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Gotte G. Effects of Pathogenic Mutants of the Neuroprotective RNase 5-Angiogenin in Amyotrophic Lateral Sclerosis (ALS). Genes (Basel) 2024; 15:738. [PMID: 38927674 PMCID: PMC11202570 DOI: 10.3390/genes15060738] [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: 05/01/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease that affects the motoneurons. More than 40 genes are related with ALS, and amyloidogenic proteins like SOD1 and/or TDP-43 mutants are directly involved in the onset of ALS through the formation of polymorphic fibrillogenic aggregates. However, efficacious therapeutic approaches are still lacking. Notably, heterozygous missense mutations affecting the gene coding for RNase 5, an enzyme also called angiogenin (ANG), were found to favor ALS onset. This is also true for the less-studied but angiogenic RNase 4. This review reports the substrate targets and illustrates the neuroprotective role of native ANG in the neo-vascularization of motoneurons. Then, it discusses the molecular determinants of many pathogenic ANG mutants, which almost always cause loss of function related to ALS, resulting in failures in angiogenesis and motoneuron protection. In addition, ANG mutations are sometimes combined with variants of other factors, thereby potentiating ALS effects. However, the activity of the native ANG enzyme should be finely balanced, and not excessive, to avoid possible harmful effects. Considering the interplay of these angiogenic RNases in many cellular processes, this review aims to stimulate further investigations to better elucidate the consequences of mutations in ANG and/or RNase 4 genes, in order to achieve early diagnosis and, possibly, successful therapies against ALS.
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Affiliation(s)
- Giovanni Gotte
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy
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2
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Dewangan D, Joshi A, Padhi AK. Long-timescale atomistic simulations uncover loss-of-function mechanisms of uncharacterized Angiogenin mutants associated with ALS. Arch Biochem Biophys 2024; 756:110000. [PMID: 38621442 DOI: 10.1016/j.abb.2024.110000] [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: 12/23/2023] [Revised: 03/19/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a devastating neurodegenerative disease characterized by progressive degeneration of motor neurons, resulting in respiratory failure and mortality within 3-5 years. Mutations in the Angiogenin (ANG) cause loss of ribonucleolytic and nuclear translocation activities, contributing to ALS pathogenesis. This study focused on investigating two uncharacterized ANG mutations, T11S and R122H, newly identified in the Project Mine consortium. Using extensive computational analysis, including structural modeling and microsecond-timescale molecular dynamics (MD) simulations, we observed conformational changes in the catalytic residue His114 of ANG induced by T11S and R122H mutations. These alterations impaired ribonucleolytic activity, as inferred through molecular docking and binding free energy calculations. Gibbs free energy landscape and residue-residue interaction network analysis further supported our findings, revealing the energetic states and allosteric pathway from the mutated site to His114. Additionally, we assessed the binding of NCI-65828, an inhibitor of ribonucleolytic activity of ANG, and found reduced effectiveness in binding to T11S and R122H mutants when His114 assumed a non-native conformation. This highlights the crucial role of His114 and its association with ALS. Elucidating the relationship between physical structure and functional dynamics of frequently mutated ANG mutants is essential for understanding ALS pathogenesis and developing more effective therapeutic interventions.
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Affiliation(s)
- Deeksha Dewangan
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Aryaman Joshi
- Department of Chemical Engineering & Technology, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India
| | - Aditya K Padhi
- Laboratory for Computational Biology & Biomolecular Design, School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India.
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3
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Culurciello R, Di Nardo I, Bosso A, Tortora F, Troisi R, Sica F, Arciello A, Notomista E, Pizzo E. Tailoring the stress response of human skin cells by substantially limiting the nuclear localization of angiogenin. Heliyon 2024; 10:e24556. [PMID: 38317956 PMCID: PMC10839879 DOI: 10.1016/j.heliyon.2024.e24556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/14/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
Human angiogenin (hANG) is the most studied stress-induced ribonuclease (RNase). In physiological conditions it performs its main functions in nucleoli, promoting cell proliferation by rDNA transcription, whereas it is strongly limited by its inhibitor (RNH1) throughout the rest of the cell. In stressed cells hANG dissociates from RNH1 and thickens in the cytoplasm where it manages the translational arrest and the recruitment of stress granules, thanks to its propensity to cleave tRNAs and to induce the release of active halves. Since it exists a clear connection between hANG roles and its intracellular routing, starting from our recent findings on heterologous ANG (ANG) properties in human keratinocytes (HaCaT cells), here we designed a variant unable to translocate into the nucleus with the aim of thoroughly verifying its potentialities under stress. This variant, widely characterized for its structural features and biological attitudes, shows more pronounced aid properties than unmodified protein. The collected evidence thus fully prove that ANG stress-induced skills in assisting cellular homeostasis are strictly due to its cytosolic localization. This study opens an interesting scenario for future studies regarding both the strengthening of skin defences and in understanding the mechanism of action of these special enzymes potentially suitable for any cell type.
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Affiliation(s)
- Rosanna Culurciello
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Ilaria Di Nardo
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Andrea Bosso
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Francesca Tortora
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
- Institute of Biostructures and Bioimaging, CNR, 80131, Naples, Italy
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Elio Pizzo
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
- Centro Servizi Metrologici e Tecnologici Avanzati (CeSMA), University of Naples Federico II, 80126, Naples, Italy
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4
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Olsen CG, Busk ØL, Holla ØL, Tveten K, Holmøy T, Tysnes OB, Høyer H. Genetic overlap between ALS and other neurodegenerative or neuromuscular disorders. Amyotroph Lateral Scler Frontotemporal Degener 2024; 25:177-187. [PMID: 37849306 DOI: 10.1080/21678421.2023.2270705] [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: 08/09/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023]
Abstract
OBJECTIVE In Norway, 89% of patients with Amyotrophic lateral sclerosis (ALS) lacks a genetic diagnose. ALS genes and genes that cause other neuromuscular or neurodegenerative disorders extensively overlap. This population-based study examined whether patients with ALS have a family history of neurological disorders and explored the occurrence of rare genetic variants associated with other neurodegenerative or neuromuscular disorders. METHODS During a two-year period, blood samples and clinical data from patients with ALS were collected from all 17 neurological departments in Norway. Our genetic analysis involved exome sequencing and bioinformatics filtering of 510 genes associated with neurodegenerative and neuromuscular disorders. The variants were interpreted using genotype-phenotype correlations and bioinformatics tools. RESULTS A total of 279 patients from a Norwegian population-based ALS cohort participated in this study. Thirty-one percent of the patients had first- or second-degree relatives with other neurodegenerative disorders, most commonly dementia and Parkinson's disease. The genetic analysis identified 20 possible pathogenic variants, in ATL3, AFG3L2, ATP7A, BICD2, HARS1, KIF1A, LRRK2, MSTO1, NEK1, NEFH, and SORL1, in 25 patients. NEK1 risk variants were present in 2.5% of this ALS cohort. Only four of the 25 patients reported relatives with other neurodegenerative or neuromuscular disorders. CONCLUSION Gene variants known to cause other neurodegenerative or neuromuscular disorders, most frequently in NEK1, were identified in 9% of the patients with ALS. Most of these patients had no family history of other neurodegenerative or neuromuscular disorders. Our findings indicated that AFG3L2, ATP7A, BICD2, KIF1A, and MSTO1 should be further explored as potential ALS-causing genes.
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Affiliation(s)
- Cathrine Goberg Olsen
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
- Institute of Clinical Medicine, University of Oslo, Nordbyhagen, Norway
| | | | | | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Trygve Holmøy
- Institute of Clinical Medicine, University of Oslo, Nordbyhagen, Norway
- Department of Neurology, Akershus University Hospital, Lørenskog, Norway, and
| | - Ole-Bjørn Tysnes
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Helle Høyer
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
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5
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Mathew BA, Katta M, Ludhiadch A, Singh P, Munshi A. Role of tRNA-Derived Fragments in Neurological Disorders: a Review. Mol Neurobiol 2023; 60:655-671. [PMID: 36348262 DOI: 10.1007/s12035-022-03078-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022]
Abstract
tRFs are small tRNA derived fragments that are emerging as novel therapeutic targets and regulatory molecules in the pathophysiology of various neurological disorders. These are derived from precursor or mature tRNA, forming different subtypes that have been reported to be involved in neurological disorders like stroke, Alzheimer's, epilepsy, Parkinson's, MELAS, autism, and Huntington's disorder. tRFs were earlier believed to be random degradation debris of tRNAs. The significant variation in the expression level of tRFs in disease conditions indicates their salient role as key players in regulation of these disorders. Various animal studies are being carried out to decipher their exact role; however, more inputs are required to transform this research knowledge into clinical application. Future investigations also call for high-throughput technologies that could help to bring out the other hidden aspects of these entities. However, studies on tRFs require further research efforts to overcome the challenges posed in quantifying tRFs, their interactions with other molecules, and the exact mechanism of function. In this review, we are abridging the current understanding of tRFs, including their biogenesis, function, relevance in clinical therapies, and potential as diagnostic and prognostic biomarkers of these neurological disorders.
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Affiliation(s)
- Blessy Aksa Mathew
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India, 151401
| | - Madhumitha Katta
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India, 151401
| | - Abhilash Ludhiadch
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India, 151401
| | - Paramdeep Singh
- Department of Radiology, All India Institute of Medical Sciences, Bathinda, Punjab, India, 151001
| | - Anjana Munshi
- Complex Disease Genomics and Precision Medicine Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India, 151401.
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6
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Sultana MF, Abo H, Kawashima H. Human and mouse angiogenins: Emerging insights and potential opportunities. Front Microbiol 2022; 13:1022945. [PMID: 36466652 PMCID: PMC9714274 DOI: 10.3389/fmicb.2022.1022945] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/01/2022] [Indexed: 12/27/2023] Open
Abstract
Angiogenin, a well-known angiogenic factor, is crucial to the angiogenesis in gastrointestinal tumors. Human angiogenin has only one gene, whereas the murine angiogenin family has extended to incorporate six genes. Evolutionary studies have suggested functional variations among murine angiogenin paralogs, even though the three-dimensional structures of angiogenin proteins are remarkably similar. In addition to angiogenesis, the ubiquitous pattern of angiogenin expression suggests a variety of functions, such as tumorigenesis, neuroprotective, antimicrobial activity, and innate immunity. Here, we comprehensively reviewed studies on the structures and functions of human and mouse angiogenins. Understanding the structure and function of angiogenins from a broader perspective could facilitate future research related to development of novel therapeutics on its biological processes, especially in gastrointestinal cancers.
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Affiliation(s)
- Mst. Farzana Sultana
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
- Department of Pharmacy, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Hirohito Abo
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Hiroto Kawashima
- Laboratory of Microbiology and Immunology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
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7
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Tobar Montilla CD, Rengifo Rodas CF, Muñoz Añasco M. Petri net transition times as training features for multiclass models to support the detection of neurodegenerative diseases. Biomed Phys Eng Express 2022; 8. [PMID: 36007476 DOI: 10.1088/2057-1976/ac8c9a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/25/2022] [Indexed: 11/12/2022]
Abstract
This paper proposes the transition times of Petri net models of human gait as training features for multiclass random forests (RFs) and classification trees (CTs). These models are designed to support screening for neurodegenerative diseases. The proposed Petri net describes gait in terms of nine cyclic phases and the timing of the nine events that mark the transition between phases. Since the transition times between strides vary, each is represented as a random variable characterized by its mean and standard deviation. These transition times are calculated using the PhysioNet database of vertical ground reaction forces (VGRFs) generated by feet-ground contact. This database comprises the VGRFs of four groups: amyotrophic lateral sclerosis, the control group, Huntington's disease, and Parkinson disease. The RF produced an overall classification accuracy of 91%, and the specificities and sensitivities for each class were between 80% and 100%. However, despite this high performance, the RF-generated models demonstrated lack of interpretability prompted the training of a CT using identical features. The obtained tree comprised only four features and required a maximum of three comparisons. However, this simplification dramatically reduced the overall accuracy from 90.6% to 62.3%. The proposed set features were compared with those included in PhysioNet database of VGRFs. In terms of both the RF and CT, more accurate models were established using our features than those of the PhysioNet.
