1
|
Lobo V, Nowak I, Fernandez C, Correa Muler AI, Westholm JO, Huang HC, Fabrik I, Huynh HT, Shcherbinina E, Poyraz M, Härtlova A, Benhalevy D, Angeletti D, Sarshad AA. Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference. Nucleic Acids Res 2024; 52:9917-9935. [PMID: 38994560 PMCID: PMC11381323 DOI: 10.1093/nar/gkae589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 05/31/2024] [Accepted: 06/25/2024] [Indexed: 07/13/2024] Open
Abstract
In mammals, RNA interference (RNAi) was historically studied as a cytoplasmic event; however, in the last decade, a growing number of reports convincingly show the nuclear localization of the Argonaute (AGO) proteins. Nevertheless, the extent of nuclear RNAi and its implication in biological mechanisms remain to be elucidated. We found that reduced Lamin A levels significantly induce nuclear influx of AGO2 in SHSY5Y neuroblastoma and A375 melanoma cancer cell lines, which normally have no nuclear AGO2. Lamin A KO manifested a more pronounced effect in SHSY5Y cells compared to A375 cells, evident by changes in cell morphology, increased cell proliferation, and oncogenic miRNA expression. Moreover, AGO fPAR-CLIP in Lamin A KO SHSY5Y cells revealed significantly reduced RNAi activity. Further exploration of the nuclear AGO interactome by mass spectrometry identified FAM120A, an RNA-binding protein and known interactor of AGO2. Subsequent FAM120A fPAR-CLIP, revealed that FAM120A co-binds AGO targets and that this competition reduces the RNAi activity. Therefore, loss of Lamin A triggers nuclear AGO2 translocation, FAM120A mediated RNAi impairment, and upregulation of oncogenic miRNAs, facilitating cancer cell proliferation.
Collapse
Affiliation(s)
- Vivian Lobo
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Iwona Nowak
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Carola Fernandez
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Ana Iris Correa Muler
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Jakub O Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121 Solna, Sweden
| | - Hsiang-Chi Huang
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Ivo Fabrik
- Biomedical Research Centre, University Hospital Hradec Kralove, Sokolska 581, 500 05 Hradec Kralove, Czech Republic
| | - Hang T Huynh
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Evgeniia Shcherbinina
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Melis Poyraz
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Anetta Härtlova
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Daniel Benhalevy
- Lab of Cellular RNA Biology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Davide Angeletti
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- SciLifeLab, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Aishe A Sarshad
- Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| |
Collapse
|
2
|
Rahman M, Marzullo BP, Lam PY, Barrow MP, Holman SW, Ray AD, O'Connor PB. Unveiling the intricacy of gapmer oligonucleotides through advanced tandem mass spectrometry approaches and scan accumulation for 2DMS. Analyst 2024; 149:4687-4701. [PMID: 39101388 PMCID: PMC11382339 DOI: 10.1039/d4an00484a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Antisense oligonucleotides (ASOs) are crucial for biological applications as they bind to complementary RNA sequences, modulating protein expression. ASOs undergo synthetic modifications like phosphorothioate (PS) backbone and locked nucleic acid (LNA) to enhance stability and specificity. Tandem mass spectrometry (MS) techniques were employed to study gapmer ASOs, which feature a DNA chain within RNA segments at both termini, revealing enhanced cleavages with ultraviolet photodissociation (UVPD) and complementary fragment ions from collision-induced dissociation (CID) and electron detachment dissociation (EDD). 2DMS, a data-independent analysis technique, allowed for comprehensive coverage and identification of shared fragments across multiple precursor ions. EDD fragmentation efficiency correlated with precursor ion charge states, with higher charges facilitating dissociation due to intramolecular repulsions. An electron energy of 22.8 eV enabled electron capture and radical-based cleavage. Accumulating multiple scans and generating average spectra improved signal intensity, aided by denoising algorithms. Data analysis utilised a custom Python script capable of handling modifications and generating unique mass lists.
Collapse
Affiliation(s)
- Mohammed Rahman
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK
| | - Bryan P Marzullo
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Pui Yiu Lam
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Mark P Barrow
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| | - Stephen W Holman
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, AstraZeneca, SK10 2NA, UK
| | - Andrew D Ray
- New Modalities & Parental Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, SK10 2NA, UK
| | - Peter B O'Connor
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.
| |
Collapse
|
3
|
Sarli SL, Fakih HH, Kelly K, Devi G, Rembetsy-Brown J, McEachern H, Ferguson C, Echeverria D, Lee J, Sousa J, Sleiman H, Khvorova A, Watts J. Quantifying the activity profile of ASO and siRNA conjugates in glioblastoma xenograft tumors in vivo. Nucleic Acids Res 2024; 52:4799-4817. [PMID: 38613388 PMCID: PMC11109979 DOI: 10.1093/nar/gkae260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/06/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Glioblastoma multiforme is a universally lethal brain tumor that largely resists current surgical and drug interventions. Despite important advancements in understanding GBM biology, the invasiveness and heterogeneity of these tumors has made it challenging to develop effective therapies. Therapeutic oligonucleotides-antisense oligonucleotides and small-interfering RNAs-are chemically modified nucleic acids that can silence gene expression in the brain. However, activity of these oligonucleotides in brain tumors remains inadequately characterized. In this study, we developed a quantitative method to differentiate oligonucleotide-induced gene silencing in orthotopic GBM xenografts from gene silencing in normal brain tissue, and used this method to test the differential silencing activity of a chemically diverse panel of oligonucleotides. We show that oligonucleotides chemically optimized for pharmacological activity in normal brain tissue do not show consistent activity in GBM xenografts. We then survey multiple advanced oligonucleotide chemistries for their activity in GBM xenografts. Attaching lipid conjugates to oligonucleotides improves silencing in GBM cells across several different lipid classes. Highly hydrophobic lipid conjugates cholesterol and docosanoic acid enhance silencing but at the cost of higher neurotoxicity. Moderately hydrophobic, unsaturated fatty acid and amphiphilic lipid conjugates still improve activity without compromising safety. These oligonucleotide conjugates show promise for treating glioblastoma.
Collapse
Affiliation(s)
- Samantha L Sarli
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hassan H Fakih
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Karen Kelly
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Gitali Devi
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Julia M Rembetsy-Brown
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Holly R McEachern
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Chantal M Ferguson
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan Lee
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jacquelyn Sousa
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, Montréal, Québec, Canada
| | - Anastasia Khvorova
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| |
Collapse
|
4
|
Nguyen L. Updates on Disease Mechanisms and Therapeutics for Amyotrophic Lateral Sclerosis. Cells 2024; 13:888. [PMID: 38891021 PMCID: PMC11172142 DOI: 10.3390/cells13110888] [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] [Received: 03/29/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
Amyotrophic lateral sclerosis (ALS), or Lou Gehrig's disease, is a motor neuron disease. In ALS, upper and lower motor neurons in the brain and spinal cord progressively degenerate during the course of the disease, leading to the loss of the voluntary movement of the arms and legs. Since its first description in 1869 by a French neurologist Jean-Martin Charcot, the scientific discoveries on ALS have increased our understanding of ALS genetics, pathology and mechanisms and provided novel therapeutic strategies. The goal of this review article is to provide a comprehensive summary of the recent findings on ALS mechanisms and related therapeutic strategies to the scientific audience. Several highlighted ALS research topics discussed in this article include the 2023 FDA approved drug for SOD1 ALS, the updated C9orf72 GGGGCC repeat-expansion-related mechanisms and therapeutic targets, TDP-43-mediated cryptic splicing and disease markers and diagnostic and therapeutic options offered by these recent discoveries.
Collapse
Affiliation(s)
- Lien Nguyen
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA;
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| |
Collapse
|
5
|
Johnson KC, Kilikevicius A, Hofman C, Hu J, Liu Y, Aguilar S, Graswich J, Han Y, Wang T, Westcott JM, Brekken RA, Peng L, Karagkounis G, Corey DR. Nuclear localization of Argonaute 2 is affected by cell density and may relieve repression by microRNAs. Nucleic Acids Res 2024; 52:1930-1952. [PMID: 38109320 PMCID: PMC10899759 DOI: 10.1093/nar/gkad1155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/20/2023] Open
Abstract
Argonaute protein is associated with post-transcriptional control of cytoplasmic gene expression through miRNA-induced silencing complexes (miRISC). Specific cellular and environmental conditions can trigger AGO protein to accumulate in the nucleus. Localization of AGO is central to understanding miRNA action, yet the consequences of AGO being in the nucleus are undefined. We show nuclear enrichment of AGO2 in HCT116 cells grown in two-dimensional culture to high density, HCT116 cells grown in three-dimensional tumor spheroid culture, and human colon tumors. The shift in localization of AGO2 from cytoplasm to nucleus de-represses cytoplasmic AGO2-eCLIP targets that were candidates for canonical regulation by miRISC. Constitutive nuclear localization of AGO2 using an engineered nuclear localization signal increases cell migration. Critical RNAi factors also affect the localization of AGO2. Knocking out an enzyme essential for miRNA biogenesis, DROSHA, depletes mature miRNAs and restricts AGO2 localization to the cytoplasm, while knocking out the miRISC scaffolding protein, TNRC6, results in nuclear localization of AGO2. These data suggest that AGO2 localization and miRNA activity can be regulated depending on environmental conditions, expression of mature miRNAs, and expression of miRISC cofactors. Localization and expression of core miRISC protein machinery should be considered when investigating the roles of miRNAs.
