. CHART-enriched RNA-sequencing reads at the genomic loci of MALAT1 and neighbouring nuclear enriched abundant transcript (NEAT1) documented direct interaction between these lncRNA transcripts. Conclusion The data suggest a molecular circuit involving the MALAT1-mascRNA system, interactions between MALAT1 and NEAT1, and key immune effector molecules, cumulatively impacting upon the development of atherosclerosis. It appears reasonable to look for therapeutic targets in this circuit and to screen for anomalies in the NEAT1-MALAT1 region in humans, too, as possible novel disease risk factors.
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Affiliation(s)
- Martina Gast
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany
| | - Bernhard H Rauch
- Institute for Pharmacology, Universitätsmedizin Greifswald, Felix-Hausdorff-Strasse 3, Greifswald, Germany.,German Center for Cardiovascular Research (DZHK), Felix-Hausdorff-Strasse 3, Greifswald, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan.,Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12 jo, Nishi 6-chome, Kita-ku, Sapporo, Japan
| | - Arash Haghikia
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Hindenburgdamm 30, Berlin, Germany
| | - Andrzej Jasina
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany
| | - Jan Haas
- Institute for Cardiomyopathies, Department of Cardiology, University Hospital Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Im Neuenheimer Feld 669, Heidelberg, Germany
| | - Neetika Nath
- Interfaculty Institute for Genetics and Functional Genome Research, University of Greifswald, Felix-Hausdorff-Strasse 8, Greifswald, Germany.,Institute for Bioinformatics, Universitätsmedizin Greifswald, Walther-Rathenau-Strasse 48, Greifswald, Germany
| | - Lars Jensen
- Interfaculty Institute for Genetics and Functional Genome Research, University of Greifswald, Felix-Hausdorff-Strasse 8, Greifswald, Germany.,Institute for Bioinformatics, Universitätsmedizin Greifswald, Walther-Rathenau-Strasse 48, Greifswald, Germany
| | - Andrea Stroux
- Institute for Biometry and Clinical Epidemiology, Charité - Universitätsmedizin Berlin, Chariteplatz 1, Berlin, Germany
| | - Andreas Böhm
- Institute for Pharmacology, Universitätsmedizin Greifswald, Felix-Hausdorff-Strasse 3, Greifswald, Germany
| | - Julian Friebel
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany
| | - Ursula Rauch
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany
| | - Carsten Skurk
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany
| | - Stefan Blankenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, Martinistrasse 52, Hamburg, Germany
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK), Site Hamburg/Lübeck/Kiel, Martinistrasse 52, Hamburg, Germany
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Chemical and Life Sciences Laboratory, 601 S. Goodwin Avenue, Urbana, IL, USA
| | - Benjamin Meder
- Institute for Cardiomyopathies, Department of Cardiology, University Hospital Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Im Neuenheimer Feld 669, Heidelberg, Germany
| | - Andreas Kuss
- Interfaculty Institute for Genetics and Functional Genome Research, University of Greifswald, Felix-Hausdorff-Strasse 8, Greifswald, Germany.,Institute for Bioinformatics, Universitätsmedizin Greifswald, Walther-Rathenau-Strasse 48, Greifswald, Germany
| | - Ulf Landmesser
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Hindenburgdamm 30, Berlin, Germany.,Berlin Institute of Health, Anna-Louisa-Karsch-Strasse 2, Berlin, Germany
| | - Wolfgang Poller
- Department of Cardiology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Hindenburgdamm 30, Berlin, Germany.,German Center for Cardiovascular Research (DZHK), Hindenburgdamm 30, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, Germany
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11
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Andersen RE, Hong SJ, Lim JJ, Cui M, Harpur BA, Hwang E, Delgado RN, Ramos AD, Liu SJ, Blencowe BJ, Lim DA. The Long Noncoding RNA Pnky Is a Trans-acting Regulator of Cortical Development In Vivo. Dev Cell 2020; 49:632-642.e7. [PMID: 31112699 DOI: 10.1016/j.devcel.2019.04.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/15/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023]
Abstract
While it is now appreciated that certain long noncoding RNAs (lncRNAs) have important functions in cell biology, relatively few have been shown to regulate development in vivo, particularly with genetic strategies that establish cis versus trans mechanisms. Pnky is a nuclear-enriched lncRNA that is transcribed divergently from the neighboring proneural transcription factor Pou3f2. Here, we show that conditional deletion of Pnky from the developing cortex regulates the production of projection neurons from neural stem cells (NSCs) in a cell-autonomous manner, altering postnatal cortical lamination. Surprisingly, Pou3f2 expression is not disrupted by deletion of the entire Pnky gene. Moreover, expression of Pnky from a BAC transgene rescues the differential gene expression and increased neurogenesis of Pnky-knockout NSCs, as well as the developmental phenotypes of Pnky-deletion in vivo. Thus, despite being transcribed divergently from a key developmental transcription factor, the lncRNA Pnky regulates development in trans.
