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Ariel F, Lucero L, Christ A, Mammarella MF, Jegu T, Veluchamy A, Mariappan K, Latrasse D, Blein T, Liu C, Benhamed M, Crespi M. R-Loop Mediated trans Action of the APOLO Long Noncoding RNA. Mol Cell 2020; 77:1055-1065.e4. [DOI: 10.1016/j.molcel.2019.12.015] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 08/30/2019] [Accepted: 12/18/2019] [Indexed: 11/25/2022]
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p53 Activates the Long Noncoding RNA Pvt1b to Inhibit Myc and Suppress Tumorigenesis. Mol Cell 2020; 77:761-774.e8. [PMID: 31973890 DOI: 10.1016/j.molcel.2019.12.014] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/20/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023]
Abstract
The tumor suppressor p53 transcriptionally activates target genes to suppress cellular proliferation during stress. p53 has also been implicated in the repression of the proto-oncogene Myc, but the mechanism has remained unclear. Here, we identify Pvt1b, a p53-dependent isoform of the long noncoding RNA (lncRNA) Pvt1, expressed 50 kb downstream of Myc, which becomes induced by DNA damage or oncogenic signaling and accumulates near its site of transcription. We show that production of the Pvt1b RNA is necessary and sufficient to suppress Myc transcription in cis without altering the chromatin organization of the locus. Inhibition of Pvt1b increases Myc levels and transcriptional activity and promotes cellular proliferation. Furthermore, Pvt1b loss accelerates tumor growth, but not tumor progression, in an autochthonous mouse model of lung cancer. These findings demonstrate that Pvt1b acts at the intersection of the p53 and Myc transcriptional networks to reinforce the anti-proliferative activities of p53.
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Abstract
Despite advanced clinical treatments, mortality in patients with metastatic colorectal cancer (CRC) remains high. Three critical determinants in CRC progression include the epithelial proliferation checkpoints, epithelial-to-mesenchymal transition (EMT) and inflammatory cytokines in the tumour microenvironment. Genes involved in these three processes are regulated at the transcriptional and post-transcriptional level. Recent studies revealed previously unappreciated roles of non-coding ribonucleic acids (ncRNAs) in modulating the proliferation checkpoints, EMT, and inflammatory gene expression in CRC. In this review, we will discuss the mechanisms underlying the roles of ncRNAs in CRC as well as examine future perspectives in this field. Better understanding of ncRNA biology will provide novel targets for future therapeutic development.
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Affiliation(s)
- Shengyun Ma
- Cellular and Molecular Medicine, University of California , San Diego, USA
| | - Tianyun Long
- Cellular and Molecular Medicine, University of California , San Diego, USA
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54
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LincRNA Cox-2 Regulates Lipopolysaccharide-Induced Inflammatory Response of Human Peritoneal Mesothelial Cells via Modulating miR-21/NF- κB Axis. Mediators Inflamm 2019; 2019:8626703. [PMID: 31885500 PMCID: PMC6914883 DOI: 10.1155/2019/8626703] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 09/08/2019] [Accepted: 09/18/2019] [Indexed: 02/07/2023] Open
Abstract
Postoperative peritoneal adhesion (PPA) is a common postoperative complication caused by any peritoneal inflammatory process. This study aimed to identify the biological function of large intergenic non-coding RNAs (lincRNAs) Cox-2 in the inflammation reaction of adhesion formation. The Cox-2 expression in peritoneal adhesion tissues and normal tissues was detected. The human peritoneal mesothelium cells (HPMCs) were treated with lipopolysaccharide (LPS) to induce inflammatory injury. The effect of Cox-2 suppression on cell viability, apoptosis and inflammatory factors of LPS induced HPMCs injury were explored. The regulatory correlation between Cox-2 and miR-21, as well as the targeted genes of miR-21 were identified. Meanwhile, the regulatory mechanism of Cox-2/miR-21 axis on NF-κB pathway was explored. It indicated that Cox-2 was highly expressed in peritoneal adhesion tissues compared with that in normal tissues. Suppression of Cox-2 ameliorated LPS induced HMPCs injury as cell viability was promoted, and cell apoptosis and the production of inflammatory factors were inhibited. And suppression of Cox-2 reversed the LPS induced HPMCs injury by regulation of miR-21 negatively. miR-21 was negatively correlated with TLR4, and TLR4 was predicted as target gene of miR-21. Furthermore, the suppression of miR-21 on LPS induced HPMCs injury was reversed by knockdown of TLR4, which could inhibited the activation of NF-κB pathway axis. It suggested that the effect of Cox-2 on LPS induced HPMCs injury was achieved by negatively regulation of miR-21 and targeted TLR4 through NF-κB pathway axis. The findings may provide a new insight into preventing postoperative peritoneal adhesion.