Collapse
Affiliation(s)
- Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Audrius Kilikevicius
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Cristina Hofman
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Jiaxin Hu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Yang Liu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Selina Aguilar
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Jon Graswich
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| | - Yi Han
- UT Southwestern Medical Center, Peter O'Donnell Jr. School of Public Health, Dallas, TX 75235, USA
| | - Tao Wang
- UT Southwestern Medical Center, Peter O'Donnell Jr. School of Public Health, Dallas, TX 75235, USA
| | - Jill M Westcott
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235, USA
| | - Rolf A Brekken
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235, USA
| | - Lan Peng
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Pathology, Dallas, TX 75235, USA
| | - Georgios Karagkounis
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235, USA
- Memorial Sloan Kettering Cancer Center, New York, NY 10022, USA
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235, USA
| |
Collapse
|
6
|
Gruber C, Gursinsky T, Gago-Zachert S, Pantaleo V, Behrens SE. Effective Antiviral Application of Antisense in Plants by Exploiting Accessible Sites in the Target RNA. Int J Mol Sci 2023; 24:17153. [PMID: 38138982 PMCID: PMC10743417 DOI: 10.3390/ijms242417153] [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: 10/18/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
Antisense oligodeoxynucleotides (ASOs) have long been used to selectively inhibit or modulate gene expression at the RNA level, and some ASOs are approved for clinical use. However, the practicability of antisense technologies remains limited by the difficulty of reliably predicting the sites accessible to ASOs in complex folded RNAs. Recently, we applied a plant-based method that reproduces RNA-induced RNA silencing in vitro to reliably identify sites in target RNAs that are accessible to small interfering RNA (siRNA)-guided Argonaute endonucleases. Here, we show that this method is also suitable for identifying ASOs that are effective in DNA-induced RNA silencing by RNases H. We show that ASOs identified in this way that target a viral genome are comparably effective in protecting plants from infection as siRNAs with the corresponding sequence. The antiviral activity of the ASOs could be further enhanced by chemical modification. This led to two important conclusions: siRNAs and ASOs that can effectively knock down complex RNA molecules can be identified using the same approach, and ASOs optimized in this way could find application in crop protection. The technology developed here could be useful not only for effective RNA silencing in plants but also in other organisms.
Collapse
Affiliation(s)
- Cornelia Gruber
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany; (C.G.); (T.G.); (S.G.-Z.)
| | - Torsten Gursinsky
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany; (C.G.); (T.G.); (S.G.-Z.)
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany; (C.G.); (T.G.); (S.G.-Z.)
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection, Department of Biology, Agricultural and Food Sciences National Research Council, Bari Unit, I-70126 Bari, Italy;
| | - Sven-Erik Behrens
- Institute of Biochemistry and Biotechnology, Section Microbial Biotechnology, Martin Luther University Halle-Wittenberg, D-06120 Halle (Saale), Germany; (C.G.); (T.G.); (S.G.-Z.)
| |
Collapse
|
7
|
Iyer AK, Schoch KM, Verbeck A, Galasso G, Chen H, Smith S, Oldenborg A, Miller TM, Karch CM, Bonni A. Targeted ASO-mediated Atp1a2 knockdown in astrocytes reduces SOD1 aggregation and accelerates disease onset in mutant SOD1 mice. PLoS One 2023; 18:e0294731. [PMID: 38015828 PMCID: PMC10683999 DOI: 10.1371/journal.pone.0294731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 11/07/2023] [Indexed: 11/30/2023] Open
Abstract
Astrocyte-specific ion pump α2-Na+/K+-ATPase plays a critical role in the pathogenesis of amyotrophic lateral sclerosis (ALS). Here, we test the effect of Atp1a2 mRNA-specific antisense oligonucleotides (ASOs) to induce α2-Na+/K+-ATPase knockdown in the widely used ALS animal model, SOD1*G93A mice. Two ASOs led to efficient Atp1a2 knockdown and significantly reduced SOD1 aggregation in vivo. Although Atp1a2 ASO-treated mice displayed no off-target or systemic toxicity, the ASO-treated mice exhibited an accelerated disease onset and shorter lifespan than control mice. Transcriptomics studies reveal downregulation of genes involved in oxidative response, metabolic pathways, trans-synaptic signaling, and upregulation of genes involved in glutamate receptor signaling and complement activation, suggesting a potential role for these molecular pathways in de-coupling SOD1 aggregation from survival in Atp1a2 ASO-treated mice. Together, these results reveal a role for α2-Na+/K+-ATPase in SOD1 aggregation and highlight the critical effect of temporal modulation of genetically validated therapeutic targets in neurodegenerative diseases.
Collapse
Affiliation(s)
- Abhirami K. Iyer
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kathleen M. Schoch
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Anthony Verbeck
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Grant Galasso
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Hao Chen
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sarah Smith
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Anna Oldenborg
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Timothy M. Miller
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Celeste M. Karch
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Azad Bonni
- Neuroscience and Rare Diseases, Roche Pharma Research and Early Development (pRED), Roche Innovation Centre Basel, Basel, Switzerland
| |
Collapse
|
8
|
Pfeiffer LS, Stafforst T. Precision RNA base editing with engineered and endogenous effectors. Nat Biotechnol 2023; 41:1526-1542. [PMID: 37735261 DOI: 10.1038/s41587-023-01927-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/26/2023] [Indexed: 09/23/2023]
Abstract
RNA base editing refers to the rewriting of genetic information within an intact RNA molecule and serves various functions, such as evasion of the endogenous immune system and regulation of protein function. To achieve this, certain enzymes have been discovered in human cells that catalyze the conversion of one nucleobase into another. This natural process could be exploited to manipulate and recode any base in a target transcript. In contrast to DNA base editing, analogous changes introduced in RNA are not permanent or inheritable but rather allow reversible and doseable effects that appeal to various therapeutic applications. The current practice of RNA base editing involves the deamination of adenosines and cytidines, which are converted to inosines and uridines, respectively. In this Review, we summarize current site-directed RNA base-editing strategies and highlight recent achievements to improve editing efficiency, precision, codon-targeting scope and in vivo delivery into disease-relevant tissues. Besides engineered editing effectors, we focus on strategies to harness endogenous adenosine deaminases acting on RNA (ADAR) enzymes and discuss limitations and future perspectives to apply the tools in basic research and as a therapeutic modality. We expect the field to realize the first RNA base-editing drug soon, likely on a well-defined genetic disease. However, the long-term challenge will be to carve out the sweet spot of the technology where its unique ability is exploited to modulate signaling cues, metabolism or other clinically relevant processes in a safe and doseable manner.
Collapse
Affiliation(s)
- Laura S Pfeiffer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Thorsten Stafforst
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
- Gene and RNA Therapy Center, Faculty of Medicine, University of Tübingen, Tübingen, Germany.
| |
Collapse
|
9
|
Kang H, Ga YJ, Kim SH, Cho YH, Kim JW, Kim C, Yeh JY. Small interfering RNA (siRNA)-based therapeutic applications against viruses: principles, potential, and challenges. J Biomed Sci 2023; 30:88. [PMID: 37845731 PMCID: PMC10577957 DOI: 10.1186/s12929-023-00981-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023] Open
Abstract
RNA has emerged as a revolutionary and important tool in the battle against emerging infectious diseases, with roles extending beyond its applications in vaccines, in which it is used in the response to the COVID-19 pandemic. Since their development in the 1990s, RNA interference (RNAi) therapeutics have demonstrated potential in reducing the expression of disease-associated genes. Nucleic acid-based therapeutics, including RNAi therapies, that degrade viral genomes and rapidly adapt to viral mutations, have emerged as alternative treatments. RNAi is a robust technique frequently employed to selectively suppress gene expression in a sequence-specific manner. The swift adaptability of nucleic acid-based therapeutics such as RNAi therapies endows them with a significant advantage over other antiviral medications. For example, small interfering RNAs (siRNAs) are produced on the basis of sequence complementarity to target and degrade viral RNA, a novel approach to combat viral infections. The precision of siRNAs in targeting and degrading viral RNA has led to the development of siRNA-based treatments for diverse diseases. However, despite the promising therapeutic benefits of siRNAs, several problems, including impaired long-term protein expression, siRNA instability, off-target effects, immunological responses, and drug resistance, have been considerable obstacles to the use of siRNA-based antiviral therapies. This review provides an encompassing summary of the siRNA-based therapeutic approaches against viruses while also addressing the obstacles that need to be overcome for their effective application. Furthermore, we present potential solutions to mitigate major challenges.
Collapse
Affiliation(s)
- Hara Kang
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Yun Ji Ga
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Soo Hyun Kim
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Young Hoon Cho
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Jung Won Kim
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
- Convergence Research Center for Insect Vectors, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Chaeyeon Kim
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea
| | - Jung-Yong Yeh
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea.
- Research Institute for New Drug Development, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea.
- Convergence Research Center for Insect Vectors, Incheon National University, Academy-Ro 119, Yeonsu-Gu, Incheon, 22012, South Korea.
- KU Center for Animal Blood Medical Science, College of Veterinary Medicine, Konkuk University, 120 Neungdong-Ro, Gwangjin-Gu, Seoul, 05029, South Korea.
| |
Collapse
|
10
|
Johnson KC, Kilikevicius A, Hofman C, Hu J, Liu Y, Aguilar S, Graswich J, Han Y, Wang T, Westcott JM, Brekken RA, Peng L, Karagkounis G, Corey DR. Nuclear Localization of Argonaute is affected by Cell Density and May Relieve Repression by microRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.548119. [PMID: 37461596 PMCID: PMC10350042 DOI: 10.1101/2023.07.07.548119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Argonaute protein is associated with post-transcriptional control of cytoplasmic gene expression through miRNA-induced silencing complexes (miRISC). Specific cellular and environmental conditions can trigger AGO protein to accumulate in the nucleus. Localization of AGO is central to understanding miRNA action, yet the consequences of AGO being in the nucleus are undefined. We show nuclear enrichment of AGO2 in HCT116 cells grown in two-dimensional culture to high density, HCT116 cells grown in three-dimensional tumor spheroid culture, and human colon tumors. The shift in localization of AGO2 from cytoplasm to nucleus de-represses cytoplasmic AGO2-eCLIP targets that were candidates for canonical regulation by miRISC. Constitutive nuclear localization of AGO2 using an engineered nuclear localization signal increases cell migration. Critical RNAi factors also affect the localization of AGO2. Knocking out an enzyme essential for miRNA biogenesis, DROSHA, depletes mature miRNAs and restricts AGO2 localization to the cytoplasm, while knocking out the miRISC scaffolding protein, TNRC6, results in nuclear localization of AGO2. These data suggest that AGO2 localization and miRNA activity can be regulated depending on environmental conditions, expression of mature miRNAs, and expression of miRISC cofactors. Localization and expression of core miRISC protein machinery should be considered when investigating the roles of miRNAs.