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Affiliation(s)
- Rebecca E Andersen
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sung Jun Hong
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Justin J Lim
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Miao Cui
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brock A Harpur
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Elizabeth Hwang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ryan N Delgado
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexander D Ramos
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Siyuan John Liu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Medical Scientist Training Program, Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Benjamin J Blencowe
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, USA.
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12
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Abstract
Biomarker-driven personalized cancer therapy is a field of growing interest, and several molecular tests have been developed to detect biomarkers that predict, e.g., response of cancers to particular therapies. Identification of these molecules and understanding their molecular mechanisms is important for cancer prognosis and the development of therapeutics for late stage diseases. In the past, significant efforts have been placed on the discovery of protein or DNA-based biomarkers while only recently the class of long non-coding RNA (lncRNA) has emerged as a new category of biomarker. The mammalian genome is pervasively transcribed yielding a vast amount of non-protein-coding RNAs including lncRNAs. Hence, these transcripts represent a rich source of information that has the potential to significantly contribute to precision medicine in the future. Importantly, many lncRNAs are differentially expressed in carcinomas and they are emerging as potent regulators of tumor progression and metastasis. Here, we will highlight prime examples of lncRNAs that serve as marker for cancer progression or therapy response and which might represent promising therapeutic targets. Furthermore, we will introduce lncRNA targeting tools and strategies, and we will discuss potential pitfalls in translating these into clinical trials.
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13
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Karlik E, Ari S, Gozukirmizi N. LncRNAs: genetic and epigenetic effects in plants. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1581085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Elif Karlik
- Department of Biotechnology Institute of Graduate Studies in Science and Engineering, Istanbul University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Science, Istinye University, Istanbul, Turkey
| | - Sule Ari
- Department of Molecular Biology and Genetics Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Nermin Gozukirmizi
- Department of Molecular Biology and Genetics Faculty of Science, Istanbul University, Istanbul, Turkey
- Department of Molecular Biology and Genetics Faculty of Science, Istinye University, Istanbul, Turkey
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14
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Komatsu T, Yokoi S, Fujii K, Mito M, Kimura Y, Iwasaki S, Nakagawa S. UPA-seq: prediction of functional lncRNAs using differential sensitivity to UV crosslinking. RNA (NEW YORK, N.Y.) 2018; 24:1785-1802. [PMID: 30232101 PMCID: PMC6239193 DOI: 10.1261/rna.067611.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/12/2018] [Indexed: 05/16/2023]
Abstract
While a large number of long noncoding RNAs (lncRNAs) are transcribed from the genome of higher eukaryotes, systematic prediction of their functionality has been challenging due to the lack of conserved sequence motifs or structures. Assuming that some lncRNAs function as large ribonucleoprotein complexes and thus are easily crosslinked to proteins upon UV irradiation, we performed RNA-seq analyses of RNAs recovered from the aqueous phase after UV irradiation and phenol-chloroform extraction (UPA-seq). As expected, the numbers of UPA-seq reads mapped to known functional lncRNAs were remarkably reduced upon UV irradiation. Comparison with ENCODE eCLIP data revealed that lncRNAs that exhibited greater decreases upon UV irradiation preferentially associated with proteins containing prion-like domains (PrLDs). Fluorescent in situ hybridization (FISH) analyses revealed the nuclear localization of novel functional lncRNA candidates, including one that accumulated at the site of transcription. We propose that UPA-seq provides a useful tool for the selection of lncRNA candidates to be analyzed in depth in subsequent functional studies.