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55
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Gil N, Ulitsky I. Regulation of gene expression by cis-acting long non-coding RNAs. Nat Rev Genet 2019; 21:102-117. [DOI: 10.1038/s41576-019-0184-5] [Citation(s) in RCA: 296] [Impact Index Per Article: 59.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/14/2022]
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56
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Lewandowski JP, Lee JC, Hwang T, Sunwoo H, Goldstein JM, Groff AF, Chang NP, Mallard W, Williams A, Henao-Meija J, Flavell RA, Lee JT, Gerhardinger C, Wagers AJ, Rinn JL. The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis. Nat Commun 2019; 10:5137. [PMID: 31723143 PMCID: PMC6853988 DOI: 10.1038/s41467-019-12970-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 10/03/2019] [Indexed: 12/13/2022] Open
Abstract
RNA has been classically known to play central roles in biology, including maintaining telomeres, protein synthesis, and in sex chromosome compensation. While thousands of long noncoding RNAs (lncRNAs) have been identified, attributing RNA-based roles to lncRNA loci requires assessing whether phenotype(s) could be due to DNA regulatory elements, transcription, or the lncRNA. Here, we use the conserved X chromosome lncRNA locus Firre, as a model to discriminate between DNA- and RNA-mediated effects in vivo. We demonstrate that (i) Firre mutant mice have cell-specific hematopoietic phenotypes, and (ii) upon exposure to lipopolysaccharide, mice overexpressing Firre exhibit increased levels of pro-inflammatory cytokines and impaired survival. (iii) Deletion of Firre does not result in changes in local gene expression, but rather in changes on autosomes that can be rescued by expression of transgenic Firre RNA. Together, our results provide genetic evidence that the Firre locus produces a trans-acting lncRNA that has physiological roles in hematopoiesis.
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Affiliation(s)
- Jordan P Lewandowski
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - James C Lee
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Taeyoung Hwang
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Hongjae Sunwoo
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Jill M Goldstein
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, 77 Louis Pasteur Avenue, Boston, MA, USA
| | - Abigail F Groff
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Nydia P Chang
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - William Mallard
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Adam Williams
- The Jackson Laboratory, JAX Genomic Medicine, Farmington, CT, USA
| | - Jorge Henao-Meija
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, USA
| | - Richard A Flavell
- Department of Immunobiology and Howard Hughes Medical Institute, Yale University, School of Medicine, New Haven, CT, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Amy J Wagers
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
- Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, 77 Louis Pasteur Avenue, Boston, MA, USA
- Joslin Diabetes Center, Boston, MA, USA
| | - John L Rinn
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
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Intranasal Delivery of lincRNA-Cox2 siRNA Loaded Extracellular Vesicles Decreases Lipopolysaccharide-Induced Microglial Proliferation in Mice. J Neuroimmune Pharmacol 2019; 15:390-399. [PMID: 31325121 DOI: 10.1007/s11481-019-09864-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022]
Abstract
Long non-coding RNAs (lncRNAs), including long intergenic non-coding RNAs (lincRNAs), play an important regulatory role in controlling various biological processes. Both in vitro and in vivo studies have demonstrated that lincRNA-Cox2 plays a global regulatory role in regulating the expression of immune genes. Extracellular vesicles (EVs) are cell-derived nanosized membrane vesicles that have gained increasing attention in recent years due to their ability to efficiently deliver therapeutics to specific target organs or cell types. In this study, we found that lincRNA-Cox2 controls the expression of a set of cell cycle genes in lipopolysaccharide (LPS)-stimulated microglial cells. Our in vitro study suggested that knocking down lincRNA-Cox2 reversed LPS-induced microglial proliferation. In addition, our in vivo study demonstrated that intranasally delivered lincRNA-Cox2-siRNA loaded EVs could reach the brain resulting in a significant decrease in the expression of lincRNA-Cox2 in the microglia. Importantly, lincRNA-Cox2-siRNA loaded EVs also decreased LPS-induced microglial proliferation in mice. These findings indicate that intranasal delivery of EV-loaded small RNA could be developed as therapeutics for treatment of a multitude of CNS disorders.