Collapse
Affiliation(s)
- Krystal C Johnson
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Audrius Kilikevicius
- current address, Eli Lilly, Lilly Cambridge Innovation Center, Cambridge, MA 02142
| | - Cristina Hofman
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Jiaxin Hu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Yang Liu
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Selina Aguilar
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Jon Graswich
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| | - Yi Han
- UT Southwestern Medical Center, Quantitative Biomedical Research Center, Department of Population and Data Sciences, Dallas, TX 75235
| | - Tao Wang
- UT Southwestern Medical Center, Quantitative Biomedical Research Center, Department of Population and Data Sciences, Dallas, TX 75235
| | - Jill M Westcott
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235
| | - Rolf A Brekken
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235
| | - Lan Peng
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Pathology, Dallas, TX 75235
| | - Georgios Karagkounis
- UT Southwestern Medical Center, Harold C. Simmons Comprehensive Cancer Center, Department of Surgery, Dallas, TX 75235
| | - David R Corey
- UT Southwestern Medical Center, Departments of Pharmacology and Biochemistry, Dallas, TX 75235
| |
Collapse
|
11
|
Safi A, Saberiyan M, Sanaei MJ, Adelian S, Davarani Asl F, Zeinaly M, Shamsi M, Ahmadi R. The role of noncoding RNAs in metabolic reprogramming of cancer cells. Cell Mol Biol Lett 2023; 28:37. [PMID: 37161350 PMCID: PMC10169341 DOI: 10.1186/s11658-023-00447-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/11/2023] [Indexed: 05/11/2023] Open
Abstract
Metabolic reprogramming is a well-known feature of cancer that allows malignant cells to alter metabolic reactions and nutrient uptake, thereby promoting tumor growth and spread. It has been discovered that noncoding RNAs (ncRNAs), including microRNA (miRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA), have a role in a variety of biological functions, control physiologic and developmental processes, and even influence disease. They have been recognized in numerous cancer types as tumor suppressors and oncogenic agents. The role of ncRNAs in the metabolic reprogramming of cancer cells has recently been noticed. We examine this subject, with an emphasis on the metabolism of glucose, lipids, and amino acids, and highlight the therapeutic use of targeting ncRNAs in cancer treatment.
Collapse
Affiliation(s)
- Amir Safi
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammadreza Saberiyan
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mohammad-Javad Sanaei
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samaneh Adelian
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Fateme Davarani Asl
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mahsa Zeinaly
- Department of Biology, Faculty of Sciences, University of Guilan, Rasht, Iran
| | - Mahdi Shamsi
- Department of Cell and Molecular Biology, Najafabad Branch, Islamic Azad University, Najafabad, Iran
| | - Reza Ahmadi
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Rahmatiyeh Region, Shahrekord, Iran.
| |
Collapse
|
12
|
Nandi S, Mondal A, Ghosh A, Mukherjee S, Das C. Lnc-ing epigenetic mechanisms with autophagy and cancer drug resistance. Adv Cancer Res 2023; 160:133-203. [PMID: 37704287 DOI: 10.1016/bs.acr.2023.03.002] [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: 09/15/2023]
Abstract
Long noncoding RNAs (lncRNAs) comprise a diverse class of RNA molecules that regulate various physiological processes and have been reported to be involved in several human pathologies ranging from neurodegenerative disease to cancer. Therapeutic resistance is a major hurdle for cancer treatment. Over the past decade, several studies has emerged on the role of lncRNAs in cancer drug resistance and many trials have been conducted employing them. LncRNAs also regulate different cell death pathways thereby maintaining a fine balance of cell survival and death. Autophagy is a complex cell-killing mechanism that has both cytoprotective and cytotoxic roles. Similarly, autophagy can lead to the induction of both chemosensitization and chemoresistance in cancer cells upon therapeutic intervention. Recently the role of lncRNAs in the regulation of autophagy has also surfaced. Thus, lncRNAs can be used in cancer therapeutics to alleviate the challenges of chemoresistance by targeting the autophagosomal axis. In this chapter, we discuss about the role of lncRNAs in autophagy-mediated cancer drug resistance and its implication in targeted cancer therapy.
Collapse
Affiliation(s)
- Sandhik Nandi
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India
| | - Atanu Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India
| | - Aritra Ghosh
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Indian Institute of Science Education and Research, Kolkata, India
| | - Shravanti Mukherjee
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhabha National Institute, Mumbai, India.
| |
Collapse
|
13
|
Vaillant A. Bepirovirsen/GSK3389404: Antisense or TLR9 agonists? J Hepatol 2023; 78:e107-e108. [PMID: 36116715 DOI: 10.1016/j.jhep.2022.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 12/04/2022]
|
14
|
Krasnodębski C, Sawuła A, Kaźmierczak U, Żuk M. Oligo-Not Only for Silencing: Overlooked Potential for Multidirectional Action in Plants. Int J Mol Sci 2023; 24:ijms24054466. [PMID: 36901895 PMCID: PMC10002457 DOI: 10.3390/ijms24054466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Oligo technology is a low-cost and easy-to-implement method for direct manipulation of gene activity. The major advantage of this method is that gene expression can be changed without requiring stable transformation. Oligo technology is mainly used for animal cells. However, the use of oligos in plants seems to be even easier. The oligo effect could be similar to that induced by endogenous miRNAs. In general, the action of exogenously introduced nucleic acids (Oligo) can be divided into a direct interaction with nucleic acids (genomic DNA, hnRNA, transcript) and an indirect interaction via the induction of processes regulating gene expression (at the transcriptional and translational levels) involving regulatory proteins using endogenous cellular mechanisms. Presumed mechanisms of oligonucleotides' action in plant cells (including differences from animal cells) are described in this review. Basic principles of oligo action in plants that allow bidirectional changes in gene activity and even those that lead to heritable epigenetic changes in gene expression are presented. The effect of oligos is related to the target sequence at which they are directed. This paper also compares different delivery methods and provides a quick guide to using IT tools to help design oligonucleotides.
Collapse
Affiliation(s)
- Cezary Krasnodębski
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Agnieszka Sawuła
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Urszula Kaźmierczak
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, 50-383 Wroclaw, Poland
| | - Magdalena Żuk
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
- Correspondence:
| |
Collapse
|
15
|
Sapkota S, Gantier MP. Selecting Therapeutic Antisense Oligonucleotides with Gene Targeting and TLR8 Potentiating Bifunctionality. Methods Mol Biol 2023; 2691:225-234. [PMID: 37355549 DOI: 10.1007/978-1-0716-3331-1_17] [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: 06/26/2023]
Abstract
A growing body of preclinical evidence has led to the hypothesis that human Toll-like receptor 8 (hTLR8) activation in the tumor microenvironment (TME) could have potent anticancer effects through its action on monocytes, myeloid dendritic cells (mDCs), and natural killer (NK) cells. This has motivated the initiation of several clinical trials for chemical hTLR8 agonists in a variety of cancers. Concurrently, a growing number of synthetic antisense oligonucleotides (ASOs) are being developed as cancer therapeutics. We have recently reported that 2'-O-methyl (2'OMe)-modified ASOs can potentiate sensing of hTLR8 chemical agonists in a sequence-dependent manner. This suggests that select gene-targeting ASOs with anticancer activity may synergize with low-dose hTLR8 agonists in the TME. Here, we provide a detailed protocol to rapidly screen and identify such synthetic bifunctional oligonucleotides with synergistic activity on hTLR8 sensing.
Collapse
Affiliation(s)
- Sunil Sapkota
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia
| | - Michael P Gantier
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.
- Department of Molecular and Translational Science, Monash University, Clayton, VIC, Australia.
| |
Collapse
|
16
|
Small Interfering RNAs Targeting a Chromatin-Associated RNA Induce Its Transcriptional Silencing in Human Cells. Mol Cell Biol 2022; 42:e0027122. [PMID: 36445136 PMCID: PMC9753735 DOI: 10.1128/mcb.00271-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Transcriptional gene silencing by small interfering RNAs (siRNAs) has been widely described in various species, including plants and yeast. In mammals, its extent remains somewhat debated. Previous studies showed that siRNAs targeting gene promoters could induce the silencing of the targeted promoter, although the involvement of off-target mechanisms was also suggested. Here, by using nascent RNA capture and RNA polymerase II chromatin immunoprecipitation, we show that siRNAs targeting a chromatin-associated noncoding RNA induced its transcriptional silencing. Deletion of the sequence targeted by one of these siRNAs on the two alleles by genome editing further showed that this silencing was due to base-pairing of the siRNA to the target. Moreover, by using cells with heterozygous deletion of the target sequence, we showed that only the wild-type allele, but not the deleted allele, was silenced by the siRNA, indicating that transcriptional silencing occurred only in cis. Finally, we demonstrated that both Ago1 and Ago2 are involved in this transcriptional silencing. Altogether, our data demonstrate that siRNAs targeting a chromatin-associated RNA at a distance from its promoter induce its transcriptional silencing. Our results thus extend the possible repertoire of endogenous or exogenous interfering RNAs.
Collapse
|
17
|
La Rosa M, Fiannaca A, La Paglia L, Urso A. A Graph Neural Network Approach for the Analysis of siRNA-Target Biological Networks. Int J Mol Sci 2022; 23:ijms232214211. [PMID: 36430688 PMCID: PMC9696923 DOI: 10.3390/ijms232214211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Many biological systems are characterised by biological entities, as well as their relationships. These interaction networks can be modelled as graphs, with nodes representing bio-entities, such as molecules, and edges representing relations among them, such as interactions. Due to the current availability of a huge amount of biological data, it is very important to consider in silico analysis methods based on, for example, machine learning, that could take advantage of the inner graph structure of the data in order to improve the quality of the results. In this scenario, graph neural networks (GNNs) are recent computational approaches that directly deal with graph-structured data. In this paper, we present a GNN network for the analysis of siRNA-mRNA interaction networks. siRNAs, in fact, are small RNA molecules that are able to bind to target genes and silence them. These events make siRNAs key molecules as RNA interference agents in many biological interaction networks related to severe diseases such as cancer. In particular, our GNN approach allows for the prediction of the siRNA efficacy, which measures the siRNA's ability to bind and silence a gene target. Tested on benchmark datasets, our proposed method overcomes other machine learning algorithms, including the state-of-the-art predictor based on the convolutional neural network, reaching a Pearson correlation coefficient of approximately 73.6%. Finally, we proposed a case study where the efficacy of a set of siRNAs is predicted for a gene of interest. To the best of our knowledge, GNNs were used for the first time in this scenario.