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Affiliation(s)
- Taiwa Komatsu
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Saori Yokoi
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Koichi Fujii
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Mari Mito
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
| | - Yusuke Kimura
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
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15
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Garcia GR, Shankar P, Dunham CL, Garcia A, La Du JK, Truong L, Tilton SC, Tanguay RL. Signaling Events Downstream of AHR Activation That Contribute to Toxic Responses: The Functional Role of an AHR-Dependent Long Noncoding RNA ( slincR) Using the Zebrafish Model. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:117002. [PMID: 30398377 PMCID: PMC6371766 DOI: 10.1289/ehp3281] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND A structurally diverse group of chemicals, including dioxins [e.g., 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)] and polycyclic aromatic hydrocarbons (PAHs), can xenobiotically activate the aryl hydrocarbon receptor (AHR) and contribute to adverse health effects in humans and wildlife. In the zebrafish model, repression of sox9b has a causal role in several AHR-mediated toxic responses, including craniofacial cartilage malformations; however, the mechanism of sox9b repression remains unknown. We previously identified a long noncoding RNA, sox9b long intergenic noncoding RNA (slincR), which is increased (in an AHR-dependent manner) by multiple AHR ligands and is required for the AHR-activated repression of sox9b. OBJECTIVE Using the zebrafish model, we aimed to enhance our understanding of the signaling events downstream of AHR activation that contribute to toxic responses by identifying: a) whether slincR is enriched on the sox9b locus, b) slincR's functional contributions to TCDD-induced toxicity, c) PAHs that increase slincR expression, and d) mammalian orthologs of slincR. METHODS We used capture hybridization analysis of RNA targets (CHART), qRT-PCR, RNA sequencing, morphometric analysis of cartilage structures, and hemorrhaging screens. RESULTS The slincR transcript was enriched at the 5' untranslated region (UTR) of the sox9b locus. Transcriptome profiling and human ortholog analyses identified processes related to skeletal and cartilage development unique to TCDD-exposed controls, and angiogenesis and vasculature development unique to TCDD-exposed zebrafish that were injected with a splice-blocking morpholino targeting slincR. In comparison to TCDD exposed control morphants, slincR morphants exposed to TCDD resulted in abnormal cartilage structures and a smaller percentage of animals displaying the hemorrhaging phenotype. In addition, slincR expression was significantly increased in six out of the sixteen PAHs we screened. CONCLUSION Our study establishes that in zebrafish, slincR is recruited to the sox9b 5' UTR to repress transcription, can regulate cartilage development, has a causal role in the TCDD-induced hemorrhaging phenotype, and is up-regulated by multiple environmentally relevant PAHs. These findings have important implications for understanding the ligand-specific mechanisms of AHR-mediated toxicity. https://doi.org/10.1289/EHP3281.
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Affiliation(s)
- Gloria R Garcia
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Prarthana Shankar
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Cheryl L Dunham
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Abraham Garcia
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Jane K La Du
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Lisa Truong
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Susan C Tilton
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
| | - Robert L Tanguay
- Department of Environmental and Molecular Toxicology, Sinnhuber Aquatic Research Laboratory, Environmental Health Sciences Center, Oregon State University, Corvallis, Oregon, USA
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16
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Bie B, Wang Y, Li L, Fang H, Liu L, Sun J. Noncoding RNAs: Potential players in the self-renewal of mammalian spermatogonial stem cells. Mol Reprod Dev 2018; 85:720-728. [PMID: 29969526 DOI: 10.1002/mrd.23041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/30/2018] [Indexed: 12/11/2022]
Abstract
Spermatogonial stem cells (SSCs), a unique population of male germ cells with self-renewal ability, are the foundation for maintenance of spermatogenesis throughout the life of the male. Although many regulatory molecules essential for SSC self-renewal have been identified, the fundamental mechanism underlying how SSCs acquire and maintain their self-renewal activity remains largely to be elucidated. In recent years, many types of noncoding RNAs (ncRNAs) have been suggested to regulate the SSC self-renewal through multiple ways, indicating ncRNAs play crucial roles in SSC self-renewal. In this paper, we mainly focus on four types of ncRNAs including microRNA, long ncRNA, piwi-interacting RNA, as well as circular RNAs, and reviewed their potential roles in SSC self-renewal that discovered recently to help us gain a better understanding of molecular mechanisms by which ncRNAs perform their function in regulating SSC self-renewal.