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Menard KL, Haskins BE, Denkers EY. Impact of Toxoplasma gondii Infection on Host Non-coding RNA Responses. Front Cell Infect Microbiol 2019; 9:132. [PMID: 31157172 PMCID: PMC6530353 DOI: 10.3389/fcimb.2019.00132] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/12/2019] [Indexed: 12/12/2022] Open
Abstract
As an intracellular microbe, Toxoplasma gondii must establish a highly intimate relationship with its host to ensure success as a parasite. Many studies over the last decade-and-a-half have highlighted how the host reshapes its immunoproteome to survive infection, and conversely how the parasite regulates host responses to ensure persistence. The role of host non-protein-coding RNA during infection is a vast and largely unexplored area of emerging interest. The potential importance of this facet of the host-parasite interaction is underscored by current estimates that as much as 80% of the host genome is transcribed into non-translated RNA. Here, we review the current state of knowledge with respect to two major classes of non-coding RNA, microRNA (miRNA) and long non-coding RNA (lncRNA), in the host response to T. gondii infection. These two classes of regulatory RNA are known to have profound and widespread effects on cell function. However, their impact on infection and immunity is not well-understood, particularly for the response to T. gondii. Nevertheless, numerous miRNAs have been identified that are upregulated by Toxoplasma, and emerging evidence suggests a functional role during infection. While the field of lncRNA is in its infancy, it is already clear that Toxoplasma is also a strong trigger for this class of regulatory RNA. Non-coding RNA responses induced by T. gondii are likely to be major determinants of the host's ability to resist infection and the parasite's ability to establish long-term latency.
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Affiliation(s)
- Kayla L Menard
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States
| | - Breanne E Haskins
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States
| | - Eric Y Denkers
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, United States
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Agliano F, Rathinam VA, Medvedev AE, Vanaja SK, Vella AT. Long Noncoding RNAs in Host-Pathogen Interactions. Trends Immunol 2019; 40:492-510. [PMID: 31053495 DOI: 10.1016/j.it.2019.04.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 02/08/2023]
Abstract
Long noncoding RNAs (lncRNAs) are key molecules that regulate gene expression in a variety of organisms. LncRNAs can drive different transcriptional and post-transcriptional events that impact cellular functions. Recent studies have identified many lncRNAs associated with immune cell development and activation; however, an understanding of their functional role in host immunity to infection is just emerging. Here, we provide a detailed and updated review of the functional roles of lncRNAs in regulating mammalian immune responses during host-pathogen interactions, because these functions may be either beneficial or detrimental to the host. With increased mechanistic insight into the roles of lncRNAs, it may be possible to design and/or improve lncRNA-based therapies to treat a variety of infectious and inflammatory diseases.
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Affiliation(s)
- Federica Agliano
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Vijay A Rathinam
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Andrei E Medvedev
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Sivapriya Kailasan Vanaja
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA.
| | - Anthony T Vella
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA.
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60
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Hadjicharalambous MR, Lindsay MA. Long Non-Coding RNAs and the Innate Immune Response. Noncoding RNA 2019; 5:ncrna5020034. [PMID: 31010202 PMCID: PMC6630897 DOI: 10.3390/ncrna5020034] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 12/12/2022] Open
Abstract
Innate immunity provides the initial defence against infection and it is now clear that long non-coding RNAs (lncRNAs) are important regulators of this response. Following activation of the innate response, we commonly see rapid induction of these lncRNAs and this is often mediated via the pro-inflammatory transcription factor, nuclear factor-κB (NF-κB). Knockdown studies have shown that lncRNAs tend to act in trans to regulate the expression of multiple inflammatory mediators and other responses. Mechanistically, many lncRNAs have demonstrated acting through heterogeneous nuclear ribonucleoproteins, complexes that are implicated chromatin re-modelling, transcription process and translation. In addition, these lncRNAs have also been shown to interact with multiple other proteins involved in the regulation of chromatin re-modelling, as well as those proteins involved in intracellular immune signalling, which include NF-κB. In this review, we will describe the evidence that supports this emerging role of lncRNA in the innate immune response.