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Affiliation(s)
| | - Carlos Felipe Rengifo Rodas
- Electronics, Instrumentation and Control, Universidad del Cauca, Calle 5 No. 4-70, Sector Tulcan, Oficina 430, Popayan, Popayan, Departamento del Cauca, 190001, COLOMBIA
| | - Mariela Muñoz Añasco
- Universidad del Cauca, Calle 5 No 4 - 70 Sector Tulcan, Oficina 430, Popayan, Popayan, 190001, COLOMBIA
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8
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Blaze J, Akbarian S. The tRNA regulome in neurodevelopmental and neuropsychiatric disease. Mol Psychiatry 2022; 27:3204-3213. [PMID: 35505091 PMCID: PMC9630165 DOI: 10.1038/s41380-022-01585-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 12/14/2022]
Abstract
Transfer (t)RNAs are 70-90 nucleotide small RNAs highly regulated by 43 different types of epitranscriptomic modifications and requiring aminoacylation ('charging') for mRNA decoding and protein synthesis. Smaller cleavage products of mature tRNAs, or tRNA fragments, have been linked to a broad variety of noncanonical functions, including translational inhibition and modulation of the immune response. Traditionally, knowledge about tRNA regulation in brain is derived from phenotypic exploration of monogenic neurodevelopmental and neurodegenerative diseases associated with rare mutations in tRNA modification genes. More recent studies point to the previously unrecognized potential of the tRNA regulome to affect memory, synaptic plasticity, and affective states. For example, in mature cortical neurons, cytosine methylation sensitivity of the glycine tRNA family (tRNAGly) is coupled to glycine biosynthesis and codon-specific alterations in ribosomal translation together with robust changes in cognition and depression-related behaviors. In this Review, we will discuss the emerging knowledge of the neuronal tRNA landscape, with a focus on epitranscriptomic tRNA modifications and downstream molecular pathways affected by alterations in tRNA expression, charging levels, and cleavage while mechanistically linking these pathways to neuropsychiatric disease and provide insight into future areas of study for this field.
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Affiliation(s)
- Jennifer Blaze
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Schahram Akbarian
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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9
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Yang H, Yuan L, Ibaragi S, Li S, Shapiro R, Vanli N, Goncalves KA, Yu W, Kishikawa H, Jiang Y, Hu AJ, Jay D, Cochran B, Holland EC, Hu GF. Angiogenin and plexin-B2 axis promotes glioblastoma progression by enhancing invasion, vascular association, proliferation and survival. Br J Cancer 2022; 127:422-435. [PMID: 35418212 PMCID: PMC9345892 DOI: 10.1038/s41416-022-01814-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/25/2022] [Accepted: 03/31/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Angiogenin is a multifunctional secreted ribonuclease that is upregulated in human cancers and downregulated or mutationally inactivated in neurodegenerative diseases. A role for angiogenin in glioblastoma was inferred from the inverse correlation of angiogenin expression with patient survival but had not been experimentally investigated. METHODS Angiogenin knockout mice were generated and the effect of angiogenin deficiency on glioblastoma progression was examined. Angiogenin and plexin-B2 genes were knocked down in glioblastoma cells and the changes in cell proliferation, invasion and vascular association were examined. Monoclonal antibodies of angiogenin and small molecules were used to assess the therapeutic activity of the angiogenin-plexin-B2 pathway in both genetic and xenograft animal models. RESULTS Deletion of Ang1 gene prolonged survival of PDGF-induced glioblastoma in mice in the Ink4a/Arf-/-:Pten-/- background, accompanied by decreased invasion, vascular association and proliferation. Angiogenin upregulated MMP9 and CD24 leading to enhanced invasion and vascular association. Inhibition of angiogenin or plexin-B2, either by shRNA, monoclonal antibody or small molecule inhibitor, decreases sphere formation of patient-derived glioma stem cells, reduces glioblastoma proliferation and invasion and inhibits glioblastoma growth in both genetic and xenograft animal models. CONCLUSIONS Angiogenin and its receptor, plexin-B2, are a pair of novel regulators that mediate invasion, vascular association and proliferation of glioblastoma cells. Inhibitors of the angiogenin-plexin-B2 axis have therapeutic potential against glioblastoma.
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Affiliation(s)
- Hailing Yang
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Program in Cellular and Molecular Physiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Liang Yuan
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Program in Cell, Molecular, and Developmental Biology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Soichiro Ibaragi
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Shuping Li
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Robert Shapiro
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Nil Vanli
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Program in Biochemistry, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Kevin A Goncalves
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Program in Cellular and Molecular Physiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Wenhao Yu
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Hiroko Kishikawa
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Yuxiang Jiang
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA
| | - Alexander J Hu
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA.,Program in Cell, Molecular, and Developmental Biology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA
| | - Daniel Jay
- Program in Cellular and Molecular Physiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA.,Program in Cell, Molecular, and Developmental Biology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA.,Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Brent Cochran
- Program in Cellular and Molecular Physiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA.,Program in Cell, Molecular, and Developmental Biology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA.,Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Guo-Fu Hu
- Division of Hematology and Oncology, Department of Medicine, Tufts Medical Center, Boston, MA, USA. .,Program in Cellular and Molecular Physiology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA. .,Program in Cell, Molecular, and Developmental Biology, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA. .,Department of Pathology, Harvard Medical School, Boston, MA, USA. .,Program in Biochemistry, Graduate School of Biomedical Sciences, Tufts University, Boston, MA, USA.
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10
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Yue Z, Tong F, Zeng C, Wei R. Identification of tRNA-Related Fragments and Their Potential Regulatory Effects in Thyroid-Associated Ophthalmopathy. Front Genet 2022; 13:878405. [PMID: 35444685 PMCID: PMC9013859 DOI: 10.3389/fgene.2022.878405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Recently, the potential role of tRNA-related fragments (tRFs) in ophthalmic diseases has been extensively researched. However, systematic studies on the potential regulatory effects of tRFs in thyroid-associated ophthalmopathy (TAO) are lacking. We used high-throughput sequencing techniques to measure expression levels of mRNAs and tRFs in patients with TAO, and the results were verified by real-time quantitative reverse transcription polymerase chain reaction (q-PCR). Next, the potential biological regulatory effect of differentially expressed tRFs was analyzed, and potential downstream target RNAs of differentially expressed tRFs were predicted to explore the potential role of tRFs as therapeutic targets and biomarkers of TAO. A total of 50 tRFs and 361 mRNAs were dysregulated in the TAO group, and tRF5-GluCTC, PMAIP1, HSD17B2 and ATF3 were verified to be significantly differentially expressed in TAO. Our research reveals that several associated pathways likely play a role in the pathogenesis of TAO. By targeting ATF3, HSD17B2 and PMAIP1, tRF5-GluCTC may play a potential role in regulating the orbital fibroblast adipogenic response and fibrotic hyperplasia in patients with TAO.
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11
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Tian H, Hu Z, Wang C. The Therapeutic Potential of tRNA-derived Small RNAs in Neurodegenerative Disorders. Aging Dis 2022; 13:389-401. [PMID: 35371602 PMCID: PMC8947841 DOI: 10.14336/ad.2021.0903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/02/2021] [Indexed: 11/01/2022] Open
Abstract
Gene expressions and functions at various levels, namely post-transcriptional, transcriptional, and epigenetic, can be regulated by transfer RNA (tRNA)-derived small RNAs (tsRNAs), which are as well-established as tRNA fragments or tRFs. This regulation occurs when tsRNAs are created through the special endonuclease-mediated cleavage of mature or precursor tRNAs. However, tsRNAs are newly discovered entities, and molecular functions associated with tsRNAs are still not clearly understood. There is increasingly robust evidence suggesting that specific tsRNAs perform fundamental tasks in the pathogenesis of neurodevelopmental, neurodegenerative, and neurobehavioral disorders. Indeed, the patterns of tsRNA expression are uncertain and could be altered in patients suffering from Parkinson's disease, pontocerebellar hypoplasia, amyotrophic lateral sclerosis, Alzheimer's disease, and other neurodegenerative disorders. In the present article, a review is conducted of recent domestic and international progress in research on the potential cellular and molecular mechanisms of tsRNA biogenesis. We also describe endogenous tsRNAs during neuronal development and neurodegenerative disorders, thereby providing theoretical support and guidance for further revealing the therapeutic potential of tsRNAs in neurodegenerative disorders.
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Affiliation(s)
- Haihua Tian
- 1Ningbo Key Laboratory of Behavioral Neuroscience, Ningbo University School of Medicine, Ningbo, Zhejiang, China.,2Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.,3Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo, Zhejiang, China.,4Department of Laboratory Medicine, Ningbo Kangning Hospital, Ningbo, Zhejiang, China
| | - Zhenyu Hu
- 5Department of Child Psychiatry, Ningbo Kanning Hospital, Ningbo, Zhejiang, China
| | - Chuang Wang
- 1Ningbo Key Laboratory of Behavioral Neuroscience, Ningbo University School of Medicine, Ningbo, Zhejiang, China.,2Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China.,3Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo, Zhejiang, China
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12
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Soelter TM, Whitlock JH, Williams AS, Hardigan AA, Lasseigne BN. Nucleic acid liquid biopsies in Alzheimer's disease: current state, challenges, and opportunities. Heliyon 2022; 8:e09239. [PMID: 35469332 PMCID: PMC9034064 DOI: 10.1016/j.heliyon.2022.e09239] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/25/2021] [Accepted: 03/30/2022] [Indexed: 11/29/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease and affects persons of all races, ethnic groups, and sexes. The disease is characterized by neuronal loss leading to cognitive decline and memory loss. There is no cure and the effectiveness of existing treatments is limited and depends on the time of diagnosis. The long prodromal period, during which patients' ability to live a normal life is not affected despite neuronal loss, often leads to a delayed diagnosis because it can be mistaken for normal aging of the brain. In order to make a substantial impact on AD patient survival, early diagnosis may provide a greater therapeutic window for future therapies to slow AD-associated neurodegeneration. Current gold standards for disease detection include magnetic resonance imaging and positron emission tomography scans, which visualize amyloid β and phosphorylated tau depositions and aggregates. Liquid biopsies, already an active field of research in precision oncology, are hypothesized to provide early disease detection through minimally or non-invasive sample collection techniques. Liquid biopsies in AD have been studied in cerebrospinal fluid, blood, ocular, oral, and olfactory fluids. However, most of the focus has been on blood and cerebrospinal fluid due to biomarker specificity and sensitivity attributed to the effects of the blood-brain barrier and inter-laboratory variation during sample collection. Many studies have identified amyloid β and phosphorylated tau levels as putative biomarkers, however, advances in next-generation sequencing-based liquid biopsy methods have led to significant interest in identifying nucleic acid species associated with AD from liquid tissues. Differences in cell-free RNAs and DNAs have been described as potential biomarkers for AD and hold the potential to affect disease diagnosis, treatment, and future research avenues.
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Affiliation(s)
- Tabea M. Soelter
- Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, AL, USA
| | - Jordan H. Whitlock
- Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, AL, USA
| | - Avery S. Williams
- Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, AL, USA
| | - Andrew A. Hardigan
- Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, AL, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, AL, USA
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13
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Weng C, Dong H, Bai R, Sheng J, Chen G, Ding K, Lin W, Chen J, Xu Z. Angiogenin promotes angiogenesis via the endonucleolytic decay of miR-141 in colorectal cancer. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 27:1010-1022. [PMID: 35228896 PMCID: PMC8844805 DOI: 10.1016/j.omtn.2022.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022]
Abstract
Mature microRNA (miRNA) decay is a key step in miRNA turnover and gene expression regulation. Angiogenin (ANG), the first human tumor-derived angiogenic protein and also a member of the RNase A superfamily, can promote tumor growth and metastasis by regulating rRNA biogenesis and tiRNA production. However, its effect on miRNA has not been explored. In this study, we find that ANG exclusively downregulates mature miR-141 in human umbilical endothelial cells (HUVECs) via its ribonuclease activity and preferably cleaves single-stranded miR-141 at the A5/C6, U7/G8, and U14/A15 sites via endonucleolytic digestion. By downregulating miR-141, ANG promotes HUVECs proliferation, migration, tube formation, and angiogenesis both in vitro and in vivo. Conversely, downregulated ANG inhibits ANG-mediated miR-141 decay, thus decreasing the angiogenesis process of HUVECs. We also find an inverse correlation between ANG and miR-141 expression in colorectal cancer (CRC) tissues. Our study indicates that ANG regulates CRC progression by disrupting miR-141 and its regulation on angiogenesis-related target genes, not only revealing a new mechanism of ANG action but also newly identifying miR-141 as a substrate of ANG. This study suggests that targeting ANG nuclease activity might be valuable in treating angiogenesis-related diseases through coordinately regulating the metabolism of rRNA, tiRNA, and miRNA.