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Affiliation(s)
- Beibei Bie
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Ya Wang
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Liang Li
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Huanle Fang
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Libing Liu
- Department of Pharmacy, Medical School, Xi'an Peihua University, Xi'an, China
| | - Jin Sun
- National & Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
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17
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Poller W, Dimmeler S, Heymans S, Zeller T, Haas J, Karakas M, Leistner DM, Jakob P, Nakagawa S, Blankenberg S, Engelhardt S, Thum T, Weber C, Meder B, Hajjar R, Landmesser U. Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives. Eur Heart J 2018; 39:2704-2716. [PMID: 28430919 PMCID: PMC6454570 DOI: 10.1093/eurheartj/ehx165] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/14/2017] [Accepted: 03/15/2017] [Indexed: 02/06/2023] Open
Abstract
Recent research has demonstrated that the non-coding genome plays a key role in genetic programming and gene regulation during development as well as in health and cardiovascular disease. About 99% of the human genome do not encode proteins, but are transcriptionally active representing a broad spectrum of non-coding RNAs (ncRNAs) with important regulatory and structural functions. Non-coding RNAs have been identified as critical novel regulators of cardiovascular risk factors and cell functions and are thus important candidates to improve diagnostics and prognosis assessment. Beyond this, ncRNAs are rapidly emgerging as fundamentally novel therapeutics. On a first level, ncRNAs provide novel therapeutic targets some of which are entering assessment in clinical trials. On a second level, new therapeutic tools were developed from endogenous ncRNAs serving as blueprints. Particularly advanced is the development of RNA interference (RNAi) drugs which use recently discovered pathways of endogenous short interfering RNAs and are becoming versatile tools for efficient silencing of protein expression. Pioneering clinical studies include RNAi drugs targeting liver synthesis of PCSK9 resulting in highly significant lowering of LDL cholesterol or targeting liver transthyretin (TTR) synthesis for treatment of cardiac TTR amyloidosis. Further novel drugs mimicking actions of endogenous ncRNAs may arise from exploitation of molecular interactions not accessible to conventional pharmacology. We provide an update on recent developments and perspectives for diagnostic and therapeutic use of ncRNAs in cardiovascular diseases, including atherosclerosis/coronary disease, post-myocardial infarction remodelling, and heart failure.
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Affiliation(s)
- Wolfgang Poller
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Center of Molecular Medicine, Johann Wolfgang Goethe Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany
- DZHK, Site Rhein-Main, Frankfurt, Germany
| | - Stephane Heymans
- Center for Heart Failure Research, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Jan Haas
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Mahir Karakas
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - David-Manuel Leistner
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Philipp Jakob
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo, Japan
| | - Stefan Blankenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Stefan Engelhardt
- Institute for Pharmacology and Toxikology, Technische Universität München, Biedersteiner Strasse 29, München, Germany
- DZHK, Site Munich, Munich, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Christian Weber
- DZHK, Site Munich, Munich, Germany
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität, Pettenkoferstrasse 8a/9, Munich, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Roger Hajjar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ulf Landmesser
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
- Berlin Institute of Health, Kapelle-Ufer 2, Berlin, Germany
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18
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Stojic L, Lun AT, Mangei J, Mascalchi P, Quarantotti V, Barr AR, Bakal C, Marioni JC, Gergely F, Odom DT. Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis. Nucleic Acids Res 2018; 46:5950-5966. [PMID: 29860520 PMCID: PMC6093183 DOI: 10.1093/nar/gky437] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 05/03/2018] [Accepted: 05/09/2018] [Indexed: 02/06/2023] Open
Abstract
Loss-of-function (LOF) methods such as RNA interference (RNAi), antisense oligonucleotides or CRISPR-based genome editing provide unparalleled power for studying the biological function of genes of interest. However, a major concern is non-specific targeting, which involves depletion of transcripts other than those intended. Little work has been performed to characterize the off-target effects of these common LOF methods at the whole-transcriptome level. Here, we experimentally compared the non-specific activity of RNAi, antisense oligonucleotides and CRISPR interference (CRISPRi). All three methods yielded non-negligible off-target effects in gene expression, with CRISPRi also exhibiting strong clonal effects. As an illustrative example, we evaluated the performance of each method for determining the role of an uncharacterized long noncoding RNA (lncRNA). Several LOF methods successfully depleted the candidate lncRNA but yielded different sets of differentially expressed genes as well as a different cellular phenotype upon depletion. Similar discrepancies between methods were observed with a protein-coding gene (Ch-TOG/CKAP5) and another lncRNA (MALAT1). We suggest that the differences between methods arise due to method-specific off-target effects and provide guidelines for mitigating such effects in functional studies. Our recommendations provide a framework with which off-target effects can be managed to improve functional characterization of genes of interest.