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Affiliation(s)
| | - Mark A Lindsay
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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61
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Habib AM, Okorokov AL, Hill MN, Bras JT, Lee MC, Li S, Gossage SJ, van Drimmelen M, Morena M, Houlden H, Ramirez JD, Bennett DLH, Srivastava D, Cox JJ. Microdeletion in a FAAH pseudogene identified in a patient with high anandamide concentrations and pain insensitivity. Br J Anaesth 2019; 123:e249-e253. [PMID: 30929760 PMCID: PMC6676009 DOI: 10.1016/j.bja.2019.02.019] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/19/2019] [Accepted: 02/22/2019] [Indexed: 01/07/2023] Open
Abstract
The study of rare families with inherited pain insensitivity can identify new human-validated analgesic drug targets. Here, a 66-yr-old female presented with nil requirement for postoperative analgesia after a normally painful orthopaedic hand surgery (trapeziectomy). Further investigations revealed a lifelong history of painless injuries, such as frequent cuts and burns, which were observed to heal quickly. We report the causative mutations for this new pain insensitivity disorder: the co-inheritance of (i) a microdeletion in dorsal root ganglia and brain-expressed pseudogene, FAAH-OUT, which we cloned from the fatty-acid amide hydrolase (FAAH) chromosomal region; and (ii) a common functional single-nucleotide polymorphism in FAAH conferring reduced expression and activity. Circulating concentrations of anandamide and related fatty-acid amides (palmitoylethanolamide and oleoylethanolamine) that are all normally degraded by FAAH were significantly elevated in peripheral blood compared with normal control carriers of the hypomorphic single-nucleotide polymorphism. The genetic findings and elevated circulating fatty-acid amides are consistent with a phenotype resulting from enhanced endocannabinoid signalling and a loss of function of FAAH. Our results highlight previously unknown complexity at the FAAH genomic locus involving the expression of FAAH-OUT, a novel pseudogene and long non-coding RNA. These data suggest new routes to develop FAAH-based analgesia by targeting of FAAH-OUT, which could significantly improve the treatment of postoperative pain and potentially chronic pain and anxiety disorders.
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Affiliation(s)
- Abdella M Habib
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK; College of Medicine, Member of Qatar Health Cluster, Qatar University, Doha, Qatar
| | - Andrei L Okorokov
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Matthew N Hill
- Hotchkiss Brain Institute, Departments of Cell Biology and Anatomy and Psychiatry, University of Calgary, Calgary, AB, Canada
| | - Jose T Bras
- UK Dementia Research Institute at UCL, London, UK; Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Man-Cheung Lee
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK; University Division of Anaesthesia, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK; Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA
| | - Shengnan Li
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Samuel J Gossage
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK
| | | | - Maria Morena
- Hotchkiss Brain Institute, Departments of Cell Biology and Anatomy and Psychiatry, University of Calgary, Calgary, AB, Canada
| | - Henry Houlden
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Juan D Ramirez
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - David L H Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | | | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London, London, UK.
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62
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Miano JM, Long X, Lyu Q. CRISPR links to long noncoding RNA function in mice: A practical approach. Vascul Pharmacol 2019; 114:1-12. [PMID: 30822570 PMCID: PMC6435418 DOI: 10.1016/j.vph.2019.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/29/2022]
Abstract
Next generation sequencing has uncovered a trove of short noncoding RNAs (e.g., microRNAs) and long noncoding RNAs (lncRNAs) that act as molecular rheostats in the control of diverse homeostatic processes. Meanwhile, the tsunamic emergence of clustered regularly interspaced short palindromic repeats (CRISPR) editing has transformed our influence over all DNA-carrying entities, heralding global CRISPRization. This is evident in biomedical research where the ease and low-cost of CRISPR editing has made it the preferred method of manipulating the mouse genome, facilitating rapid discovery of genome function in an in vivo context. Here, CRISPR genome editing components are updated for elucidating lncRNA function in mice. Various strategies are highlighted for understanding the function of lncRNAs residing in intergenic sequence space, as host genes that harbor microRNAs or other genes, and as natural antisense, overlapping or intronic genes. Also discussed is CRISPR editing of mice carrying human lncRNAs as well as the editing of competing endogenous RNAs. The information described herein should assist labs in the rigorous design of experiments that interrogate lncRNA function in mice where complex disease processes can be modeled thus accelerating translational discovery.
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Affiliation(s)
- Joseph M Miano
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America.
| | - Xiaochun Long
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, United States of America
| | - Qing Lyu
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY, United States of America
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