Collapse
|
18
|
Amanat M, Nemeth CL, Fine AS, Leung DG, Fatemi A. Antisense Oligonucleotide Therapy for the Nervous System: From Bench to Bedside with Emphasis on Pediatric Neurology. Pharmaceutics 2022; 14:2389. [PMID: 36365206 PMCID: PMC9695718 DOI: 10.3390/pharmaceutics14112389] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 09/05/2023] Open
Abstract
Antisense oligonucleotides (ASOs) are disease-modifying agents affecting protein-coding and noncoding ribonucleic acids. Depending on the chemical modification and the location of hybridization, ASOs are able to reduce the level of toxic proteins, increase the level of functional protein, or modify the structure of impaired protein to improve function. There are multiple challenges in delivering ASOs to their site of action. Chemical modifications in the phosphodiester bond, nucleotide sugar, and nucleobase can increase structural thermodynamic stability and prevent ASO degradation. Furthermore, different particles, including viral vectors, conjugated peptides, conjugated antibodies, and nanocarriers, may improve ASO delivery. To date, six ASOs have been approved by the US Food and Drug Administration (FDA) in three neurological disorders: spinal muscular atrophy, Duchenne muscular dystrophy, and polyneuropathy caused by hereditary transthyretin amyloidosis. Ongoing preclinical and clinical studies are assessing the safety and efficacy of ASOs in multiple genetic and acquired neurological conditions. The current review provides an update on underlying mechanisms, design, chemical modifications, and delivery of ASOs. The administration of FDA-approved ASOs in neurological disorders is described, and current evidence on the safety and efficacy of ASOs in other neurological conditions, including pediatric neurological disorders, is reviewed.
Collapse
Affiliation(s)
- Man Amanat
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christina L. Nemeth
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amena Smith Fine
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Doris G. Leung
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Genetic Muscle Disorders, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Ali Fatemi
- Moser Center for Leukodystrophies, Kennedy Krieger Institute, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| |
Collapse
|
19
|
Vaillant A. Oligonucleotide-Based Therapies for Chronic HBV Infection: A Primer on Biochemistry, Mechanisms and Antiviral Effects. Viruses 2022; 14:v14092052. [PMID: 36146858 PMCID: PMC9502277 DOI: 10.3390/v14092052] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/21/2022] Open
Abstract
Three types of oligonucleotide-based medicines are under clinical development for the treatment of chronic HBV infection. Antisense oligonucleotides (ASOs) and synthetic interfering RNA (siRNA) are designed to degrade HBV mRNA, and nucleic acid polymers (NAPs) stop the assembly and secretion of HBV subviral particles. Extensive clinical development of ASOs and siRNA for a variety of liver diseases has established a solid understanding of their pharmacodynamics, accumulation in different tissue types in the liver, pharmacological effects, off-target effects and how chemical modifications and delivery approaches affect these parameters. These effects are highly conserved for all ASO and siRNA used in human studies to date. The clinical assessment of several ASO and siRNA compounds in chronic HBV infection in recent years is complicated by the different delivery approaches used. Moreover, these assessments have not considered the large clinical database of ASO/siRNA function in other liver diseases and known off target effects in other viral infections. The goal of this review is to summarize the current understanding of ASO/siRNA/NAP pharmacology and integrate these concepts into current clinical results for these compounds in the treatment of chronic HBV infection.
Collapse
Affiliation(s)
- Andrew Vaillant
- Replicor Inc., 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada
| |
Collapse
|
20
|
Eptaminitaki GC, Stellas D, Bonavida B, Baritaki S. Long Non-coding RNAs (lncRNAs) signaling in Cancer Chemoresistance: From Prediction to Druggability. Drug Resist Updat 2022; 65:100866. [DOI: 10.1016/j.drup.2022.100866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/03/2022]
|
21
|
Bocos-Asenjo IT, Niño-Sánchez J, Ginésy M, Diez JJ. New Insights on the Integrated Management of Plant Diseases by RNA Strategies: Mycoviruses and RNA Interference. Int J Mol Sci 2022; 23:9236. [PMID: 36012499 PMCID: PMC9409477 DOI: 10.3390/ijms23169236] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
RNA-based strategies for plant disease management offer an attractive alternative to agrochemicals that negatively impact human and ecosystem health and lead to pathogen resistance. There has been recent interest in using mycoviruses for fungal disease control after it was discovered that some cause hypovirulence in fungal pathogens, which refers to a decline in the ability of a pathogen to cause disease. Cryphonectria parasitica, the causal agent of chestnut blight, has set an ideal model of management through the release of hypovirulent strains. However, mycovirus-based management of plant diseases is still restricted by limited approaches to search for viruses causing hypovirulence and the lack of protocols allowing effective and systemic virus infection in pathogens. RNA interference (RNAi), the eukaryotic cell system that recognizes RNA sequences and specifically degrades them, represents a promising. RNA-based disease management method. The natural occurrence of cross-kingdom RNAi provides a basis for host-induced gene silencing, while the ability of most pathogens to uptake exogenous small RNAs enables the use of spray-induced gene silencing techniques. This review describes the mechanisms behind and the potential of two RNA-based strategies, mycoviruses and RNAi, for plant disease management. Successful applications are discussed, as well as the research gaps and limitations that remain to be addressed.
Collapse
Affiliation(s)
- Irene Teresa Bocos-Asenjo
- Department of Plant Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
- iuFOR-Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
| | - Jonatan Niño-Sánchez
- Department of Plant Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
- iuFOR-Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
| | - Mireille Ginésy
- Department of Plant Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
- iuFOR-Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
| | - Julio Javier Diez
- Department of Plant Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
- iuFOR-Sustainable Forest Management Research Institute, University of Valladolid-INIA, 34004 Palencia, Spain
| |
Collapse
|
22
|
Targeting Subviral Particles: A Critical Step in Achieving HBV Functional Cure but Where Are We with Current Agents in Clinical Development? Viruses 2022; 14:v14061193. [PMID: 35746664 PMCID: PMC9227515 DOI: 10.3390/v14061193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023] Open
|
23
|
Shen Q, Zhou H, Zhang M, Wu R, Wang L, Wang Y, Chen J. Super enhancer-LncRNA SENCR promoted cisplatin resistance and growth of NSCLC through upregulating FLI1. J Clin Lab Anal 2022; 36:e24460. [PMID: 35500152 PMCID: PMC9169188 DOI: 10.1002/jcla.24460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/13/2022] [Accepted: 04/10/2022] [Indexed: 01/21/2023] Open
Abstract
Background Super enhancer‐lncRNA smooth muscle and endothelial cell‐enriched migration/differentiation‐associated lncRNA (SENCR) were highly overexpressed in cisplatin‐resistant A549/DDP cells, while the mechanism was unclear. Methods SE‐lncRNA SENCR and FLI1 mRNA expression in A549/DDP cell, LAD tissues were detected. SENCR knockdown of A549/DDP cell and SENCR overexpression of cisplatin‐sensitive A549 cell were constructed. Experiments of cell‐confirmed function of SENCR and the correlation between SENCR and FLI1 were validated. Results The expression of SENCR and FLI1 mRNA in A549/DDP cell were both upregulated and mainly localized in the nucleus. Compared with DDP‐sensitive tissues with disease relief, SENCR expression was higher in DDP‐resistant tissues with disease progression from LAD. Knockdown of SENCR in A549/DDP reduced proliferation ability and cisplatin resistance, consistent with the decreased levels of proteins PCNA, MDMX, and P‐gp. Besides, whatever without cisplatin or with 2 μg/ml cisplatin, knockdown of SENCR reduced the migration, invasion, and colony formation abilities of A549/DDP cell and promoted apoptosis. However, when SENCR was overexpressed in A549 cell, all above results were reversed. Mechanistically, FLI1 expression was reduced after knocking down SENCR, while overexpressing SENCR increased FLI1 expression. Conclusion SE‐LncRNA SENCR was upregulated in A549/DDP, which could promote cisplatin resistance and growth of NSCLC cell through upregulating FLI1 expression.
Collapse
Affiliation(s)
- Qiang Shen
- First People's Hospital of Linping District, Hangzhou, China
| | - Huixin Zhou
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Zhejiang, China
| | - Meijuan Zhang
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Zhejiang, China
| | - Ruihao Wu
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Zhejiang, China
| | - Liangxing Wang
- First People's Hospital of Linping District, Hangzhou, China
| | - Yumin Wang
- Department of Respiratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jie Chen
- Department of Intensive Care Unit, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
24
|
Yamada T, Murata D, Kleiner DE, Anders R, Rosenberg AZ, Kaplan J, Hamilton JP, Aghajan M, Levi M, Wang NY, Dawson TM, Yanagawa T, Powers AF, Iijima M, Sesaki H. Prevention and regression of megamitochondria and steatosis by blocking mitochondrial fusion in the liver. iScience 2022; 25:103996. [PMID: 35310936 PMCID: PMC8927900 DOI: 10.1016/j.isci.2022.103996] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/06/2022] [Accepted: 02/24/2022] [Indexed: 02/07/2023] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a most common chronic liver disease that is manifested by steatosis, inflammation, fibrosis, and tissue damage. Hepatocytes produce giant mitochondria termed megamitochondria in patients with NASH. It has been shown that gene knockout of OPA1, a mitochondrial dynamin-related GTPase that mediates mitochondrial fusion, prevents megamitochondria formation and liver damage in a NASH mouse model induced by a methionine-choline-deficient (MCD) diet. However, it is unknown whether blocking mitochondrial fusion mitigates NASH pathologies. Here, we acutely depleted OPA1 using antisense oligonucleotides in the NASH mouse model before or after megamitochondria formation. When OPA1 ASOs were applied at the disease onset, they effectively prevented megamitochondria formation and liver pathologies in the MCD model. Notably, even when applied after mice robustly developed NASH pathologies, OPA1 targeting effectively regressed megamitochondria and the disease phenotypes. Thus, our data show the efficacy of mitochondrial dynamics as a unique therapy for megamitochondria-associated liver disease.