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14
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Fiskum V, Sandvig A, Sandvig I. Silencing of Activity During Hypoxia Improves Functional Outcomes in Motor Neuron Networks in vitro. Front Integr Neurosci 2021; 15:792863. [PMID: 34975426 PMCID: PMC8716921 DOI: 10.3389/fnint.2021.792863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/01/2021] [Indexed: 11/13/2022] Open
Abstract
The effects of hypoxia, or reduced oxygen supply, to brain tissue can be disastrous, leading to extensive loss of function. Deoxygenated tissue becomes unable to maintain healthy metabolism, which leads to increased production of reactive oxygen species (ROS) and loss of calcium homoeostasis, with damaging downstream effects. Neurons are a highly energy demanding cell type, and as such they are highly sensitive to reductions in oxygenation and some types of neurons such as motor neurons are even more susceptible to hypoxic damage. In addition to the immediate deleterious effects hypoxia can have on neurons, there can be delayed effects which lead to increased risk of developing neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), even if no immediate consequences are apparent. Furthermore, impairment of the function of various hypoxia-responsive factors has been shown to increase the risk of developing several neurodegenerative disorders. Longitudinal assessment of electrophysiological network activity is underutilised in assessing the effects of hypoxia on neurons and how their activity and communication change over time following a hypoxic challenge. This study utilised multielectrode arrays and motor neuron networks to study the response to hypoxia and the subsequent development of the neuronal activity over time, as well as the effect of silencing network activity during the hypoxic challenge. We found that motor neuron networks exposed to hypoxic challenge exhibited a delayed fluctuation in multiple network activity parameters compared to normoxic networks. Silencing of activity during the hypoxic challenge leads to maintained bursting activity, suggesting that functional outcomes are better maintained in these networks and that there are activity-dependent mechanisms involved in the network damage following hypoxia.
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Affiliation(s)
- Vegard Fiskum
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Axel Sandvig
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Neurology, St. Olav’s Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Pharmacology and Clinical Neurosciences, Division of Neuro, Head, and Neck, Umeå University Hospital, Umeå, Sweden
- Department of Community Medicine and Rehabilitation, Umeå University, Umeå, Sweden
| | - Ioanna Sandvig
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
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15
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Pandey KK, Madhry D, Ravi Kumar YS, Malvankar S, Sapra L, Srivastava RK, Bhattacharyya S, Verma B. Regulatory roles of tRNA-derived RNA fragments in human pathophysiology. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:161-173. [PMID: 34513302 PMCID: PMC8413677 DOI: 10.1016/j.omtn.2021.06.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hundreds of tRNA genes and pseudogenes are encoded by the human genome. tRNAs are the second most abundant type of RNA in the cell. Advancement in deep-sequencing technologies have revealed the presence of abundant expression of functional tRNA-derived RNA fragments (tRFs). They are either generated from precursor (pre-)tRNA or mature tRNA. They have been found to play crucial regulatory roles during different pathological conditions. Herein, we briefly summarize the discovery and recent advances in deciphering the regulatory role played by tRFs in the pathophysiology of different human diseases.
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Affiliation(s)
- Kush Kumar Pandey
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Deeksha Madhry
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Y S Ravi Kumar
- Department of Biotechnology, M.S. Ramaiah, Institute of Technology, MSR Nagar, Bengaluru, India
| | - Shivani Malvankar
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Leena Sapra
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Rupesh K Srivastava
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Sankar Bhattacharyya
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Bhupendra Verma
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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16
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Dimerization of Human Angiogenin and of Variants Involved in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms221810068. [PMID: 34576228 PMCID: PMC8468037 DOI: 10.3390/ijms221810068] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/25/2022] Open
Abstract
Human Angiogenin (hANG, or ANG, 14.1 kDa) promotes vessel formation and is also called RNase 5 because it is included in the pancreatic-type ribonuclease (pt-RNase) super-family. Although low, its ribonucleolytic activity is crucial for angiogenesis in tumor tissues but also in the physiological development of the Central Nervous System (CNS) neuronal progenitors. Nevertheless, some ANG variants are involved in both neurodegenerative Parkinson disease (PD) and Amyotrophic Lateral Sclerosis (ALS). Notably, some pt-RNases acquire new biological functions upon oligomerization. Considering neurodegenerative diseases correlation with massive protein aggregation, we analyzed the aggregation propensity of ANG and of three of its pathogenic variants, namely H13A, S28N, and R121C. We found no massive aggregation, but wt-ANG, as well as S28N and R121C variants, can form an enzymatically active dimer, which is called ANG-D. By contrast, the enzymatically inactive H13A-ANG does not dimerize. Corroborated by a specific cross-linking analysis and by the behavior of H13A-ANG that in turn lacks one of the two His active site residues necessary for pt-RNases to self-associate through the three-dimensional domain swapping (3D-DS), we demonstrate that ANG actually dimerizes through 3D-DS. Then, we deduce by size exclusion chromatography (SEC) and modeling that ANG-D forms through the swapping of ANG N-termini. In light of these novelties, we can expect future investigations to unveil other ANG determinants possibly related with the onset and/or development of neurodegenerative pathologies.
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17
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Tabbì G, Cucci LM, Pinzino C, Munzone A, Marzo T, Pizzanelli S, Satriano C, Magrì A, La Mendola D. Peptides Derived from Angiogenin Regulate Cellular Copper Uptake. Int J Mol Sci 2021; 22:9530. [PMID: 34502439 PMCID: PMC8430698 DOI: 10.3390/ijms22179530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 12/31/2022] Open
Abstract
The angiogenin protein (ANG) is one of the most potent endogenous angiogenic factors. In this work we characterized by means of potentiometric, spectroscopic and voltammetric techniques, the copper complex species formed with peptide fragments derived from the N-terminal domain of the protein, encompassing the sequence 1-17 and having free amino, Ang1-17, or acetylated N-terminus group, AcAng1-17, so to explore the role of amino group in metal binding and cellular copper uptake. The obtained data show that amino group is the main copper anchoring site for Ang1-17. The affinity constant values, metal coordination geometry and complexes redox-potentials strongly depend, for both peptides, on the number of copper equivalents added. Confocal laser scanning microscope analysis on neuroblastoma cells showed that in the presence of one equivalent of copper ion, the free amino Ang1-17 increases cellular copper uptake while the acetylated AcAng1-17 strongly decreases the intracellular metal level. The activity of peptides was also compared to that of the protein normally present in the plasma (wtANG) as well as to the recombinant form (rANG) most commonly used in literature experiments. The two protein isoforms bind copper ions but with a different coordination environment. Confocal laser scanning microscope data showed that the wtANG induces a strong increase in intracellular copper compared to control while the rANG decreases the copper signal inside cells. These data demonstrate the relevance of copper complexes' geometry to modulate peptides' activity and show that wtANG, normally present in the plasma, can affect cellular copper uptake.
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Affiliation(s)
- Giovanni Tabbì
- Institute of Crystallography—National Council of Research—CNR, via Paolo Gaifami 18, 95126 Catania, Italy;
| | - Lorena Maria Cucci
- Nano Hybrid BioInterfaces Lab (NHBIL), Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Calogero Pinzino
- Institute for the Chemistry of OrganoMetallic Compounds (ICCOM), National Council of Research—CNR, via G. Moruzzi 1, 56124 Pisa, Italy;
| | - Alessia Munzone
- Aix-Marseille Univesité, 52 Avenue Escadrille Normandie Niemen, 13013 Marseille, France;
| | - Tiziano Marzo
- Department of Pharmacy, University of Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy;
| | - Silvia Pizzanelli
- Institute for the Chemistry of OrganoMetallic Compounds (ICCOM), National Council of Research—CNR, via G. Moruzzi 1, 56124 Pisa, Italy;
| | - Cristina Satriano
- Nano Hybrid BioInterfaces Lab (NHBIL), Department of Chemical Sciences, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy;
| | - Antonio Magrì
- Institute of Crystallography—National Council of Research—CNR, via Paolo Gaifami 18, 95126 Catania, Italy;
| | - Diego La Mendola
- Department of Pharmacy, University of Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy;
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18
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Richard P, Kozlowski L, Guillorit H, Garnier P, McKnight NC, Danchin A, Manière X. Queuine, a bacterial-derived hypermodified nucleobase, shows protection in in vitro models of neurodegeneration. PLoS One 2021; 16:e0253216. [PMID: 34379627 PMCID: PMC8357117 DOI: 10.1371/journal.pone.0253216] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/29/2021] [Indexed: 11/26/2022] Open
Abstract
Growing evidence suggests that human gut bacteria, which comprise the microbiome, are linked to several neurodegenerative disorders. An imbalance in the bacterial population in the gut of Parkinson's disease (PD) and Alzheimer's disease (AD) patients has been detected in several studies. This dysbiosis very likely decreases or increases microbiome-derived molecules that are protective or detrimental, respectively, to the human body and those changes are communicated to the brain through the so-called 'gut-brain-axis'. The microbiome-derived molecule queuine is a hypermodified nucleobase enriched in the brain and is exclusively produced by bacteria and salvaged by humans through their gut epithelium. Queuine replaces guanine at the wobble position (position 34) of tRNAs with GUN anticodons and promotes efficient cytoplasmic and mitochondrial mRNA translation. Queuine depletion leads to protein misfolding and activation of the endoplasmic reticulum stress and unfolded protein response pathways in mice and human cells. Protein aggregation and mitochondrial impairment are often associated with neural dysfunction and neurodegeneration. To elucidate whether queuine could facilitate protein folding and prevent aggregation and mitochondrial defects that lead to proteinopathy, we tested the effect of chemically synthesized queuine, STL-101, in several in vitro models of neurodegeneration. After neurons were pretreated with STL-101 we observed a significant decrease in hyperphosphorylated alpha-synuclein, a marker of alpha-synuclein aggregation in a PD model of synucleinopathy, as well as a decrease in tau hyperphosphorylation in an acute and a chronic model of AD. Additionally, an associated increase in neuronal survival was found in cells pretreated with STL-101 in both AD models as well as in a neurotoxic model of PD. Measurement of queuine in the plasma of 180 neurologically healthy individuals suggests that healthy humans maintain protective levels of queuine. Our work has identified a new role for queuine in neuroprotection uncovering a therapeutic potential for STL-101 in neurological disorders.
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Affiliation(s)
- Patricia Richard
- Stellate Therapeutics Inc., JLABS @ NYC, New York, New York, United States of America
| | | | - Hélène Guillorit
- Stellate Therapeutics SAS, Paris, France
- Institut de Génomique Fonctionnelle, Montpellier, France
| | | | - Nicole C. McKnight
- Stellate Therapeutics Inc., JLABS @ NYC, New York, New York, United States of America
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19
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Grenn FP, Moore A, Bandres-Ciga S, Krohn L, Blauwendraat C. Assessment of ANG variants in Parkinson's disease. Neurobiol Aging 2021; 104:111.e1-111.e4. [PMID: 33875291 PMCID: PMC8225568 DOI: 10.1016/j.neurobiolaging.2021.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/01/2020] [Accepted: 03/09/2021] [Indexed: 11/23/2022]
Abstract
Genetic risk factors are occasionally shared between different neurodegenerative diseases. Previous studies have linked ANG, a gene encoding angiogenin, to both Parkinson's disease (PD) and amyotrophic lateral sclerosis (ALS). Functional studies suggest ANG plays a neuroprotective role in both PD and amyotrophic lateral sclerosis by reducing cell death. We further explored the genetic association between ANG and PD by analyzing genotype data from the International Parkinson's Disease Genomics Consortium (14,671 cases and 17,667 controls) and whole genome sequencing data from the Accelerating Medicines Partnership - Parkinson's disease initiative (AMP-PD, https://amp-pd.org/) (1,647 cases and 1,050 controls). Our analysis did not replicate the findings of previous studies and identified no significant association between ANG variants and PD risk.