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Affiliation(s)
- Lovorka Stojic
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Aaron T L Lun
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Jasmin Mangei
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Patrice Mascalchi
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Valentina Quarantotti
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Alexis R Barr
- Institute of Cancer Research, 237 Fulham Road London SW3 6JB, UK
| | - Chris Bakal
- Institute of Cancer Research, 237 Fulham Road London SW3 6JB, UK
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Fanni Gergely
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
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19
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Luo Y, Xu Y, Liang C, Xing W, Zhang T. The mechanism of myocardial hypertrophy regulated by the interaction between mhrt and myocardin. Cell Signal 2017; 43:11-20. [PMID: 29199045 DOI: 10.1016/j.cellsig.2017.11.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/17/2017] [Accepted: 11/27/2017] [Indexed: 12/11/2022]
Abstract
As a strong transactivator of promoters containing CarG boxes, myocardin was critical for the cardiac muscle program and necessary for normal cardiogenesis. So it probably represents a viable therapeutic biomarker in the setting of cardiac hypertrophy and failure. In recent years, the studies of regulation of cardiac hypertrophy via myocardin are so common, and the molecular mechanism is becoming more and more clear. Here, we have revealed a kind of interaction between mhrt and myocardin shown as a feedback regulatory mechanism in the regulation of cardiac hypertrophy. That is, the lncRNA mhrt can affect the acetylation of myocardin by HDAC5 to inhibit cardiac hypertrophy induced by myocardin. Moreover, myocardin also can directly activate the mhrt transcription through binding to the CarG box. Thus, mhrt and myocardin form a regulation loop in the process of cardiac hypertrophy. This finding may play a positive role in revealing the complete mechanisms of cardiac hypertrophy.
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Affiliation(s)
- Ying Luo
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Yao Xu
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Chen Liang
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Weibing Xing
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan 430065, China.
| | - Tongcun Zhang
- Institute of Biology and Medicine, Wuhan University of Science and Technology, Wuhan 430065, China.
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20
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Salehi S, Taheri MN, Azarpira N, Zare A, Behzad-Behbahani A. State of the art technologies to explore long non-coding RNAs in cancer. J Cell Mol Med 2017. [PMID: 28631377 PMCID: PMC5706582 DOI: 10.1111/jcmm.13238] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Long non‐coding RNAs (lncRNAs) comprise a vast repertoire of RNAs playing a wide variety of crucial roles in tissue physiology in a cell‐specific manner. Despite being engaged in myriads of regulatory mechanisms, many lncRNAs have still remained to be assigned any functions. A constellation of experimental techniques including single‐molecule RNA in situ hybridization (sm‐RNA FISH), cross‐linking and immunoprecipitation (CLIP), RNA interference (RNAi), Clustered regularly interspaced short palindromic repeats (CRISPR) and so forth has been employed to shed light on lncRNA cellular localization, structure, interaction networks and functions. Here, we review these and other experimental approaches in common use for identification and characterization of lncRNAs, particularly those involved in different types of cancer, with focus on merits and demerits of each technique.