Collapse
Affiliation(s)
- Tatsuya Yamada
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daisuke Murata
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David E. Kleiner
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD, USA
| | - Robert Anders
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Avi Z. Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeffrey Kaplan
- Department of Pathology, University of Colorado School of Medicine, Aurora, CO, USA
| | - James P. Hamilton
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Moshe Levi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Nae-Yuh Wang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ted M. Dawson
- Departments of Neurology and Neuroscience and Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Toru Yanagawa
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | | | - Miho Iijima
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hiromi Sesaki
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
25
|
Mangraviti N, De Windt LJ. Long Non-Coding RNAs in Cardiac Hypertrophy. FRONTIERS IN MOLECULAR MEDICINE 2022; 2:836418. [PMID: 39086960 PMCID: PMC11285587 DOI: 10.3389/fmmed.2022.836418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/08/2022] [Indexed: 08/02/2024]
Abstract
Heart disease represents one of the main challenges in modern medicine with insufficient treatment options. Whole genome sequencing allowed for the discovery of several classes of non-coding RNA (ncRNA) and widened our understanding of disease regulatory circuits. The intrinsic ability of long ncRNAs (lncRNAs) and circular RNAs (circRNAs) to regulate gene expression by a plethora of mechanisms make them candidates for conceptually new treatment options. However, important questions remain to be addressed before we can fully exploit the therapeutic potential of these molecules. Increasing our knowledge of their mechanisms of action and refining the approaches for modulating lncRNAs expression are just a few of the challenges we face. The accurate identification of novel lncRNAs is hampered by their relatively poor cross-species sequence conservation and their low and context-dependent expression pattern. Nevertheless, progress has been made in their annotation in recent years, while a few experimental studies have confirmed the value of lncRNAs as new mechanisms in the development of cardiac hypertrophy and other cardiovascular diseases. Here, we explore cardiac lncRNA biology and the evidence that this class of molecules has therapeutic benefit to treat cardiac hypertrophy.
Collapse
Affiliation(s)
| | - Leon J. De Windt
- Department of Molecular Genetics, Faculty of Science and Engineering, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| |
Collapse
|
26
|
Kordyś M, Sen R, Warkocki Z. Applications of the versatile CRISPR-Cas13 RNA targeting system. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1694. [PMID: 34553495 DOI: 10.1002/wrna.1694] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas are adaptable natural prokaryotic defense systems that act against invading viruses and plasmids. Among the six currently known major CRISPR-Cas types, the type VI CRISPR-Cas13 is the only one known to exclusively bind and cleave foreign RNA. Within the last couple of years, this system has been adapted to serve numerous, and sometimes not obvious, applications, including some that might be developed as effective molecular therapies. Indeed, Cas13 has been adapted to kill antibiotic-resistant bacteria. In a cell-free environment, Cas13 has been used in the development of highly specific, sensitive, multiplexing-capable, and field-adaptable detection tools. Importantly, Cas13 can be reprogrammed and applied to eukaryotes to either combat pathogenic RNA viruses or in the regulation of gene expression, facilitating the knockdown of mRNA, circular RNA, and noncoding RNA. Furthermore, Cas13 has been harnessed for in vivo RNA modifications including programmable regulation of alternative splicing, A-to-I and C to U editing, and m6A modifications. Finally, approaches allowing for the detection and characterization of RNA-interacting proteins have also been demonstrated. Here, we provide a comprehensive overview of the applications utilizing CRISPR-Cas13 that illustrate its versatility. We also discuss the most important limitations of the CRISPR-Cas13-based technologies, and controversies regarding them. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Martyna Kordyś
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | | |
Collapse
|
27
|
Jurgielewicz B, Stice S, Yao Y. Therapeutic Potential of Nucleic Acids when Combined with Extracellular Vesicles. Aging Dis 2021; 12:1476-1493. [PMID: 34527423 PMCID: PMC8407886 DOI: 10.14336/ad.2021.0708] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs), endogenous nanocarriers of proteins, lipids, and genetic material, have been harnessed as intrinsic delivery vectors for nucleic acid therapies. EVs are nanosized lipid bilayer bound vesicles released from most cell types responsible for delivery of functional biologic material to mediate intercellular communication and to modulate recipient cell phenotypes. Due to their innate biological role and composition, EVs possess several advantages as delivery vectors for nucleic acid based therapies including low immunogenicity and toxicity, high bioavailability, and ability to be engineered to enhance targeting to specific recipient cells in vivo. In this review, the current understanding of the biological role of EVs as well as the advancements in loading EVs to deliver nucleic acid therapies are summarized. We discuss the current methods and associated challenges in loading EVs and the prospects of utilizing the inherent characteristics of EVs as a delivery vector of nucleic acid therapies for genetic disorders.
Collapse
Affiliation(s)
- Brian Jurgielewicz
- 1Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA.,2Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA 30602, USA
| | - Steven Stice
- 1Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA.,2Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA 30602, USA.,3ArunA Bio, Athens, GA 30602, USA
| | - Yao Yao
- 1Regenerative Bioscience Center, University of Georgia, Athens, GA 30602, USA.,2Department of Animal and Dairy Science, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
28
|
Abstract
PURPOSE OF REVIEW The current aim in the HBV landscape is to develop therapeutic strategies to achieve a functional cure of infection, characterized by a sustained loss of HBsAg off-treatment. Current treatment options, that is, nucleos(t)ide analogues and IFN are effective at viral suppression but very poor at achieving HBsAg loss. This article is designed to summarize the HBV life cycle in order to review the current treatment strategies and compounds targeting different points of the virus life cycle, which are either in preclinical or clinical phases. RECENT FINDINGS Recently our developed understanding of the HBV life cycle has enabled the development of multiple novel treatment options, all aiming for functional cure. SUMMARY It is likely that combinations of novel treatments will be needed to achieve a functional cure, including those that target the virus itself as well as those that target the immune system.
Collapse
|
29
|
Krappinger JC, Bonstingl L, Pansy K, Sallinger K, Wreglesworth NI, Grinninger L, Deutsch A, El-Heliebi A, Kroneis T, Mcfarlane RJ, Sensen CW, Feichtinger J. Non-coding Natural Antisense Transcripts: Analysis and Application. J Biotechnol 2021; 340:75-101. [PMID: 34371054 DOI: 10.1016/j.jbiotec.2021.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/30/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Non-coding natural antisense transcripts (ncNATs) are regulatory RNA sequences that are transcribed in the opposite direction to protein-coding or non-coding transcripts. These transcripts are implicated in a broad variety of biological and pathological processes, including tumorigenesis and oncogenic progression. With this complex field still in its infancy, annotations, expression profiling and functional characterisations of ncNATs are far less comprehensive than those for protein-coding genes, pointing out substantial gaps in the analysis and characterisation of these regulatory transcripts. In this review, we discuss ncNATs from an analysis perspective, in particular regarding the use of high-throughput sequencing strategies, such as RNA-sequencing, and summarize the unique challenges of investigating the antisense transcriptome. Finally, we elaborate on their potential as biomarkers and future targets for treatment, focusing on cancer.
Collapse
Affiliation(s)
- Julian C Krappinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
| | - Lilli Bonstingl
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Katrin Pansy
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Katja Sallinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Nick I Wreglesworth
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Lukas Grinninger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Austrian Biotech University of Applied Sciences, Konrad Lorenz-Straße 10, 3430 Tulln an der Donau, Austria
| | - Alexander Deutsch
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Amin El-Heliebi
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Thomas Kroneis
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Ramsay J Mcfarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Christoph W Sensen
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria; Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; HCEMM Kft., Római blvd. 21, 6723 Szeged, Hungary
| | - Julia Feichtinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
| |
Collapse
|
30
|
Niu D, Hamby R, Sanchez JN, Cai Q, Yan Q, Jin H. RNAs - a new frontier in crop protection. Curr Opin Biotechnol 2021; 70:204-212. [PMID: 34217122 PMCID: PMC8957476 DOI: 10.1016/j.copbio.2021.06.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022]
Abstract
Small RNA (sRNA)-mediated RNA interference (RNAi) is a regulatory mechanism conserved in almost all eukaryotes. sRNAs play a critical role in host pathogen interactions either endogenously or by traveling between the interacting organisms and inducing 'cross-Kingdom RNAi' in the counterparty. Cross-kingdom RNAi is the mechanistic basis of host-induced gene silencing (HIGS), which relies on genetically expressing pathogen-gene targeting RNAs in crops, and has been successfully utilized against both microbial pathogens and pests. HIGS is limited by the need to produce genetically engineered crops. Recent studies have demonstrated that double-stranded RNAs and sRNAs can be efficiently taken up by many fungal pathogens, and induce gene silencing in fungal cells. This mechanism, termed 'environmental RNAi', allows direct application of pathogen-gene targeting RNAs onto crops to silence fungal virulence-related genes for plant protection. In this review, we will focus on how we can leverage cross-kingdom RNAi and environmental RNAi for crop disease control.
Collapse
Affiliation(s)
- Dongdong Niu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Rachael Hamby
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Jonatan Nino Sanchez
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qin Yan
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Hailing Jin
- Department of Microbiology & Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
| |
Collapse
|
31
|
Therapeutically viable generation of neurons with antisense oligonucleotide suppression of PTB. Nat Neurosci 2021; 24:1089-1099. [PMID: 34083786 PMCID: PMC8338913 DOI: 10.1038/s41593-021-00864-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 04/29/2021] [Indexed: 02/07/2023]
Abstract
Methods to enhance adult neurogenesis by reprogramming glial cells into neurons enable production of new neurons in the adult nervous system. Development of therapeutically viable approaches to induce new neurons is now required to bring this concept to clinical application. Here, we successfully generate new neurons in the cortex and dentate gyrus of the aged adult mouse brain by transiently suppressing polypyrimidine tract binding protein 1 using an antisense oligonucleotide delivered by a single injection into cerebral spinal fluid. Radial glial-like cells and other GFAP-expressing cells convert into new neurons that, over a 2-month period, acquire mature neuronal character in a process mimicking normal neuronal maturation. The new neurons functionally integrate into endogenous circuits and modify mouse behavior. Thus, generation of new neurons in the dentate gyrus of the aging brain can be achieved with a therapeutically feasible approach, thereby opening prospects for production of neurons to replace those lost to neurodegenerative disease.