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Affiliation(s)
- Francis P Grenn
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Anni Moore
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Sara Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Lynne Krohn
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada; Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Cornelis Blauwendraat
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
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20
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Fagan SG, Helm M, Prehn JHM. tRNA-derived fragments: A new class of non-coding RNA with key roles in nervous system function and dysfunction. Prog Neurobiol 2021; 205:102118. [PMID: 34245849 DOI: 10.1016/j.pneurobio.2021.102118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 01/12/2023]
Abstract
tRNA-derived small RNAs (tsRNA) are a recently identified family of non-coding RNA that have been associated with a variety of cellular functions including the regulation of protein translation and gene expression. Recent sequencing and bioinformatic studies have identified the broad spectrum of tsRNA in the nervous system and demonstrated that this new class of non-coding RNA is produced from tRNA by specific cleavage events catalysed by ribonucleases such as angiogenin and dicer. Evidence is also accumulating that production of tsRNA is increased during disease processes where they regulate stress responses, proteostasis, and neuronal survival. Mutations to tRNA cleaving and modifying enzymes have been implicated in several neurodegenerative disorders, and tsRNA levels in the blood are advancing as biomarkers for neurological disease. In this review we summarize the physiological importance of tsRNA in the central nervous system and their relevance to neurological disease.
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Affiliation(s)
- Steven G Fagan
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen'S Green, Dublin 2, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences - IPBS, Johannes Gutenberg-University, 55128, Mainz, Germany
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen'S Green, Dublin 2, Ireland; SFI FutureNeuro Research Centre, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland.
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21
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Krishna S, Raghavan S, DasGupta R, Palakodeti D. tRNA-derived fragments (tRFs): establishing their turf in post-transcriptional gene regulation. Cell Mol Life Sci 2021; 78:2607-2619. [PMID: 33388834 PMCID: PMC11073306 DOI: 10.1007/s00018-020-03720-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/02/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Transfer RNA (tRNA)-derived fragments (tRFs) are an emerging class of conserved small non-coding RNAs that play important roles in post-transcriptional gene regulation. High-throughput sequencing of multiple biological samples have identified heterogeneous species of tRFs with distinct functionalities. These small RNAs have garnered a lot of scientific attention due to their ubiquitous expression and versatility in regulating various biological processes. In this review, we highlight our current understanding of tRF biogenesis and their regulatory functions. We summarize the diverse modes of biogenesis through which tRFs are generated and discuss the mechanism through which different tRF species regulate gene expression and the biological implications. Finally, we conceptualize research areas that require focus to strengthen our understanding of the biogenesis and function of tRFs.
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Affiliation(s)
- Srikar Krishna
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Srikala Raghavan
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, India.
| | - Ramanuj DasGupta
- Precision Oncology, Genome Institute of Singapore, Singapore City, Singapore.
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22
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Lee SM, Jun DW, Kang HT, Oh JH, Saeed WK, Ahn SB. Optimal Hypoxic Preconditioning of Human Embryonic Stem Cell-Derived Mesenchymal Stem Cells (hES-MSCs) and Their Characteristics. Int J Stem Cells 2021; 14:221-228. [PMID: 33632987 PMCID: PMC8138663 DOI: 10.15283/ijsc20096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 12/17/2022] Open
Abstract
Background and Objectives Hypoxia is frequently used to enhance stem cell function. However, the optimal level of hypoxia for growth and function of human embryonic stem cell-derived mesenchymal stem cells (hES-MSCs) is yet to be determined. The purpose of this study was to find the optimal level of hypoxia for hES-MSCs and characteristics of hES-MSCs cultured under these optimal hypoxic conditions. Methods and Results Cell viability and changes in the morphology of hES-MSCs were determined through cell proliferation and CCK-8 assay. The hES-MSCs were preconditioned under various hypoxic conditions (0.5∼5% O2 and 24∼72 h). The expression of cytokines in each culture condition was compared using cytokine array analysis. The morphology of hES-MSCs did not change under various hypoxic culture conditions. hES-MSCs viability after 48 h incubation in 2% O2 condition was higher than that in normoxic condition. HIF1α expression was increased up to six folds after 48 h of hypoxic preconditioning. HIF1α expression in hES-MSCs peaked after 48 h of incubation in 1% O2 condition. The expressions of PDGF-BB, IGFBP-6, VEGF-A, and angiogenin were increased after hES-MSCs were incubated for 48 h in 2% O2 condition. Conclusions The hES-MSCs viability and expressions of PDGF-BB, IGFBP-6, VEGF-A, and angiogenin increased after 48 h incubation in 2% O2 condition.
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Affiliation(s)
- Seung Min Lee
- Department of Translational Medicine, Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea
| | - Dae Won Jun
- Department of Translational Medicine, Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea.,Department of Internal Medicine, Hanyang University School of Medicine, Seoul, Korea
| | - Hyeon Tae Kang
- Department of Translational Medicine, Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea
| | - Ju Hee Oh
- Department of Translational Medicine, Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, Korea
| | - Waqar Khalid Saeed
- Department of Biomedical Sciences, Pak-Austria Fachhochschule: Institute of Applied Sciences and Technology, Mang, Haripur, Pakistan
| | - Sang Bong Ahn
- Department of Internal Medicine, Eulji University School of Medicine, Seoul, Korea
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23
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Fagagnini A, Garavís M, Gómez-Pinto I, Fasoli S, Gotte G, Laurents DV. NMR Characterization of Angiogenin Variants and tRNA Ala Products Impacting Aberrant Protein Oligomerization. Int J Mol Sci 2021; 22:1439. [PMID: 33535464 PMCID: PMC7867098 DOI: 10.3390/ijms22031439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 11/25/2022] Open
Abstract
Protein oligomerization is key to countless physiological processes, but also to abnormal amyloid conformations implicated in over 25 mortal human diseases. Human Angiogenin (h-ANG), a ribonuclease A family member, produces RNA fragments that regulate ribosome formation, the creation of new blood vessels and stress granule function. Too little h-ANG activity leads to abnormal protein oligomerization, resulting in Amyotrophic Lateral Sclerosis (ALS) or Parkinson's disease. While a score of disease linked h-ANG mutants has been studied by X-ray diffraction, some elude crystallization. There is also a debate regarding the structure that RNA fragments adopt after cleavage by h-ANG. Here, to better understand the beginning of the process that leads to aberrant protein oligomerization, the solution secondary structure and residue-level dynamics of WT h-ANG and two mutants i.e., H13A and R121C, are characterized by multidimensional heteronuclear NMR spectroscopy under near-physiological conditions. All three variants are found to adopt well folded and highly rigid structures in the solution, although the elements of secondary structure are somewhat shorter than those observed in crystallography studies. R121C alters the environment of nearby residues only. By contrast, the mutation H13A affects local residues as well as nearby active site residues K40 and H114. The conformation characterization by CD and 1D 1H NMR spectroscopies of tRNAAla before and after h-ANG cleavage reveals a retention of the duplex structure and little or no G-quadruplex formation.
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Affiliation(s)
- Andrea Fagagnini
- Dipartimento di Neuroscienze, Biomedicina e Movimento, Sezione di Chimica Biologica, Università di Verona, Strada Le Grazie 8, I-37134 Verona, Italy; (A.F.); (S.F.)
| | - Miguel Garavís
- Instituto de Química Física “Rocasolano”, Consejo Superior de Investigaciones Científicas, c/Serrano 119, E-28006 Madrid, Spain; (M.G.); (I.G.-P.)
| | - Irene Gómez-Pinto
- Instituto de Química Física “Rocasolano”, Consejo Superior de Investigaciones Científicas, c/Serrano 119, E-28006 Madrid, Spain; (M.G.); (I.G.-P.)
| | - Sabrina Fasoli
- Dipartimento di Neuroscienze, Biomedicina e Movimento, Sezione di Chimica Biologica, Università di Verona, Strada Le Grazie 8, I-37134 Verona, Italy; (A.F.); (S.F.)
| | - Giovanni Gotte
- Dipartimento di Neuroscienze, Biomedicina e Movimento, Sezione di Chimica Biologica, Università di Verona, Strada Le Grazie 8, I-37134 Verona, Italy; (A.F.); (S.F.)
| | - Douglas V. Laurents
- Instituto de Química Física “Rocasolano”, Consejo Superior de Investigaciones Científicas, c/Serrano 119, E-28006 Madrid, Spain; (M.G.); (I.G.-P.)
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Tosar JP, Witwer K, Cayota A. Revisiting Extracellular RNA Release, Processing, and Function. Trends Biochem Sci 2021; 46:438-445. [PMID: 33413996 DOI: 10.1016/j.tibs.2020.12.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/26/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023]
Abstract
It is assumed that RNAs enriched in extracellular samples were selected for release by their parental cells. However, recent descriptions of extracellular RNA (exRNA) biogenesis and their differential stabilities question this assumption, as they could produce identical outcomes. Here, we share our opinion about the importance of considering both selective and nonselective mechanisms for RNA release into the extracellular environment. In doing so, we provide new perspectives on RNA-mediated intercellular communication, including an analogy to communication through social media. We also argue that technical limitations have restricted the study of some of the most abundant exRNAs, both inside and outside extracellular vesicles (EVs). These RNAs may be better positioned to induce a response in recipient cells compared with low abundance miRNAs.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit, Nuclear Research Center, School of Science, Universidad de la República, Montevideo, Uruguay; Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.
| | - Kenneth Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alfonso Cayota
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay; Department of Medicine, University Hospital, Universidad de la República, Montevideo, Uruguay
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25
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Tosar JP, Segovia M, Castellano M, Gámbaro F, Akiyama Y, Fagúndez P, Olivera Á, Costa B, Possi T, Hill M, Ivanov P, Cayota A. Fragmentation of extracellular ribosomes and tRNAs shapes the extracellular RNAome. Nucleic Acids Res 2020; 48:12874-12888. [PMID: 32785615 PMCID: PMC7736827 DOI: 10.1093/nar/gkaa674] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/19/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022] Open
Abstract
A major proportion of extracellular RNAs (exRNAs) do not copurify with extracellular vesicles (EVs) and remain in ultracentrifugation supernatants of cell-conditioned medium or mammalian blood serum. However, little is known about exRNAs beyond EVs. We have previously shown that the composition of the nonvesicular exRNA fraction is highly biased toward specific tRNA-derived fragments capable of forming RNase-protecting dimers. To solve the problem of stability in exRNA analysis, we developed a method based on sequencing the size exclusion chromatography (SEC) fractions of nonvesicular extracellular samples treated with RNase inhibitors (RI). This method revealed dramatic compositional changes in exRNA population when enzymatic RNA degradation was inhibited. We demonstrated the presence of ribosomes and full-length tRNAs in cell-conditioned medium of a variety of mammalian cell lines. Their fragmentation generates some small RNAs that are highly resistant to degradation. The extracellular biogenesis of some of the most abundant exRNAs demonstrates that extracellular abundance is not a reliable input to estimate RNA secretion rates. Finally, we showed that chromatographic fractions containing extracellular ribosomes are probably not silent from an immunological perspective and could possibly be decoded as damage-associated molecular patterns.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit. Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mercedes Segovia
- Laboratory of Immunoregulation and Inflammation, Institut Pasteur de Montevideo, Uruguay. Immunobiology Department, Faculty of Medicine, Universidad de la República, Uruguay
| | - Mauricio Castellano
- Analytical Biochemistry Unit. Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Fabiana Gámbaro
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
- Molecular Virology Laboratory, Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
| | - Yasutoshi Akiyama
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Pablo Fagúndez
- Analytical Biochemistry Unit. Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Álvaro Olivera
- Centro Universitario Regional Este, Universidad de la República, Uruguay
| | - Bruno Costa
- Analytical Biochemistry Unit. Nuclear Research Center. Faculty of Science. Universidad de la República, Uruguay
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Tania Possi
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
| | - Marcelo Hill
- Laboratory of Immunoregulation and Inflammation, Institut Pasteur de Montevideo, Uruguay. Immunobiology Department, Faculty of Medicine, Universidad de la República, Uruguay
| | - Pavel Ivanov
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and M.I.T., Cambridge, MA, USA
| | - Alfonso Cayota
- Functional Genomics Unit, Institut Pasteur de Montevideo, Uruguay
- Department of Medicine, University Hospital, Universidad de la República, Uruguay
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26
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Zhu XL, Li T, Cao Y, Yao QP, Liu X, Li Y, Guan YY, Deng JJ, Jiang R, Jiang J. tRNA-derived fragments tRF GlnCTG induced by arterial injury promote vascular smooth muscle cell proliferation. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 23:603-613. [PMID: 33552681 PMCID: PMC7819823 DOI: 10.1016/j.omtn.2020.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 12/09/2020] [Indexed: 01/20/2023]
Abstract
tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs) are originated from the specific cleavage of endogenous tRNAs or their precursors and regulate gene expression when the cells are in stressful circumstances. Here, we replicated the rat common carotid artery (CCA) intimal hyperplasia model and investigated the expression of tRFs/tiRNAs in the artery. The normal and the balloon-injured rat CCAs were subjected to small RNA sequencing, and then the differentially expressed tRFs/tiRNAs were identified and analyzed. The expression profiles of tRFs/tiRNAs in the healthy and injured CCAs were remarkably different. tRNAGlnCTG-derived fragments (tRFGlnCTG) were found to be overexpressed with a high abundance in the injured CCA. In in vitro experiments, the synthetic tRFGlnCTG mimetics elevated the proliferation and migration of rat vascular smooth muscle cells (VSMCs). Through bioinformatics analysis and an overexpression experiment, tRFGlnCTG was found to negatively regulate the expression of FAS cell surface death receptor (FAS). This study revealed that tRFGlnCTG is a crucial regulator in promoting VSMC proliferation. The investigation of the roles of tRFs/tiRNAs is of significance for understanding the mechanism, diagnosis, and treatment of intimal hyperplasia.