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Affiliation(s)
- Saeede Salehi
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Naser Taheri
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Negar Azarpira
- Transplant Research Center, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdolhossein Zare
- Transplant Research Center, Namazi Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Behzad-Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
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21
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Ottaviani L, da Costa Martins PA. Non-coding RNAs in cardiac hypertrophy. J Physiol 2017; 595:4037-4050. [PMID: 28233323 PMCID: PMC5471409 DOI: 10.1113/jp273129] [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: 10/17/2016] [Accepted: 02/21/2017] [Indexed: 12/23/2022] Open
Abstract
Heart failure is one of the largest contributors to disease burden and healthcare outflow in the Western world. Despite significant progress in the treatment of heart failure, disease prognosis remains very poor, with the only curative therapy still being heart transplantation. To counteract the current situation, efforts have been made to better understand the underlying molecular pathways in the progression of cardiac disease towards heart failure, and to link the disease to novel therapeutic targets such as non‐coding RNAs. The non‐coding part of the genome has gained prominence over the last couple of decades, opening a completely new research field and establishing different non‐coding RNAs species as fundamental regulators of cellular functions. Not surprisingly, their dysregulation is increasingly being linked to pathology, including to cardiac disease. Pre‐clinically, non‐coding RNAs have been shown to be of great value as therapeutic targets in pathological cardiac remodelling and also as diagnostic/prognostic biomarkers for heart failure. Therefore, it is to be expected that non‐coding RNA‐based therapeutic strategies will reach the bedside in the future and provide new and more efficient treatments for heart failure. Here, we review recent discoveries linking the function and molecular interactions of non‐coding RNAs with the pathophysiology of cardiac hypertrophy and heart failure.
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Affiliation(s)
- Lara Ottaviani
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Paula A da Costa Martins
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands.,Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
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22
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Rutenberg-Schoenberg M, Sexton AN, Simon MD. The Properties of Long Noncoding RNAs That Regulate Chromatin. Annu Rev Genomics Hum Genet 2016; 17:69-94. [PMID: 27147088 DOI: 10.1146/annurev-genom-090314-024939] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Beyond coding for proteins, RNA molecules have well-established functions in the posttranscriptional regulation of gene expression. Less clear are the upstream roles of RNA in regulating transcription and chromatin-based processes in the nucleus. RNA is transcribed in the nucleus, so it is logical that RNA could play diverse and broad roles that would impact human physiology. Indeed, this idea is supported by well-established examples of noncoding RNAs that affect chromatin structure and function. There has been dramatic growth in studies focused on the nuclear roles of long noncoding RNAs (lncRNAs). Although little is known about the biochemical mechanisms of these lncRNAs, there is a developing consensus regarding the challenges of defining lncRNA function and mechanism. In this review, we examine the definition, discovery, functions, and mechanisms of lncRNAs. We emphasize areas where challenges remain and where consensus among laboratories has underscored the exciting ways in which human lncRNAs may affect chromatin biology.
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Affiliation(s)
- Michael Rutenberg-Schoenberg
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; , , .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | - Alec N Sexton
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; , , .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511; , , .,Chemical Biology Institute, Yale University, West Haven, Connecticut 06516
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23