Collapse
|
32
|
Wang C, Deng J, Deng H, Kang Z, Huang Z, Ding Z, Dong L, Chen J, Zhang J, Zang Y. A Novel Sox9/lncRNA H19 Axis Contributes to Hepatocyte Death and Liver Fibrosis. Toxicol Sci 2021; 177:214-225. [PMID: 32579217 DOI: 10.1093/toxsci/kfaa097] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Sox9 has been previously characterized as a transcription factor responsible for the extracellular matrix production during liver fibrosis. However, the deregulation and functional role of hepatocyte Sox9 in the progression of liver fibrosis remains elusive. Here, we found a significant increase of Sox9 in the hepatocytes isolated from CCl4-induced fibrotic liver and showed that antisense oligoribonucleotides depletion of Sox9 was sufficient to attenuate CCl4-induced liver fibrosis. Notably, the increase of Sox9 in hepatocyte was associated with the upregulation of long noncoding RNA H19 in both in vitro and in vivo systems. Mechanistic studies revealed that Sox9 induced H19 by binding to a conserved promoter region of H19. In vitro, hepatocyte injury triggered the increase of Sox9/H19 axis, whereas silence of H19 greatly alleviated the H2O2-induced hepatocyte apoptosis, suggesting that H19 functions as a downstream effector of Sox9 signaling and is involved in hepatocyte apoptosis. In animal experiments, inhibition of H19 alleviated the activation of hepatic stellate cells and reduced the extent of liver fibrosis, whereas ectopic expression of H19 abolished the inhibitory effects of Sox9 depletion on liver fibrosis, suggesting that the profibrotic effect of hepatocyte Sox9 depends on H19. Finally, we investigated the clinical relevance of Sox9/H19 axis to liver fibrosis and identified the increase of Sox9/H19 axis in liver cirrhosis patients. In conclusion, our findings link Sox9/H19 axis to the intrinsic mechanisms of hepatocyte apoptosis and may represent a hitherto unknown paradigm in hepatocyte injury associated with the progression of liver fibrosis.
Collapse
Affiliation(s)
- Chenqi Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University
| | - Jia Deng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University
| | - Hao Deng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University
| | - Zhiqian Kang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University
| | - Zhen Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University
| | - Zhi Ding
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University
| | - Lei Dong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University
| | - Jiangning Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University.,State Key Laboratory of Analytical Chemistry for Life Sciences and Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing 210093, P.R. China
| | - Junfeng Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University
| | - Yuhui Zang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University
| |
Collapse
|
33
|
Vaillant A. HBsAg, Subviral Particles, and Their Clearance in Establishing a Functional Cure of Chronic Hepatitis B Virus Infection. ACS Infect Dis 2021; 7:1351-1368. [PMID: 33302622 DOI: 10.1021/acsinfecdis.0c00638] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In diverse viral infections, the production of excess viral particles containing only viral glycoproteins (subviral particles or SVP) is commonly observed and is a commonly evolved mechanism for immune evasion. In hepatitis B virus (HBV) infection, spherical particles contain the hepatitis B surface antigen, outnumber infectious virus 10 000-100 000 to 1, and have diverse inhibitory effects on the innate and adaptive immune response, playing a major role in the chronic nature of HBV infection. The current goal of therapies in development for HBV infection is a clinical outcome called functional cure, which signals a persistent and effective immune control of the infection. Although removal of spherical SVP (and the HBsAg they carry) is an important milestone in achieving functional cure, this outcome is rarely achieved with current therapies due to distinct mechanisms for assembly, secretion, and persistence of SVP, which are poorly targeted by direct acting antivirals or immunotherapies. In this Review, the current understanding of the distinct mechanisms involved in the production and persistence of spherical SVP in chronic HBV infection and their immunoinhibitory activity will be reviewed as well as current therapies in development with the goal of clearing spherical SVP and achieving functional cure.
Collapse
Affiliation(s)
- Andrew Vaillant
- Replicor Inc., 6100 Royalmount Avenue, Montreal, Quebec H8Y 3E6, Canada
| |
Collapse
|
34
|
Raghav PK, Kalyanaraman K, Kumar D. Human cell receptors: potential drug targets to combat COVID-19. Amino Acids 2021; 53:813-842. [PMID: 33950300 PMCID: PMC8097256 DOI: 10.1007/s00726-021-02991-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 04/21/2021] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19). The World Health Organization (WHO) has announced that COVID-19 is a pandemic having a higher spread rate rather than the mortality. Identification of a potential approach or therapy against COVID-19 is still under consideration. Therefore, it is essential to have an insight into SARS-CoV-2, its interacting partner, and domains for an effective treatment. The present study is divided into three main categories, including SARS-CoV-2 prominent receptor and its expression levels, other interacting partners, and their binding domains. The first section focuses primarily on coronaviruses' general aspects (SARS-CoV-2, SARS-CoV, and the Middle East Respiratory Syndrome Coronaviruses (MERS-CoV)) their structures, similarities, and mode of infections. The second section discusses the host receptors which includes the human targets of coronaviruses like dipeptidyl peptidase 4 (DPP4), CD147, CD209L, Angiotensin-Converting Enzyme 2 (ACE2), and other miscellaneous targets (type-II transmembrane serine proteases (TTSPs), furin, trypsin, cathepsins, thermolysin, elastase, phosphatidylinositol 3-phosphate 5-kinase, two-pore segment channel, and epithelium sodium channel C-α subunit). The human cell receptor, ACE2 plays an essential role in the Renin-Angiotensin system (RAS) pathway and COVID-19. Thus, this section also discusses the ACE2 expression and risk of COVID-19 infectivity in various organs and tissues such as the liver, lungs, intestine, heart, and reproductive system in the human body. Absence of ACE2 protein expression in immune cells could be used for limiting the SARS-CoV-2 infection. The third section covers the current available approaches for COVID-19 treatment. Overall, this review focuses on the critical role of human cell receptors involved in coronavirus pathogenesis, which would likely be used in designing target-specific drugs to combat COVID-19.
Collapse
Affiliation(s)
| | - Keerthana Kalyanaraman
- Amity Institute of Biotechnology, Amity University, Sector-125, Noida, Uttar Pradesh, India
| | - Dinesh Kumar
- ICMR-National Institute of Cancer Prevention & Research, Noida, 201301, India.
| |
Collapse
|
35
|
Antisense technology: an overview and prospectus. Nat Rev Drug Discov 2021; 20:427-453. [PMID: 33762737 DOI: 10.1038/s41573-021-00162-z] [Citation(s) in RCA: 302] [Impact Index Per Article: 100.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2021] [Indexed: 12/13/2022]
Abstract
Antisense technology is now beginning to deliver on its promise to treat diseases by targeting RNA. Nine single-stranded antisense oligonucleotide (ASO) drugs representing four chemical classes, two mechanisms of action and four routes of administration have been approved for commercial use, including the first RNA-targeted drug to be a major commercial success, nusinersen. Although all the approved drugs are for use in patients with rare diseases, many of the ASOs in late- and middle-stage clinical development are intended to treat patients with very common diseases. ASOs in development are showing substantial improvements in potency and performance based on advances in medicinal chemistry, understanding of molecular mechanisms and targeted delivery. Moreover, the ASOs in development include additional mechanisms of action and routes of administration such as aerosol and oral formulations. Here, we describe the key technological advances that have enabled this progress and discuss recent clinical trials that illustrate the impact of these advances on the performance of ASOs in a wide range of therapeutic applications. We also consider strategic issues such as target selection and provide perspectives on the future of the field.
Collapse
|
36
|
Nishikawa M, Yanagawa N. Knockdown of Nuclear lncRNAs by Locked Nucleic Acid (LNA) Gapmers in Nephron Progenitor Cells. Methods Mol Biol 2021; 2161:29-36. [PMID: 32681503 DOI: 10.1007/978-1-0716-0680-3_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite recent advance in our understanding on the role of long noncoding RNAs (lncRNAs), the function of the vast majority of lncRNAs remains poorly understood. To characterize the function of lncRNAs, knockdown studies are essential. However, the conventional silencing methods for mRNA, such as RNA interference (RNAi), may not be as efficient against lncRNAs, partly due to the mismatch of the localization of lncRNAs and RNAi machinery. To circumvent such limitation, a new technique has recently been developed, i.e., locked nucleic acid (LNA) gapmers. This system utilizes RNase H that distributes evenly in both nucleus and cytoplasm and is expected to knock down lncRNAs of interest more consistently regardless of their localization in the cell. In this chapter, we describe the procedure with tips to silence lncRNAs by LNA gapmers, by using mouse nephron progenitor cells as an example.
Collapse
Affiliation(s)
- Masaki Nishikawa
- School of Engineering, Chemical System Engineering, University of Tokyo, Tokyo, Japan.
| | - Norimoto Yanagawa
- Medical and Research Services, Greater Los Angeles Veterans Affairs Healthcare System at Sepulveda, North Hills, CA, USA.
- David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
37
|
de Vrieze E, Cañas Martín J, Peijnenborg J, Martens A, Oostrik J, van den Heuvel S, Neveling K, Pennings R, Kremer H, van Wijk E. AON-based degradation of c.151C>T mutant COCH transcripts associated with dominantly inherited hearing impairment DFNA9. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 24:274-283. [PMID: 33815940 PMCID: PMC7985667 DOI: 10.1016/j.omtn.2021.02.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/24/2021] [Indexed: 01/22/2023]
Abstract
The c.151C>T founder mutation in COCH is a frequent cause of late-onset, dominantly inherited hearing impairment and vestibular dysfunction (DFNA9) in the Dutch/Belgian population. The initial clinical symptoms only manifest between the 3rd and 5th decade of life, which leaves ample time for therapeutic intervention. The dominant inheritance pattern and established non-haploinsufficiency disease mechanism indicate that suppressing translation of mutant COCH transcripts has high therapeutic potential. Single-molecule real-time (SMRT) sequencing resulted in the identification of 11 variants with a low population frequency (<10%) that are specific to the c.151C>T mutant COCH allele. Proof of concept was obtained that gapmer antisense oligonucleotides (AONs), directed against the c.151C>T mutation or mutant allele-specific intronic variants, are able to induce mutant COCH transcript degradation when delivered to transgenic cells expressing COCH minigenes. The most potent AON, directed against the c.151C>T mutation, was able to induce a 60% decrease in mutant COCH transcripts without affecting wild-type COCH transcript levels. Allele specificity decreased when increasing concentrations of AON were delivered to the cells. With the proven safety of AONs in humans, and rapid advancements in inner ear drug delivery, our in vitro studies indicate that AONs offer a promising treatment modality for DFNA9.