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Affiliation(s)
- Xiao-Ling Zhu
- Department of Thyroid Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Tao Li
- Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Yu Cao
- Department of Thyroid Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qing-Ping Yao
- Institute of Mechanobiology & Medical Engineering, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xing Liu
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Ying Li
- Department of Thyroid Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yang-Yang Guan
- Department of Thyroid Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Ji-Jun Deng
- Department of Thyroid Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Rui Jiang
- Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Corresponding author: Rui Jiang, Department of Urology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000 Sichuan Province, China.
| | - Jun Jiang
- Department of Thyroid Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Southwest Medical University, Luzhou, China
- Corresponding author: Jun Jiang, Department of Thyroid Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000 Sichuan Province, China.
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Gámez-Valero A, Guisado-Corcoll A, Herrero-Lorenzo M, Solaguren-Beascoa M, Martí E. Non-Coding RNAs as Sensors of Oxidative Stress in Neurodegenerative Diseases. Antioxidants (Basel) 2020; 9:E1095. [PMID: 33171576 PMCID: PMC7695195 DOI: 10.3390/antiox9111095] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022] Open
Abstract
Oxidative stress (OS) results from an imbalance between the production of reactive oxygen species and the cellular antioxidant capacity. OS plays a central role in neurodegenerative diseases, where the progressive accumulation of reactive oxygen species induces mitochondrial dysfunction, protein aggregation and inflammation. Regulatory non-protein-coding RNAs (ncRNAs) are essential transcriptional and post-transcriptional gene expression controllers, showing a highly regulated expression in space (cell types), time (developmental and ageing processes) and response to specific stimuli. These dynamic changes shape signaling pathways that are critical for the developmental processes of the nervous system and brain cell homeostasis. Diverse classes of ncRNAs have been involved in the cell response to OS and have been targeted in therapeutic designs. The perturbed expression of ncRNAs has been shown in human neurodegenerative diseases, with these changes contributing to pathogenic mechanisms, including OS and associated toxicity. In the present review, we summarize existing literature linking OS, neurodegeneration and ncRNA function. We provide evidences for the central role of OS in age-related neurodegenerative conditions, recapitulating the main types of regulatory ncRNAs with roles in the normal function of the nervous system and summarizing up-to-date information on ncRNA deregulation with a direct impact on OS associated with major neurodegenerative conditions.
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Affiliation(s)
- Ana Gámez-Valero
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain; (A.G.-V.); (A.G.-C.); (M.H.-L.); (M.S.-B.)
| | - Anna Guisado-Corcoll
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain; (A.G.-V.); (A.G.-C.); (M.H.-L.); (M.S.-B.)
| | - Marina Herrero-Lorenzo
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain; (A.G.-V.); (A.G.-C.); (M.H.-L.); (M.S.-B.)
| | - Maria Solaguren-Beascoa
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain; (A.G.-V.); (A.G.-C.); (M.H.-L.); (M.S.-B.)
| | - Eulàlia Martí
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain; (A.G.-V.); (A.G.-C.); (M.H.-L.); (M.S.-B.)
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Ministerio de Ciencia Innovación y Universidades, 28046 Madrid, Spain
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28
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Acharya S, Salgado-Somoza A, Stefanizzi FM, Lumley AI, Zhang L, Glaab E, May P, Devaux Y. Non-Coding RNAs in the Brain-Heart Axis: The Case of Parkinson's Disease. Int J Mol Sci 2020; 21:E6513. [PMID: 32899928 PMCID: PMC7555192 DOI: 10.3390/ijms21186513] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/27/2020] [Accepted: 09/02/2020] [Indexed: 02/08/2023] Open
Abstract
Parkinson's disease (PD) is a complex and heterogeneous disorder involving multiple genetic and environmental influences. Although a wide range of PD risk factors and clinical markers for the symptomatic motor stage of the disease have been identified, there are still no reliable biomarkers available for the early pre-motor phase of PD and for predicting disease progression. High-throughput RNA-based biomarker profiling and modeling may provide a means to exploit the joint information content from a multitude of markers to derive diagnostic and prognostic signatures. In the field of PD biomarker research, currently, no clinically validated RNA-based biomarker models are available, but previous studies reported several significantly disease-associated changes in RNA abundances and activities in multiple human tissues and body fluids. Here, we review the current knowledge of the regulation and function of non-coding RNAs in PD, focusing on microRNAs, long non-coding RNAs, and circular RNAs. Since there is growing evidence for functional interactions between the heart and the brain, we discuss the benefits of studying the role of non-coding RNAs in organ interactions when deciphering the complex regulatory networks involved in PD progression. We finally review important concepts of harmonization and curation of high throughput datasets, and we discuss the potential of systems biomedicine to derive and evaluate RNA biomarker signatures from high-throughput expression data.
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Affiliation(s)
- Shubhra Acharya
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
- Faculty of Science, Technology and Medicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg
| | - Antonio Salgado-Somoza
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Francesca Maria Stefanizzi
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Andrew I. Lumley
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Lu Zhang
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg; (E.G.); (P.M.)
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4365 Esch-sur-Alzette, Luxembourg; (E.G.); (P.M.)
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (S.A.); (A.S.-S.); (F.M.S.); (A.I.L.); (L.Z.)
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29
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Jia Y, Tan W, Zhou Y. Transfer RNA-derived small RNAs: potential applications as novel biomarkers for disease diagnosis and prognosis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1092. [PMID: 33145311 PMCID: PMC7575943 DOI: 10.21037/atm-20-2797] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transfer RNA-derived small RNA (tsRNA)s are novel non-coding RNAs, expressed in a variety of tissues and organs. Two subtypes of tsRNAs have been reported: tRNA-derived stress-induced RNA (tiRNA)s and tRNA-derived fragment (tRF)s. tsRNAs have been reported to play essential roles and possess different biological functions in a variety of physiological activities. Recently, tsRNAs have been implicated in a large number of diseases, such as cancers (including breast cancer, ovarian cancer, lung cancer, prostate cancer, colorectal cancer, etc.), neurological disorders, viral infections, metabolic diseases and angiogenesis-related diseases. Although the biological functions of tsRNAs are still poorly understood, correlations between dysregulated tsRNA expression and disease development have been recently reported. Additionally, their capabilities as potential biomarkers for disease diagnosis and prognosis have been revealed in clinical studies. In this review, we summarize the current knowledge of tsRNAs, and discuss their potential clinical applications as biomarkers in different diseases. Although the regulation of tsRNAs is similar to miRNAs in regards to the related physiological and pathological processes, the higher stability and expression levels of tsRNAs place them as ideal biomarkers for the diagnosis and prognosis in cancer and other diseases. Therefore, it is worth to verify the possibility and reliability of these reported tsRNAs as potential biomarkers for clinical applications in disease diagnosis and prognosis.
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Affiliation(s)
- Yang Jia
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Tan
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
| | - Yedi Zhou
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
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30
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van Es MA, Goedee HS, Westeneng HJ, Nijboer TCW, van den Berg LH. Is it accurate to classify ALS as a neuromuscular disorder? Expert Rev Neurother 2020; 20:895-906. [PMID: 32749157 DOI: 10.1080/14737175.2020.1806061] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Amyotrophic lateral sclerosis (ALS) is a fatal disorder characterized by the progressive loss of upper and lower motor neurons. ALS has traditionally been classified within the domain of neuromuscular diseases, which are a unique spectrum of disorders that predominantly affect the peripheral nervous system. However, over the past decades compounding evidence has emerged that there is extensive involvement of the central nervous system. Therefore, one can question whether it remains accurate to classify ALS as a neuromuscular disorder. AREAS COVERED In this review, the authors sought to discuss current approaches toward disease classification and how we should classify ALS based on novel insights from clinical, imaging, pathophysiological, neuropathological and genetic studies. EXPERT OPINION ALS exhibits the cardinal features of a neurodegenerative disease. Therefore, classifying ALS as a neuromuscular disease in the strict sense has become untenable. Diagnosing ALS however does require significant neuromuscular expertise and therefore neuromuscular specialists remain best equipped to evaluate this category of patients. Designating motor neuron diseases as a separate category in the ICD-11 is justified and adequately deals with this issue. However, to drive effective therapy development the fields of motor neuron disease and neurodegenerative disorders must come together.
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Affiliation(s)
- Michael A van Es
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht , Utrecht, The Netherlands
| | - H Stephan Goedee
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht , Utrecht, The Netherlands
| | - Henk-Jan Westeneng
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht , Utrecht, The Netherlands
| | - Tanja C W Nijboer
- Center of Excellence for Rehabilitation Medicine, UMC Utrecht Brain Center, University Medical Center Utrecht, and De Hoogstraat Rehabilitation , Utrecht, Netherlands.,Department of Experimental Psychology, Helmholtz Institute, Utrecht University , Utrecht, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht , Utrecht, The Netherlands
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31
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Hogg MC, Rayner M, Susdalzew S, Monsefi N, Crivello M, Woods I, Resler A, Blackbourn L, Fabbrizio P, Trolese MC, Nardo G, Bendotti C, van den Berg LH, van Es MA, Prehn JHM. 5'ValCAC tRNA fragment generated as part of a protective angiogenin response provides prognostic value in amyotrophic lateral sclerosis. Brain Commun 2020; 2:fcaa138. [PMID: 33543130 PMCID: PMC7850272 DOI: 10.1093/braincomms/fcaa138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/02/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
Loss-of-function mutations in the ribonuclease angiogenin are associated with amyotrophic lateral sclerosis. Angiogenin has been shown to cleave transfer RNAs during stress to produce ‘transfer-derived stress-induced RNAs’. Stress-induced tRNA cleavage is preserved from single-celled organisms to humans indicating it represents part of a highly conserved stress response. However, to date, the role of tRNA cleavage in amyotrophic lateral sclerosis remains to be fully elucidated. To this end, we performed small RNA sequencing on a human astrocytoma cell line to identify the complete repertoire of tRNA fragments generated by angiogenin. We found that only a specific subset of tRNAs is cleaved by angiogenin and identified 5′ValCAC transfer-derived stress-induced RNA to be secreted from neural cells. 5′ValCAC was quantified in spinal cord and serum from SOD1G93A amyotrophic lateral sclerosis mouse models where we found it to be significantly elevated at symptom onset correlating with increased angiogenin expression, imbalanced protein translation initiation factors and slower disease progression. In amyotrophic lateral sclerosis patient serum samples, we found 5′ValCAC to be significantly higher in patients with slow disease progression, and interestingly, we find 5′ValCAC to hold prognostic value for amyotrophic lateral sclerosis patients. Here, we report that angiogenin cleaves a specific subset of tRNAs and provide evidence for 5′ValCAC as a prognostic biomarker in amyotrophic lateral sclerosis. We propose that increased serum 5′ValCAC levels indicate an enhanced angiogenin-mediated stress response within motor neurons that correlates with increased survival. These data suggest that the previously reported beneficial effects of angiogenin in SOD1G93A mice may result from elevated levels of 5′ValCAC transfer RNA fragment.