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Peters T, Hermans-Beijnsberger S, Beqqali A, Bitsch N, Nakagawa S, Prasanth KV, de Windt LJ, van Oort RJ, Heymans S, Schroen B. Long Non-Coding RNA Malat-1 Is Dispensable during Pressure Overload-Induced Cardiac Remodeling and Failure in Mice. PLoS One 2016; 11:e0150236. [PMID: 26919721 PMCID: PMC4769011 DOI: 10.1371/journal.pone.0150236] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/10/2016] [Indexed: 12/30/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are a class of RNA molecules with diverse regulatory functions during embryonic development, normal life, and disease in higher organisms. However, research on the role of lncRNAs in cardiovascular diseases and in particular heart failure is still in its infancy. The exceptionally well conserved nuclear lncRNA Metastasis associated in lung adenocarcinoma transcript 1 (Malat-1) is a regulator of mRNA splicing and highly expressed in the heart. Malat-1 modulates hypoxia-induced vessel growth, activates ERK/MAPK signaling, and scavenges the anti-hypertrophic microRNA-133. We therefore hypothesized that Malat-1 may act as regulator of cardiac hypertrophy and failure during cardiac pressure overload induced by thoracic aortic constriction (TAC) in mice. Results Absence of Malat-1 did not affect cardiac hypertrophy upon pressure overload: Heart weight to tibia length ratio significantly increased in WT mice (sham: 5.78±0.55, TAC 9.79±1.82 g/mm; p<0.001) but to a similar extend also in Malat-1 knockout (KO) mice (sham: 6.21±1.12, TAC 8.91±1.74 g/mm; p<0.01) with no significant difference between genotypes. As expected, TAC significantly reduced left ventricular fractional shortening in WT (sham: 38.81±6.53%, TAC: 23.14±11.99%; p<0.01) but to a comparable degree also in KO mice (sham: 37.01±4.19%, TAC: 25.98±9.75%; p<0.05). Histological hallmarks of myocardial remodeling, such as cardiomyocyte hypertrophy, increased interstitial fibrosis, reduced capillary density, and immune cell infiltration, did not differ significantly between WT and KO mice after TAC. In line, the absence of Malat-1 did not significantly affect angiotensin II-induced cardiac hypertrophy, dysfunction, and overall remodeling. Above that, pressure overload by TAC significantly induced mRNA levels of the hypertrophy marker genes Nppa, Nppb and Acta1, to a similar extend in both genotypes. Alternative splicing of Ndrg2 after TAC was apparent in WT (isoform ratio; sham: 2.97±0.26, TAC 1.57±0.40; p<0.0001) and KO mice (sham: 3.64±0.37; TAC: 2.24±0.76; p<0.0001) and interestingly differed between genotypes both at baseline and after pressure overload (p<0.05 each). Conclusion These findings confirm a role for the lncRNA Malat-1 in mRNA splicing. However, no critical role for Malat-1 was found in pressure overload-induced heart failure in mice, despite its reported role in vascularization, ERK/MAPK signaling, and regulation of miR-133.
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Affiliation(s)
- Tim Peters
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Steffie Hermans-Beijnsberger
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Abdelaziz Beqqali
- Department of Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Nicole Bitsch
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | | | - Kannanganattu V. Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Leon J. de Windt
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
| | - Ralph J. van Oort
- Department of Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Stephane Heymans
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
- Netherlands Heart Institute (ICIN), Utrecht, The Netherlands
- Centre for Molecular and Vascular Biology (CMVB), Department of Cardiovascular Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Blanche Schroen
- Center for Heart Failure Research, Department of Cardiology, CARIM School for Cardiovascular Diseases, Maastricht University, Maastricht, The Netherlands
- * E-mail:
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24
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Qi X. The role of miR-9 during neuron differentiation of mouse retinal stem cells. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2015; 44:1883-1890. [PMID: 26701739 DOI: 10.3109/21691401.2015.1111231] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Retinal stem cells (RSCs) have been defined as neural cells with the potential to self-renew and to generate all the different cell types of the nervous system following differentiation, which are an ideal engraft in retinal regeneration. In this research, mouse RSCs were isolated from retina, induced differentiation into neuron cells in vitro after over-expression of miR-9. The results showed that the RSCs could induce differentiation into neuron cells under the special medium, but when the miR-9 was over-expressed, the differentiated efficiency of neuron cells from RSCs could be promoted. This reason was demonstrated that polypyrimidine tract-binding protein 1 (PTBP1) was a repressor for polypyrimidine tract-binding protein 2 (PTBP2), during neuronal differentiation, miR-9 reduced PTBP1 levels, leading to the accumulation of correctly spliced PTBP2 mRNA and a dramatic increase in PTBP2 protein. And then miR-9 promoted neuron cells from RSCs were successful colonized into injured spinal cord for participation in tissue-repair. In conclusion, our research showed that the miR-9 promoted the differentiation of neuronal cells from RSCs, and this mechanism was miR-9 reduced the expression of PTBP1, increased the expression of PTBP2.
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Affiliation(s)
- Xin Qi
- a Department of Ophthalmology, Beijing Chaoyang Hospital , Capital Medical University , Beijing , P.R. China
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