Collapse
Affiliation(s)
- Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Corresponding author: Erik de Vrieze, Department of Otorhinolaryngology, Radboud University Medical Center, P.O. Box 9101, 6525 GA Nijmegen (Route 855), the Netherlands.
| | - Jorge Cañas Martín
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Jolien Peijnenborg
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Aniek Martens
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Jaap Oostrik
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Simone van den Heuvel
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Ronald Pennings
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| |
Collapse
|
38
|
Nowak I, Sarshad AA. Argonaute Proteins Take Center Stage in Cancers. Cancers (Basel) 2021; 13:cancers13040788. [PMID: 33668654 PMCID: PMC7918559 DOI: 10.3390/cancers13040788] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The dysregulation of RNA interference (RNAi) has often been observed in cancers, where the main focus of research has been on the small RNA molecules directing RNAi. In this review, we focus on the activity of Argonaute proteins, central components of RNAi, in tumorigenesis, and also highlight their potential applications in grading tumors and anti-cancer therapies. Abstract Argonaute proteins (AGOs) play crucial roles in RNA-induced silencing complex (RISC) formation and activity. AGOs loaded with small RNA molecules (miRNA or siRNA) either catalyze endoribonucleolytic cleavage of target RNAs or recruit factors responsible for translational silencing and target destabilization. miRNAs are well characterized and broadly studied in tumorigenesis; nevertheless, the functions of the AGOs in cancers have lagged behind. Here, we discuss the current state of knowledge on the role of AGOs in tumorigenesis, highlighting canonical and non-canonical functions of AGOs in cancer cells, as well as the biomarker potential of AGO expression in different of tumor types. Furthermore, we point to the possible application of the AGOs in development of novel therapeutic approaches.
Collapse
Affiliation(s)
- Iwona Nowak
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Aishe A. Sarshad
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
- Correspondence:
| |
Collapse
|
39
|
Crooke ST, Liang XH, Baker BF, Crooke RM. Antisense technology: A review. J Biol Chem 2021; 296:100416. [PMID: 33600796 PMCID: PMC8005817 DOI: 10.1016/j.jbc.2021.100416] [Citation(s) in RCA: 146] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Antisense technology is beginning to deliver on the broad promise of the technology. Ten RNA-targeted drugs including eight single-strand antisense drugs (ASOs) and two double-strand ASOs (siRNAs) have now been approved for commercial use, and the ASOs in phase 2/3 trials are innovative, delivered by multiple routes of administration and focused on both rare and common diseases. In fact, two ASOs are used in cardiovascular outcome studies and several others in very large trials. Interest in the technology continues to grow, and the field has been subject to a significant number of reviews. In this review, we focus on the molecular events that result in the effects observed and use recent clinical results involving several different ASOs to exemplify specific molecular mechanisms and specific issues. We conclude with the prospective on the technology.
Collapse
Affiliation(s)
- Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA.
| | - Xue-Hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Brenda F Baker
- Development Communication, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| | - Rosanne M Crooke
- Antisense Drug Discovery, Ionis Pharmaceuticals, Inc, Carlsbad, California, USA
| |
Collapse
|
40
|
Zhou H, Simion V, Pierce JB, Haemmig S, Chen AF, Feinberg MW. LncRNA-MAP3K4 regulates vascular inflammation through the p38 MAPK signaling pathway and cis-modulation of MAP3K4. FASEB J 2020; 35:e21133. [PMID: 33184917 DOI: 10.1096/fj.202001654rr] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/23/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022]
Abstract
Chronic vascular inflammation plays a key role in the pathogenesis of atherosclerosis. Long non-coding RNAs (lncRNAs) have emerged as essential inflammation regulators. We identify a novel lncRNA termed lncRNA-MAP3K4 that is enriched in the vessel wall and regulates vascular inflammation. In the aortic intima, lncRNA-MAP3K4 expression was reduced by 50% during the progression of atherosclerosis (chronic inflammation) and 70% during endotoxemia (acute inflammation). lncRNA-MAP3K4 knockdown reduced the expression of key inflammatory factors (eg, ICAM-1, E-selectin, MCP-1) in endothelial cells or vascular smooth muscle cells and decreased monocytes adhesion to endothelium, as well as reducing TNF-α, IL-1β, COX2 expression in macrophages. Mechanistically, lncRNA-MAP3K4 regulates inflammation through the p38 MAPK signaling pathway. lncRNA-MAP3K4 shares a bidirectional promoter with MAP3K4, an upstream regulator of the MAPK signaling pathway, and regulates its transcription in cis. lncRNA-MAP3K4 and MAP3K4 show coordinated expression in response to inflammation in vivo and in vitro. Similar to lncRNA-MAP3K4, MAP3K4 knockdown reduced the expression of inflammatory factors in several different vascular cells. Furthermore, lncRNA-MAP3K4 and MAP3K4 knockdown showed cooperativity in reducing inflammation in endothelial cells. Collectively, these findings unveil the role of a novel lncRNA in vascular inflammation by cis-regulating MAP3K4 via a p38 MAPK pathway.
Collapse
Affiliation(s)
- Haoyang Zhou
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Viorel Simion
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jacob B Pierce
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Stefan Haemmig
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alex F Chen
- Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Mark W Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
41
|
Yu AM, Choi YH, Tu MJ. RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges. Pharmacol Rev 2020; 72:862-898. [PMID: 32929000 PMCID: PMC7495341 DOI: 10.1124/pr.120.019554] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA-based therapies, including RNA molecules as drugs and RNA-targeted small molecules, offer unique opportunities to expand the range of therapeutic targets. Various forms of RNAs may be used to selectively act on proteins, transcripts, and genes that cannot be targeted by conventional small molecules or proteins. Although development of RNA drugs faces unparalleled challenges, many strategies have been developed to improve RNA metabolic stability and intracellular delivery. A number of RNA drugs have been approved for medical use, including aptamers (e.g., pegaptanib) that mechanistically act on protein target and small interfering RNAs (e.g., patisiran and givosiran) and antisense oligonucleotides (e.g., inotersen and golodirsen) that directly interfere with RNA targets. Furthermore, guide RNAs are essential components of novel gene editing modalities, and mRNA therapeutics are under development for protein replacement therapy or vaccination, including those against unprecedented severe acute respiratory syndrome coronavirus pandemic. Moreover, functional RNAs or RNA motifs are highly structured to form binding pockets or clefts that are accessible by small molecules. Many natural, semisynthetic, or synthetic antibiotics (e.g., aminoglycosides, tetracyclines, macrolides, oxazolidinones, and phenicols) can directly bind to ribosomal RNAs to achieve the inhibition of bacterial infections. Therefore, there is growing interest in developing RNA-targeted small-molecule drugs amenable to oral administration, and some (e.g., risdiplam and branaplam) have entered clinical trials. Here, we review the pharmacology of novel RNA drugs and RNA-targeted small-molecule medications, with a focus on recent progresses and strategies. Challenges in the development of novel druggable RNA entities and identification of viable RNA targets and selective small-molecule binders are discussed. SIGNIFICANCE STATEMENT: With the understanding of RNA functions and critical roles in diseases, as well as the development of RNA-related technologies, there is growing interest in developing novel RNA-based therapeutics. This comprehensive review presents pharmacology of both RNA drugs and RNA-targeted small-molecule medications, focusing on novel mechanisms of action, the most recent progress, and existing challenges.
Collapse
MESH Headings
- Aptamers, Nucleotide/pharmacology
- Aptamers, Nucleotide/therapeutic use
- Betacoronavirus
- COVID-19
- Chemistry Techniques, Analytical/methods
- Chemistry Techniques, Analytical/standards
- Clustered Regularly Interspaced Short Palindromic Repeats
- Coronavirus Infections/drug therapy
- Drug Delivery Systems/methods
- Drug Development/organization & administration
- Drug Discovery
- Humans
- MicroRNAs/pharmacology
- MicroRNAs/therapeutic use
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- Pandemics
- Pneumonia, Viral/drug therapy
- RNA/adverse effects
- RNA/drug effects
- RNA/pharmacology
- RNA, Antisense/pharmacology
- RNA, Antisense/therapeutic use
- RNA, Messenger/drug effects
- RNA, Messenger/pharmacology
- RNA, Ribosomal/drug effects
- RNA, Ribosomal/pharmacology
- RNA, Small Interfering/pharmacology
- RNA, Small Interfering/therapeutic use
- RNA, Viral/drug effects
- Ribonucleases/metabolism
- Riboswitch/drug effects
- SARS-CoV-2
Collapse
Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Young Hee Choi
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| |
Collapse
|
42
|
Langner HK, Jastrzebska K, Caruthers MH. Synthesis and Characterization of Thiophosphoramidate Morpholino Oligonucleotides and Chimeras. J Am Chem Soc 2020; 142:16240-16253. [PMID: 32866014 DOI: 10.1021/jacs.0c04335] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This Article outlines the optimized chemical synthesis and preliminary biochemical characterization of a new oligonucleotide analogue called thiophosphoramidate morpholinos (TMOs). Their rational design hinges upon integrating two well-studied pharmacophores, namely, phosphorothioates (pS) and morpholinos, to create morpholino-pS hybrid oligonucleotides. Our simple synthesis strategy enables the easy incorporation of morpholino-pS moieties and therapeutically relevant sugar modifications in tandem to create novel oligonucleotide (ON) analogues that are hitherto unexplored in the oligotherapeutics arena. Exclusively TMO-modified ONs demonstrate high stability toward 3'-exonuclease. Hybridization studies show that TMO chimeras consisting of alternating TMO and DNA-pS subunits exhibit higher binding affinity toward complementary RNA relative to the canonical DNA/RNA duplex (∼10 °C). Oligonucleotides that consist entirely of TMO linkages also show higher RNA binding affinity but do not recruit ribonuclease H1 (RNase H1). Chimeric TMO analogues demonstrate high gene silencing efficacy, comparable to that of a chimeric 2'-OMe-pS/pO control, during in vitro bioassay screens designed to evaluate their potential as microRNA inhibitors of hsa-miR-15b-5p in HeLa cells.
Collapse
Affiliation(s)
- Heera K Langner
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Katarzyna Jastrzebska
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| | - Marvin H Caruthers
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, United States
| |
Collapse
|
43
|
Antisense drug discovery and development technology considered in a pharmacological context. Biochem Pharmacol 2020; 189:114196. [PMID: 32800852 DOI: 10.1016/j.bcp.2020.114196] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023]
Abstract
When coined, the term "antisense" included oligonucleotides of any structure, with any chemical modification and designed to work through any post-RNA hybridization mechanism. However, in practice the term "antisense" has been used to describe single stranded oligonucleotides (ss ASOs) designed to hybridize to RNAswhile the term "siRNA" has come to mean double stranded oligonucleotides designed to activate Ago2. However, the two approaches share many common features. The medicinal chemistry developed for ASOs greatly facilitated the development of siRNA technology and remains the chemical basis for both approaches. Many of challenges faced and solutions achieved share many common features. In fact, because ss ASOs can be designed to activate Ago2, the two approaches intersect at this remarkably important protein. There are also meaningful differences. The pharmacokinetic properties are quite different and thus potential routes of delivery differ. ASOs may be designedto use a variety of post-RNA binding mechanismswhile siRNAs depend solely on the robust activity of Ago2. However, siRNAs and ASOs are both used for therapeutic purposes and both must be and can be understood in a pharmacological context. Thus, the goals of this review are to put ASOs in pharmacological context and compare their behavior as pharmacological agents to the those of siRNAs.