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Affiliation(s)
- Marion C Hogg
- Department of Physiology and Medical Physics, Royal College of Surgeons In Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Megan Rayner
- Department of Physiology and Medical Physics, Royal College of Surgeons In Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Sergej Susdalzew
- Department of Physiology and Medical Physics, Royal College of Surgeons In Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Naser Monsefi
- Department of Physiology and Medical Physics, Royal College of Surgeons In Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Martin Crivello
- Department of Physiology and Medical Physics, Royal College of Surgeons In Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Ina Woods
- Department of Physiology and Medical Physics, Royal College of Surgeons In Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Alexa Resler
- Department of Physiology and Medical Physics, Royal College of Surgeons In Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Lisle Blackbourn
- Department of Physiology and Medical Physics, Royal College of Surgeons In Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
| | - Paola Fabbrizio
- Laboratory of Molecular Neurobiology, Department of Neuroscience, IRCCS - Mario Negri Institute for Pharmacological Research, Via, La Masa, 19, 20156 Milan, Italy
| | - Maria Chiara Trolese
- Laboratory of Molecular Neurobiology, Department of Neuroscience, IRCCS - Mario Negri Institute for Pharmacological Research, Via, La Masa, 19, 20156 Milan, Italy
| | - Giovanni Nardo
- Laboratory of Molecular Neurobiology, Department of Neuroscience, IRCCS - Mario Negri Institute for Pharmacological Research, Via, La Masa, 19, 20156 Milan, Italy
| | - Caterina Bendotti
- Laboratory of Molecular Neurobiology, Department of Neuroscience, IRCCS - Mario Negri Institute for Pharmacological Research, Via, La Masa, 19, 20156 Milan, Italy
| | - Leonard H van den Berg
- Department of Neurology, Brain Centre Rudolf Magnus, University Medical Centre, University Utrecht, The Netherlands
| | - Michael A van Es
- Department of Neurology, Brain Centre Rudolf Magnus, University Medical Centre, University Utrecht, The Netherlands
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons In Ireland, St. Stephen's Green, Dublin, D02 YN77, Ireland
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Ng Kee Kwong KC, Mehta AR, Nedergaard M, Chandran S. Defining novel functions for cerebrospinal fluid in ALS pathophysiology. Acta Neuropathol Commun 2020; 8:140. [PMID: 32819425 PMCID: PMC7439665 DOI: 10.1186/s40478-020-01018-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 08/10/2020] [Indexed: 12/11/2022] Open
Abstract
Despite the considerable progress made towards understanding ALS pathophysiology, several key features of ALS remain unexplained, from its aetiology to its epidemiological aspects. The glymphatic system, which has recently been recognised as a major clearance pathway for the brain, has received considerable attention in several neurological conditions, particularly Alzheimer's disease. Its significance in ALS has, however, been little addressed. This perspective article therefore aims to assess the possibility of CSF contribution in ALS by considering various lines of evidence, including the abnormal composition of ALS-CSF, its toxicity and the evidence for impaired CSF dynamics in ALS patients. We also describe a potential role for CSF circulation in determining disease spread as well as the importance of CSF dynamics in ALS neurotherapeutics. We propose that a CSF model could potentially offer additional avenues to explore currently unexplained features of ALS, ultimately leading to new treatment options for people with ALS.
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Affiliation(s)
- Koy Chong Ng Kee Kwong
- UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Arpan R Mehta
- UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Siddharthan Chandran
- UK Dementia Research Institute at University of Edinburgh, Edinburgh, UK.
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK.
- Centre for Brain Development and Repair, inStem, Bangalore, India.
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Nechooshtan G, Yunusov D, Chang K, Gingeras TR. Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment. Nucleic Acids Res 2020; 48:8035-8049. [PMID: 32609822 PMCID: PMC7430647 DOI: 10.1093/nar/gkaa526] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/07/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022] Open
Abstract
Extracellular RNAs participate in intercellular communication, and are being studied as promising minimally invasive diagnostic markers. Several studies in recent years showed that tRNA halves and distinct Y RNA fragments are abundant in the extracellular space, including in biofluids. While their regulatory and diagnostic potential has gained a substantial amount of attention, the biogenesis of these extracellular RNA fragments remains largely unexplored. Here, we demonstrate that these fragments are produced by RNase 1, a highly active secreted nuclease. We use RNA sequencing to investigate the effect of a null mutation of RNase 1 on the levels of tRNA halves and Y RNA fragments in the extracellular environment of cultured human cells. We complement and extend our RNA sequencing results with northern blots, showing that tRNAs and Y RNAs in the non-vesicular extracellular compartment are released from cells as full-length precursors and are subsequently cleaved to distinct fragments. In support of these results, formation of tRNA halves is recapitulated by recombinant human RNase 1 in our in vitro assay. These findings assign a novel function for RNase 1, and position it as a strong candidate for generation of tRNA halves and Y RNA fragments in biofluids.
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Affiliation(s)
- Gal Nechooshtan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Dinar Yunusov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Kenneth Chang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Karousi P, Adamopoulos PG, Papageorgiou SG, Pappa V, Scorilas A, Kontos CK. A novel, mitochondrial, internal tRNA-derived RNA fragment possesses clinical utility as a molecular prognostic biomarker in chronic lymphocytic leukemia. Clin Biochem 2020; 85:20-26. [PMID: 32745483 DOI: 10.1016/j.clinbiochem.2020.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Chronic lymphocytic leukemia (CLL) is the most common leukemia among adults. The prognosis of CLL patients varies considerably. Transfer RNA-derived RNA fragments (tRFs) constitute a class of small non-coding RNA fragments excised from mature tRNAs and pre-tRNAs located in nuclei as well as in mitochondria. In this study, the clinical utility of i-tRF-PheGAA, a novel mitochondrial tRF, was investigated in CLL. DESIGN AND METHODS Peripheral blood mononuclear cells (PBMCs) were isolated from 91 CLL patients and 43 non-leukemic controls. Total RNA was isolated from each sample, polyadenylated at the 3' end and reversely transcribed. An in-house developed real-time quantitative PCR assay was developed and applied, and the results were biostatistically analyzed. For the normalization of the i-tRF-PheGAA expression levels, the expression of a small nucleolar RNA (RNU48) was used as reference. RESULTS Mann-Whitney U test showed that i-tRF-PheGAA can distinguish between CLL samples and normal controls (p < 0.001). As determined by Kaplan-Meier survival analysis, overexpression of i-tRF-PheGAA was related to poor overall survival of the CLL patients (p < 0.001). Univariate bootstrap Cox regression analysis exhibited a higher hazard ratio of 7.95 (95% CI = 2.37-26.72, p < 0.001) for patients with positive i-tRF-PheGAA expression status. Multivariate bootstrap Cox regression analysis showed that the prognostic value of this tRF is independent of clinical stage, mutational status of the immunoglobulin heavy chain variable (IGHV) genetic locus, and CD38 expression status (p = 0.010). CONCLUSIONS Our results show that i-tRF-PheGAA can serve as a molecular biomarker of poor prognosis in CLL, alongside with the existing factors for CLL prognosis.
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Affiliation(s)
- Paraskevi Karousi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens GR-15701, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens GR-15701, Greece
| | - Sotirios G Papageorgiou
- Second Department of Internal Medicine and Research Unit, University General Hospital "Attikon", 1 Rimini St., Haidari, GR 12462 Athens, Greece
| | - Vasiliki Pappa
- Second Department of Internal Medicine and Research Unit, University General Hospital "Attikon", 1 Rimini St., Haidari, GR 12462 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens GR-15701, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens GR-15701, Greece.
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Green JA, Ansari MY, Ball H, Haqqi TM. tRNA-derived fragments (tRFs) regulate post-transcriptional gene expression via AGO-dependent mechanism in IL-1β stimulated chondrocytes. Osteoarthritis Cartilage 2020; 28:1102-1110. [PMID: 32407895 PMCID: PMC8418333 DOI: 10.1016/j.joca.2020.04.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 04/15/2020] [Accepted: 04/29/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVES Recent studies have shown that tRNA-derived RNA fragments (tRFs) are novel regulators of post-transcriptional gene expression. However, the expression profiles and their role in post-transcriptional gene regulation in chondrocytes is unknown. Here, we determined tRFs expression profile and explored tRF-3003a role in post-transcriptional gene regulation in IL-1β stimulated chondrocytes. METHODS We used qPCR arrays to determine tRNAs and tRFs expression in age- and sex-matched primary human OA chondrocytes and TC28/I2 cells stimulated with IL-1β. Chondrocytes were transfected with tRNA-CysGCA overexpression plasmid or tRF-3003a mimic and 3'UTR luciferase reporter plasmids of mRNAs harboring predicted tRF target "seed sequence". The AGO-RNA-induced silencing complex (AGO-RISC)-dependent repressive activity of tRF-3003a was determined by siRNA-mediated knockdown of AGO2. RESULTS IL-1β increased the expression levels of specific tRNAs and of tRF-3003a, a type 3 tRF produced by the cleavage of tRNA-CysGCA. tRF-3003a "seed sequence" was identified in the 3'UTR of JAK3 mRNA and tRNA-CysGCA overexpression or transfection of a tRF-3003a mimic in chondrocytes downregulated JAK3 expression and significantly reduced the activity of the 3'UTR reporter. RIP assay showed enrichment of tRF-3003a into AGO2/RISC in IL-1β treated chondrocytes. The suppressive effect of tRF-3003a on JAK3 3'UTR reporter was abrogated with siRNA-mediated depletion of AGO2. CONCLUSIONS We demonstrate that under pathological conditions chondrocytes display perturbations in the expression profile of specific tRNAs and tRFs. Furthermore, a specific tRF namely tRF-3003a can post-transcriptionally regulate JAK3 expression via AGO/RISC formation in chondrocytes. Identification of this novel mechanism may be of value in the design of precision therapies for OA.
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Affiliation(s)
- J. A. Green
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272
| | - M. Y. Ansari
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272
| | - H.C. Ball
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272
| | - T. M. Haqqi
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH 44272,Corresponding author: Prof. Dr. Tariq M. Haqqi; Department of Anatomy & Neurobiology, Northeast Ohio Medical University, 4209 St Rt 44, Rootstown, OH 44272
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A Novel Nonsense Angiogenin Mutation is Associated With Alzheimer Disease. Alzheimer Dis Assoc Disord 2020; 33:163-165. [PMID: 30188356 DOI: 10.1097/wad.0000000000000272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Prehn JHM, Jirström E. Angiogenin and tRNA fragments in Parkinson's disease and neurodegeneration. Acta Pharmacol Sin 2020; 41:442-446. [PMID: 32144338 PMCID: PMC7470775 DOI: 10.1038/s41401-020-0375-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 01/27/2020] [Indexed: 12/11/2022] Open
Abstract
In this review, we summarise the evidence for a role of the ribonuclease angiogenin in the pathophysiology of neurodegenerative disorders, with a specific focus on Parkinson’s disease (PD). Angiogenin is a stress-induced, secreted ribonuclease with both nuclear and cytosolic activities. Loss-of-function mutations in the angiogenin gene (ANG) have been initially discovered in familial cases of amyotrophic lateral sclerosis (ALS), however, variants in ANG have subsequently been identified in PD and Alzheimer’s disease. Delivery of angiogenin protein reduces neurodegeneration and delays disease progression in in vitro and in vivo models of ALS and in vitro models of PD. In the nucleus, angiogenin promotes ribosomal RNA transcription. Under stress conditions, angiogenin also translocates to the cytosol where it cleaves non-coding RNA into RNA fragments, in particular transfer RNAs (tRNAs). Stress-induced tRNA fragments have been proposed to have multiple cellular functions, including inhibition of ribosome biogenesis, inhibition of protein translation and inhibition of apoptosis. We will discuss recent evidence of tRNA fragment accumulation in PD, as well as their potential neuroprotective activities.
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Aluri KC, Salisbury JP, Prehn JHM, Agar JN. Loss of angiogenin function is related to earlier ALS onset and a paradoxical increase in ALS duration. Sci Rep 2020; 10:3715. [PMID: 32111867 PMCID: PMC7048737 DOI: 10.1038/s41598-020-60431-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
0.5-1% of ALS (Amyotrophic Lateral Sclerosis) and Parkinson's disease (PD) are associated with mutations in the angiogenin (ANG). These mutations are thought to cause disease through a loss of ANG function, but this hypothesis has not been evaluated statistically. In addition, the potential for ANG to promote disease has not been considered. With the goal of better defining the etiology of ANG-ALS, we assembled all clinical onset and disease duration data and determined if these were correlated with biochemical properties of ANG variants. Loss of ANG stability and ribonuclease activity were found to correlate with early ALS onset, confirming an aspect of the prevailing model of ANG-ALS. Conversely, loss of ANG stability and ribonuclease activity correlated with longer survival following diagnosis, which is inconsistent with the prevailing model. These results indicate that functional ANG appears to decrease the risk of developing ALS but exacerbate ALS once in progress. These findings are rationalized in terms of studies demonstrating that distinct mechanisms contribute to ALS onset and progression and propose that ANG replacement or stabilization would benefit pre-symptomatic ANG-ALS patients. However, this study challenges the prevailing hypothesis that augmenting ANG will benefit symptomatic ANG-ALS patients. Instead, our results suggest that silencing of ANG activity may be beneficial for symptomatic ALS patients. This study will serve as a call-to-arms for neurologists to consistently publish ALS and PD patient's clinical data-if all ANG-ALS patients' data were available our findings could be tested with considerable statistical power.
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Affiliation(s)
- Krishna C Aluri
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts, 02115, United States
| | - Joseph P Salisbury
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts, 02115, United States
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, SFI Future-Neuro Centre, Royal College of Surgeons in Ireland, Dublin, 2, Ireland
| | - Jeffrey N Agar
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, 02115, USA.
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts, 02115, United States.
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts, 02115, United States.
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Abstract
Over the past decades, tRNA was found to be a rich hub of RNA modifications such as 1-methyladenosine and 5-methycytosine modifications and others, holding more than half of all modifications occurring in RNA molecules. Moreover, tRNA was discovered to be a source of various small noncoding RNA species, such as the stress induced angiogenin cleaved tRNA halves (tiRNA) or the miRNA like tRNA derived fragments. tRNA cleavage under stress was fist discovered in bacteria and later was found to be conserved across different species, including mammals. Under cellular stress conditions, tRNA undergoes conformational changes and angiogenin cleaves it into 3' and 5' halves. 5'tiRNA halves were shown to repress protein translations. tRNA cleavage is thought of to be a cytoprotective mechanism by which cells evade apoptosis, however some data hints to the opposite; that tiRNA are cytotoxic or at least related to apoptosis initiation. tRNA cleavage also was shown to be affected by tRNA modifications via different enzymes in the cytosol and mitochondria. In this review, we will highlight the biology of tRNA cleavage, show the evidence of it being cytoprotective or a marker of cell death and shed a light on its role in disease models and human diseases as well as possible future directions in this field of RNA research.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgery; Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgery; Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine; Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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40
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Qin C, Xu PP, Zhang X, Zhang C, Liu CB, Yang DG, Gao F, Yang ML, Du LJ, Li JJ. Pathological significance of tRNA-derived small RNAs in neurological disorders. Neural Regen Res 2020; 15:212-221. [PMID: 31552886 PMCID: PMC6905339 DOI: 10.4103/1673-5374.265560] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are a type of RNA that is not translated into proteins. Transfer RNAs (tRNAs), a type of ncRNA, are the second most abundant type of RNA in cells. Recent studies have shown that tRNAs can be cleaved into a heterogeneous population of ncRNAs with lengths of 18–40 nucleotides, known as tRNA-derived small RNAs (tsRNAs). There are two main types of tsRNA, based on their length and the number of cleavage sites that they contain: tRNA-derived fragments and tRNA-derived stress-induced RNAs. These RNA species were first considered to be byproducts of tRNA random cleavage. However, mounting evidence has demonstrated their critical functional roles as regulatory factors in the pathophysiological processes of various diseases, including neurological diseases. However, the underlying mechanisms by which tsRNAs affect specific cellular processes are largely unknown. Therefore, this study comprehensively summarizes the following points: (1) The biogenetics of tsRNA, including their discovery, classification, formation, and the roles of key enzymes. (2) The main biological functions of tsRNA, including its miRNA-like roles in gene expression regulation, protein translation regulation, regulation of various cellular activities, immune mediation, and response to stress. (3) The potential mechanisms of pathophysiological changes in neurological diseases that are regulated by tsRNA, including neurodegeneration and neurotrauma. (4) The identification of the functional diversity of tsRNA may provide valuable information regarding the physiological and pathophysiological mechanisms of neurological disorders, thus providing a new reference for the clinical treatment of neurological diseases. Research into tsRNAs in neurological diseases also has the following challenges: potential function and mechanism studies, how to accurately quantify expression, and the exact relationship between tsRNA and miRNA. These challenges require future research efforts.
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Affiliation(s)
- Chuan Qin
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Pei-Pei Xu
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Xin Zhang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chao Zhang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chang-Bin Liu
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - De-Gang Yang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Feng Gao
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Ming-Liang Yang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Liang-Jie Du
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Jian-Jun Li
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
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Gotte G, Menegazzi M. Biological Activities of Secretory RNases: Focus on Their Oligomerization to Design Antitumor Drugs. Front Immunol 2019; 10:2626. [PMID: 31849926 PMCID: PMC6901985 DOI: 10.3389/fimmu.2019.02626] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022] Open
Abstract
Ribonucleases (RNases) are a large number of enzymes gathered into different bacterial or eukaryotic superfamilies. Bovine pancreatic RNase A, bovine seminal BS-RNase, human pancreatic RNase 1, angiogenin (RNase 5), and amphibian onconase belong to the pancreatic type superfamily, while binase and barnase are in the bacterial RNase N1/T1 family. In physiological conditions, most RNases secreted in the extracellular space counteract the undesired effects of extracellular RNAs and become protective against infections. Instead, if they enter the cell, RNases can digest intracellular RNAs, becoming cytotoxic and having advantageous effects against malignant cells. Their biological activities have been investigated either in vitro, toward a number of different cancer cell lines, or in some cases in vivo to test their potential therapeutic use. However, immunogenicity or other undesired effects have sometimes been associated with their action. Nevertheless, the use of RNases in therapy remains an appealing strategy against some still incurable tumors, such as mesothelioma, melanoma, or pancreatic cancer. The RNase inhibitor (RI) present inside almost all cells is the most efficacious sentry to counteract the ribonucleolytic action against intracellular RNAs because it forms a tight, irreversible and enzymatically inactive complex with many monomeric RNases. Therefore, dimerization or multimerization could represent a useful strategy for RNases to exert a remarkable cytotoxic activity by evading the interaction with RI by steric hindrance. Indeed, the majority of the mentioned RNases can hetero-dimerize with antibody derivatives, or even homo-dimerize or multimerize, spontaneously or artificially. This can occur through weak interactions or upon introducing covalent bonds. Immuno-RNases, in particular, are fusion proteins representing promising drugs by combining high target specificity with easy delivery in tumors. The results concerning the biological features of many RNases reported in the literature are described and discussed in this review. Furthermore, the activities displayed by some RNases forming oligomeric complexes, the mechanisms driving toward these supramolecular structures, and the biological rebounds connected are analyzed. These aspects are offered with the perspective to suggest possible efficacious therapeutic applications for RNases oligomeric derivatives that could contemporarily lack, or strongly reduce, immunogenicity and other undesired side-effects.
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Affiliation(s)
- Giovanni Gotte
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Marta Menegazzi
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
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Ferguson R, Subramanian V. The secretion of the angiogenic and neurotrophic factor angiogenin is COPII and microtubule dependent. Exp Cell Res 2019; 381:265-279. [PMID: 31128105 DOI: 10.1016/j.yexcr.2019.05.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/10/2019] [Accepted: 05/19/2019] [Indexed: 10/26/2022]
Abstract
The RNaseA superfamily member Angiogenin (ANG) is a secreted protein involved in neovascularization, cell proliferation and stress response. Dysregulation of ANG expression is found in many cancers with poor prognosis and mutations in ANG are associated with neurodegenerative diseases. While the uptake and nuclear translocation of ANG is relatively well characterised, little is known about how it reaches the plasma membrane and its mode of secretion. We generated SH-SY5Y neuroblastoma cell lines constitutively expressing wild type (WT) Hemagglutinin (HA) epitope tagged mouse Ang1 (mAng1), and two amyotrophic lateral sclerosis associated ANG variants (C39W and K40I). Herein, we show that these cell lines secrete mAng1 into the culture media. Using small molecule inhibitors we probed the route taken between the endoplasmic reticulum and trans-Golgi network during secretion and have characterised it as COPII and microtubule dependent. In addition, we show that disruption by the PI3-kinase inhibitor wortmannin of the later stages of transit to the plasma membrane leads to mAng1 trafficking to lysosomal compartments. This suggests an autophagy dependent regulation of secretion.
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Affiliation(s)
- Ross Ferguson
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Vasanta Subramanian
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
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Tripolszki K, Danis J, Padhi AK, Gomes J, Bozó R, Nagy ZF, Nagy D, Klivényi P, Engelhardt JI, Széll M. Angiogenin mutations in Hungarian patients with amyotrophic lateral sclerosis: Clinical, genetic, computational, and functional analyses. Brain Behav 2019; 9:e01293. [PMID: 31025543 PMCID: PMC6576160 DOI: 10.1002/brb3.1293] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/28/2019] [Accepted: 04/03/2019] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Mutations in the angiogenin (ANG) gene are known to be associated with both familial and sporadic amyotrophic lateral sclerosis (ALS). The majority of disease-causing mutations of ANG result in loss of either ribonucleolytic activity, nuclear translocation activity or both. METHODS We sequenced ANG gene from a total of 136 sporadic ALS patients and 112 healthy controls of Hungarian origin. To elucidate the role of the R33W mutation in the disease mechanism, computational, and functional analyses were performed. RESULTS Mutation screening revealed a mutation located in the signal peptide (M-24I) and two mutations that affect the mature protein (R33W, V103I). The R33W mutation, which has not been previously detected in ALS patients, affects the key amino acid of the nuclear translocation signal of the ANG protein. Molecular dynamics simulations suggested that the R33W mutation results in partial loss of ribonucleolytic activity and reduced nuclear translocation activity. The ribonucleolytic assay and nuclear translocation assay of the R33W ANG protein confirmed the molecular dynamics results. CONCLUSIONS In the Hungarian ALS population, the observed frequency of ANG mutations was 2.9%, which is higher than previously reported for sporadic cohorts. The evidence from computational and functional analyses support the deleterious effect of the novel R33W variant detected in this study.
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Affiliation(s)
| | - Judit Danis
- MTA-SZTE Dermatological Research Group, Szeged, Hungary
| | - Aditya K Padhi
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi, India
| | - James Gomes
- Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, New Delhi, India
| | - Renáta Bozó
- Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - Zsófia F Nagy
- Department of Medical Genetics, University of Szeged, Szeged, Hungary
| | - Dóra Nagy
- Department of Medical Genetics, University of Szeged, Szeged, Hungary
| | - Péter Klivényi
- Department of Neurology, University of Szeged, Szeged, Hungary
| | | | - Márta Széll
- Department of Medical Genetics, University of Szeged, Szeged, Hungary.,MTA-SZTE Dermatological Research Group, Szeged, Hungary
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Watson CN, Belli A, Di Pietro V. Small Non-coding RNAs: New Class of Biomarkers and Potential Therapeutic Targets in Neurodegenerative Disease. Front Genet 2019; 10:364. [PMID: 31080456 PMCID: PMC6497742 DOI: 10.3389/fgene.2019.00364] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/05/2019] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative diseases (NDs) are becoming increasingly prevalent in the world, with an aging population. In the last few decades, due to the devastating nature of these diseases, the research of biomarkers has become crucial to enable adequate treatments and to monitor the progress of disease. Currently, gene mutations, CSF and blood protein markers together with the neuroimaging techniques are the most used diagnostic approaches. However, despite the efforts in the research, conflicting data still exist, highlighting the need to explore new classes of biomarkers, particularly at early stages. Small non-coding RNAs (MicroRNA, Small nuclear RNA, Small nucleolar RNA, tRNA derived small RNA and Piwi-interacting RNA) can be considered a "relatively" new class of molecule that have already proved to be differentially regulated in many NDs, hence they represent a new potential class of biomarkers to be explored. In addition, understanding their involvement in disease development could depict the underlying pathogenesis of particular NDs, so novel treatment methods that act earlier in disease progression can be developed. This review aims to describe the involvement of small non-coding RNAs as biomarkers of NDs and their potential role in future clinical applications.