Collapse
|
44
|
Mind the Gapmer: Implications of Co-transcriptional Cleavage by Antisense Oligonucleotides. Mol Cell 2020; 77:932-933. [PMID: 32142690 DOI: 10.1016/j.molcel.2020.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
While gapmers efficiently knock down as well as terminate transcription of nascent lncRNAs and mRNAs, Lee and Mendell (2020) and Lai et al. (2020) also demonstrate that Pol II termination is not observed with gapmers targeting the 3' terminal portions of the transcript.
Collapse
|
45
|
Xia X, Pollock N, Zhou J, Rossi J. Tissue-Specific Delivery of Oligonucleotides. Methods Mol Biol 2020; 2036:17-50. [PMID: 31410789 DOI: 10.1007/978-1-4939-9670-4_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
From the initial discovery of short-interfering RNA (siRNA) and antisense oligonucleotides for specific gene knockdown at the posttranscriptional level to the current CRISPR-Cas9 system offering gene editing at the genomic level, oligonucleotides, in addition to their biological functions in storing and conveying genetic information, provide the most prominent solutions to targeted gene therapies. Nonetheless, looking into the future of curing cancer and acute diseases, researchers are only cautiously optimistic as the cellular delivery of these polyanionic biomacromolecules is still the biggest hurdle for their therapeutic realization. To overcome the delivery obstacle, oligonucleotides have been encapsulated within or conjugated with delivery vehicles for enhanced membrane penetration, improved payload, and tissue-specific delivery. Such delivery systems include but not limited to virus-based vehicles, gold-nanoparticle vehicles, formulated liposomes, and synthetic polymers. In this chapter, delivery challenges imposed by biological barriers are briefly discussed; followed by recent advances in tissue-specific oligonucleotide delivery utilizing both viral and nonviral delivery vectors, discussing their advantages, and how judicious design and formulation could improve and expand their potential as delivery vehicles.
Collapse
Affiliation(s)
- Xin Xia
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Nicolette Pollock
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - John Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA.
| |
Collapse
|
46
|
Long non-coding RNAs in immune regulation and their potential as therapeutic targets. Int Immunopharmacol 2020; 81:106279. [PMID: 32058929 DOI: 10.1016/j.intimp.2020.106279] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 12/18/2022]
Abstract
Long non-coding RNAs (lncRNAs) are potent regulators of immune cell development and function. Their implication in multiple immune-mediated disorders highlights lncRNAs as exciting biomarkers and potential drug targets. Recent technological innovations in oligo-based therapeutics, development of RNA-targeting small molecules, and CRISPR-based approaches, position RNA as the next therapeutic frontier. Here, we review the latest advances made toward understanding the role of lncRNAs in human immunological disorders and further discuss RNA-targeting approaches that could be potentially exploited to manipulate lncRNA function as a clinical intervention.
Collapse
|
47
|
Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination. Mol Cell 2020; 77:1032-1043.e4. [PMID: 31924447 DOI: 10.1016/j.molcel.2019.12.029] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/20/2019] [Accepted: 12/25/2019] [Indexed: 11/22/2022]
Abstract
An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism. Here we show that RNase H ASOs targeted to introns or exons robustly reduce the level of spliced RNA associated with chromatin. Surprisingly, intron-targeted ASOs reduce the level of pre-mRNA associated with chromatin to a greater extent than exon-targeted ASOs. This indicates that exon-targeted ASOs achieve full activity after the pre-mRNA has undergone splicing, but before the mRNA is released from chromatin. Even though RNase H ASOs can reduce the level of RNA associated with chromatin, the effect of ASO-directed RNA degradation on transcription has never been documented. Here we show that intron-targeted ASOs and, to a lesser extent, exon-targeted ASOs cause RNA polymerase II (Pol II) transcription termination in cultured cells and mice. Furthermore, ASO-directed transcription termination is mediated by the nuclear exonuclease XRN2.
Collapse
|
48
|
Awwad DA. Beyond classic editing: innovative CRISPR approaches for functional studies of long non-coding RNA. Biol Methods Protoc 2019; 4:bpz017. [PMID: 32161809 PMCID: PMC6994087 DOI: 10.1093/biomethods/bpz017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 09/06/2019] [Accepted: 11/19/2019] [Indexed: 12/26/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) makeup a considerable part of the non-coding human genome and had been well-established as crucial players in an array of biological processes. In spite of their abundance and versatile roles, their functional characteristics remain largely undiscovered mainly due to the lack of suitable genetic manipulation tools. The emerging CRISPR/Cas9 technology has been widely adapted in several studies that aim to screen and identify novel lncRNAs as well as interrogate the functional properties of specific lncRNAs. However, the complexity of lncRNAs genes and the regulatory mechanisms that govern their transcription, as well as their unique functionality pose several limitations the utilization of classic CRISPR methods in lncRNAs functional studies. Here, we overview the unique characteristics of lncRNAs transcription and function and the suitability of the CRISPR toolbox for applications in functional characterization of lncRNAs. We discuss some of the novel variations to the classic CRISPR/Cas9 system that have been tailored and applied previously to study several aspects of lncRNAs functionality. Finally, we share perspectives on the potential applications of various CRISPR systems, including RNA-targeting, in the direct editing and manipulation of lncRNAs.
Collapse
Affiliation(s)
- Dahlia A Awwad
- Center of X-Ray Determination of Structure of Matter (CXDS), Helmi Institute of Biomedical Research, Zewail City of Science and Technology, Giza, Cairo, Egypt
| |
Collapse
|
49
|
Chen CJ, Sgritta M, Mays J, Zhou H, Lucero R, Park J, Wang IC, Park JH, Kaipparettu BA, Stoica L, Jafar-Nejad P, Rigo F, Chin J, Noebels JL, Costa-Mattioli M. Therapeutic inhibition of mTORC2 rescues the behavioral and neurophysiological abnormalities associated with Pten-deficiency. Nat Med 2019; 25:1684-1690. [PMID: 31636454 PMCID: PMC7082835 DOI: 10.1038/s41591-019-0608-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/10/2019] [Indexed: 01/05/2023]
Abstract
Dysregulation of the mammalian target of rapamycin (mTOR) signaling, which is mediated by two structurally and functionally distinct complexes, mTORC1 and mTORC2, has been implicated in several neurological disorders1-3. Individuals carrying loss-of-function mutations in the phosphatase and tensin homolog (PTEN) gene, a negative regulator of mTOR signaling, are prone to developing macrocephaly, autism spectrum disorder (ASD), seizures and intellectual disability2,4,5. It is generally believed that the neurological symptoms associated with loss of PTEN and other mTORopathies (for example, mutations in the tuberous sclerosis genes TSC1 or TSC2) are due to hyperactivation of mTORC1-mediated protein synthesis1,2,4,6,7. Using molecular genetics, we unexpectedly found that genetic deletion of mTORC2 (but not mTORC1) activity prolonged lifespan, suppressed seizures, rescued ASD-like behaviors and long-term memory, and normalized metabolic changes in the brain of mice lacking Pten. In a more therapeutically oriented approach, we found that administration of an antisense oligonucleotide (ASO) targeting mTORC2's defining component Rictor specifically inhibits mTORC2 activity and reverses the behavioral and neurophysiological abnormalities in adolescent Pten-deficient mice. Collectively, our findings indicate that mTORC2 is the major driver underlying the neuropathophysiology associated with Pten-deficiency, and its therapeutic reduction could represent a promising and broadly effective translational therapy for neurological disorders where mTOR signaling is dysregulated.
Collapse
Affiliation(s)
- Chien-Ju Chen
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Martina Sgritta
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Jacqunae Mays
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Hongyi Zhou
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Rocco Lucero
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Jin Park
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - I-Ching Wang
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Jun Hyoung Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Benny Abraham Kaipparettu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Loredana Stoica
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, CA, USA
| | - Jeannie Chin
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey L Noebels
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Mauro Costa-Mattioli
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Memory and Brain Research Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
50
|
Ruiz-Hernández A, Romero-Nava R, Huang F, Hong E, Villafaña S. Altered function and expression of the orphan GPR135 at the cardiovascular level in diabetic Wistar rats. J Recept Signal Transduct Res 2019; 38:484-491. [PMID: 31038027 DOI: 10.1080/10799893.2019.1597116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cardiovascular complications are the main cause of mortality in patients with diabetes, these have been associated with changes in function and expression of receptors coupled to G proteins (GPCR), which include orphan receptors which some of them tend to modify in diabetes, although others are not known, such as GPR135. For this reason, the objective of this work was to study the expression of the orphan receptor GPR135 in brain, heart, kidney, aorta, lung, spleen and liver of diabetic rats, as well as its function by the administration of siRNA (small interfering RNA) and curves to isoproterenol. Our results showed that GPR135 is expressed in all tissues analyzed and its expression is modified due to diabetes, we also observed that the responses to isoproterenol increase in diabetic rats administered with siRNA. Therefore, we conclude that the orphan receptor GPR135 is expressed in different tissues and its expression tends to be modified due to diabetes, besides that it is functional and that it seems to be coupled to Gi/o protein which has negative chronotropic and inotropic effects, therefore, we do not rule out that it participates in the cardiovascular complications associated with diabetes.
Collapse
Affiliation(s)
- Armando Ruiz-Hernández
- a Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional , Ciudad de México , México
| | - Rodrigo Romero-Nava
- b Laboratorio de Investigación en Farmacología, Hospital Infantil de México "Federico Gómez" , Ciudad de México , México
| | - Fengyang Huang
- b Laboratorio de Investigación en Farmacología, Hospital Infantil de México "Federico Gómez" , Ciudad de México , México
| | - Enrique Hong
- c Departamento de Farmacobiología, CINVESTAV , Ciudad de México , México
| | - Santiago Villafaña
- a Laboratorio de Señalización Intracelular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional , Ciudad de México , México
| |
Collapse
|