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Affiliation(s)
- Callum N. Watson
- Neuroscience and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Antonio Belli
- Neuroscience and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Valentina Di Pietro
- Neuroscience and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, United States
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Lee HH, Wang YN, Hung MC. Functional roles of the human ribonuclease A superfamily in RNA metabolism and membrane receptor biology. Mol Aspects Med 2019; 70:106-116. [PMID: 30902663 DOI: 10.1016/j.mam.2019.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 03/17/2019] [Indexed: 02/08/2023]
Abstract
The human ribonuclease A (hRNase A) superfamily is comprised of 13 members of secretory RNases, most of which are recognized as catabolic enzymes for their ribonucleolytic activity to degrade ribonucleic acids (RNAs) in the extracellular space, where they play a role in innate host defense and physiological homeostasis. Interestingly, human RNases 9-13, which belong to a non-canonical subgroup of the hRNase A superfamily, are ribonucleolytic activity-deficient proteins with unclear biological functions. Moreover, accumulating evidence indicates that secretory RNases, such as human RNase 5, can be internalized into cells facilitated by membrane receptors like the epidermal growth factor receptor to regulate intracellular RNA species, in particular non-coding RNAs, and signaling pathways by either a ribonucleolytic activity-dependent or -independent manner. In this review, we summarize the classical role of hRNase A superfamily in the metabolism of extracellular and intracellular RNAs and update its non-classical function as a cognate ligand of membrane receptors. We further discuss the biological significance and translational potential of using secretory RNases as predictive biomarkers or therapeutic agents in certain human diseases and the pathological settings for future investigations.
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Affiliation(s)
- Heng-Huan Lee
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Unit 108, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Ying-Nai Wang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Unit 108, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Unit 108, 1515 Holcombe Boulevard, Houston, TX, 77030, USA; Graduate Institute of Biomedical Sciences and Center for Molecular Medicine, China Medical University, Taichung, 404, Taiwan; Department of Biotechnology, Asia University, Taichung 413, Taiwan.
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Combined Tissue-Fluid Proteomics to Unravel Phenotypic Variability in Amyotrophic Lateral Sclerosis. Sci Rep 2019; 9:4478. [PMID: 30872628 PMCID: PMC6418138 DOI: 10.1038/s41598-019-40632-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/12/2019] [Indexed: 12/12/2022] Open
Abstract
The lack of biomarkers for early diagnosis, clinical stratification and to monitor treatment response has hampered the development of new therapies for amyotrophic lateral sclerosis (ALS), a clinically heterogeneous neurodegenerative disorder with a variable site of disease initiation and rate of progression. To identify new biomarkers and therapeutic targets, two separate proteomic workflows were applied to study the immunological response and the plasma/brain proteome in phenotypic variants of ALS. Conventional multiplex (TMT) proteomic analysis of peripheral blood mononuclear cells (PBMCs) was performed alongside a recently introduced method to profile neuronal-derived proteins in plasma using brain tissue-enhanced isobaric tagging (TMTcalibrator). The combined proteomic analysis allowed the detection of regulated proteins linked to ALS pathogenesis (RNA-binding protein FUS, superoxide dismutase Cu-Zn and neurofilaments light polypeptide) alongside newly identified candidate biomarkers (myosin-9, fructose-bisphosphate aldolase and plectin). In line with the proteomic results, orthogonal immunodetection showed changes in neurofilaments and ApoE in bulbar versus limb onset fast progressing ALS. Functional analysis of significantly regulated features showed enrichment of pathways involved in regulation of the immune response, Rho family GTPases, semaphorin and integrin signalling. Our cross-phenotype investigation of PBMCs and plasma/brain proteins provides a more sensitive biomarker exploratory platform than conventional case-control studies in a single matrix. The reported regulated proteins may represent novel biomarker candidates and potentially druggable targets.
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Tuorto F, Parlato R. rRNA and tRNA Bridges to Neuronal Homeostasis in Health and Disease. J Mol Biol 2019; 431:1763-1779. [PMID: 30876917 DOI: 10.1016/j.jmb.2019.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/11/2022]
Abstract
Dysregulation of protein translation is emerging as a unifying mechanism in the pathogenesis of many neuronal disorders. Ribosomal RNA (rRNA) and transfer RNA (tRNA) are structural molecules that have complementary and coordinated functions in protein synthesis. Defects in both rRNAs and tRNAs have been described in mammalian brain development, neurological syndromes, and neurodegeneration. In this review, we present the molecular mechanisms that link aberrant rRNA and tRNA transcription, processing and modifications to translation deficits, and neuropathogenesis. We also discuss the interdependence of rRNA and tRNA biosynthesis and how their metabolism brings together proteotoxic stress and impaired neuronal homeostasis.
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Affiliation(s)
- Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
| | - Rosanna Parlato
- Institute of Applied Physiology, University of Ulm, Albert Einstein Allee 11, 89081 Ulm, Germany; Institute of Anatomy and Cell Biology, Medical Cell Biology, University of Heidelberg, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany.
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48
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Mathis S, Goizet C, Soulages A, Vallat JM, Masson GL. Genetics of amyotrophic lateral sclerosis: A review. J Neurol Sci 2019; 399:217-226. [PMID: 30870681 DOI: 10.1016/j.jns.2019.02.030] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/01/2019] [Accepted: 02/20/2019] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder of the motor pathways, invariably leading to death within a few years of onset. Most cases of ALS are sporadic, but familial forms of the disease (FALS) constitute 10% of the cases. Since the first identification of a causative gene in the 1990s and with recent advances in genetics, more than twenty genes have now been linked to FALS. This increased number of genes led to a tremendous amount of research, clearly contributed to a better understanding of the pathophysiology of this disorder, and paved the way for the development of new therapeutics and new hope for this fatal disease.
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Affiliation(s)
- Stéphane Mathis
- Department of Neurology, Nerve-Muscle Unit, CHU Bordeaux, (Pellegrin Hospital), University of Bordeaux, F-33000 Bordeaux, France; ALS Center, Nerve-Muscle Unit, CHU Bordeaux, (Pellegrin Hospital), University of Bordeaux, F-33000 Bordeaux, France.
| | - Cyril Goizet
- Department of Medical Genetics, 'Centre de Référence Maladies Rares Neurogénétique', CHU Bordeaux (Pellegrin Hospital), University of Bordeaux, 33000 Bordeaux, France; Laboratoire MRGM, INSERM U1211, F-33000 Bordeaux, France
| | - Antoine Soulages
- Department of Neurology, Nerve-Muscle Unit, CHU Bordeaux, (Pellegrin Hospital), University of Bordeaux, F-33000 Bordeaux, France
| | - Jean-Michel Vallat
- Department of Neurology, 'Centre de référence neuropathies rares', 2 avenue Martin Luther King, F-87000 Limoges, France
| | - Gwendal Le Masson
- Department of Neurology, Nerve-Muscle Unit, CHU Bordeaux, (Pellegrin Hospital), University of Bordeaux, F-33000 Bordeaux, France; Neurocentre Magendie, 'Physiopathologie de la Plasticité Neuronale', University of Bordeaux, U862, F-33000 Bordeaux, France; INSERM, Neurocentre Magendie, 'Physiopathologie de la Plasticité Neuronale', U862, F-33000 Bordeaux, France
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Ferguson R, Holloway DE, Chandrasekhar A, Acharya KR, Subramanian V. The catalytic activity and secretion of zebrafish RNases are essential for their in vivo function in motor neurons and vasculature. Sci Rep 2019; 9:1107. [PMID: 30710110 PMCID: PMC6358602 DOI: 10.1038/s41598-018-37140-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/29/2018] [Indexed: 12/14/2022] Open
Abstract
Angiogenin (hANG), a member of the Ribonuclease A superfamily has angiogenic, neurotrophic and neuroprotective activities. Mutations in hANG have been found in patients with Amyotrophic lateral sclerosis (ALS). The zebrafish (Danio rerio) rnasel-1, 2 and 3 are orthologues of hANG and of these only Rnasel-1 and Rnasel-2 have been shown to be angiogenic. Herein we show that NCI-65828, a potent and specific small molecule inhibitor of hANG inhibits Rnasel-1 to a similar extent. Treatment of early zebrafish embryos with NCI-65828, or with terrein, a fungal metabolite which prevents the secretion of hANG, resulted in spinal neuron aberrations as well defects in trunk vasculature. Our detailed expression analysis and inhibitor studies suggest that Rnasel-1 plays important roles in neuronal migration and pathfinding as well as in angiogenesis in zebrafish. Our studies suggest the usefulness of the zebrafish as a model to dissect the molecular consequences of the ANG ALS variants.
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Affiliation(s)
- Ross Ferguson
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Daniel E Holloway
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Anand Chandrasekhar
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211-7310, USA
| | - K Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Vasanta Subramanian
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
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50
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Pereira GC, Sanchez L, Schaughency PM, Rubio-Roldán A, Choi JA, Planet E, Batra R, Turelli P, Trono D, Ostrow LW, Ravits J, Kazazian HH, Wheelan SJ, Heras SR, Mayer J, García-Pérez JL, Goodier JL. Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis. Mob DNA 2018; 9:35. [PMID: 30564290 PMCID: PMC6295051 DOI: 10.1186/s13100-018-0138-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving loss of motor neurons and having no known cure and uncertain etiology. Several studies have drawn connections between altered retrotransposon expression and ALS. Certain features of the LINE-1 (L1) retrotransposon-encoded ORF1 protein (ORF1p) are analogous to those of neurodegeneration-associated RNA-binding proteins, including formation of cytoplasmic aggregates. In this study we explore these features and consider possible links between L1 expression and ALS. RESULTS We first considered factors that modulate aggregation and subcellular distribution of LINE-1 ORF1p, including nuclear localization. Changes to some ORF1p amino acid residues alter both retrotransposition efficiency and protein aggregation dynamics, and we found that one such polymorphism is present in endogenous L1s abundant in the human genome. We failed, however, to identify CRM1-mediated nuclear export signals in ORF1p nor strict involvement of cell cycle in endogenous ORF1p nuclear localization in human 2102Ep germline teratocarcinoma cells. Some proteins linked with ALS bind and colocalize with L1 ORF1p ribonucleoprotein particles in cytoplasmic RNA granules. Increased expression of several ALS-associated proteins, including TAR DNA Binding Protein (TDP-43), strongly limits cell culture retrotransposition, while some disease-related mutations modify these effects. Using quantitative reverse transcription PCR (RT-qPCR) of ALS tissues and reanalysis of publicly available RNA-Seq datasets, we asked if changes in expression of retrotransposons are associated with ALS. We found minimal altered expression in sporadic ALS tissues but confirmed a previous report of differential expression of many repeat subfamilies in C9orf72 gene-mutated ALS patients. CONCLUSIONS Here we extended understanding of the subcellular localization dynamics of the aggregation-prone LINE-1 ORF1p RNA-binding protein. However, we failed to find compelling evidence for misregulation of LINE-1 retrotransposons in sporadic ALS nor a clear effect of ALS-associated TDP-43 protein on L1 expression. In sum, our study reveals that the interplay of active retrotransposons and the molecular features of ALS are more complex than anticipated. Thus, the potential consequences of altered retrotransposon activity for ALS and other neurodegenerative disorders are worthy of continued investigation.
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Affiliation(s)
- Gavin C. Pereira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Paul M. Schaughency
- Oncology Center-Cancer Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Alejandro Rubio-Roldán
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Jungbin A. Choi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ranjan Batra
- Department of Neurosciences, School of Medicine, University of California at San Diego, San Diego, California USA
| | - Priscilla Turelli
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Lyle W. Ostrow
- Neuromuscular Division, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, University of California at San Diego, San Diego, California USA
| | - Haig H. Kazazian
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Sarah J. Wheelan
- Oncology Center-Cancer Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Sara R. Heras
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jens Mayer
- Department of Human Genetics, Medical Faculty, University of Saarland, Homburg/Saar, Germany
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John L. Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
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