1
|
Tak H, Cha S, Hong Y, Jung M, Ryu S, Han S, Jeong SM, Kim W, Lee EK. The miR-30-5p/TIA-1 axis directs cellular senescence by regulating mitochondrial dynamics. Cell Death Dis 2024; 15:404. [PMID: 38858355 PMCID: PMC11164864 DOI: 10.1038/s41419-024-06797-1] [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: 11/12/2023] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/12/2024]
Abstract
Senescent cells exhibit a diverse spectrum of changes in their morphology, proliferative capacity, senescence-associated secretory phenotype (SASP) production, and mitochondrial homeostasis. These cells often manifest with elongated mitochondria, a hallmark of cellular senescence. However, the precise regulatory mechanisms orchestrating this phenomenon remain predominantly unexplored. In this study, we provide compelling evidence for decreases in TIA-1, a pivotal regulator of mitochondrial dynamics, in models of both replicative senescence and ionizing radiation (IR)-induced senescence. The downregulation of TIA-1 was determined to trigger mitochondrial elongation and enhance the expression of senescence-associated β-galactosidase, a marker of cellular senescence, in human foreskin fibroblast HS27 cells and human keratinocyte HaCaT cells. Conversely, the overexpression of TIA-1 mitigated IR-induced cellular senescence. Notably, we identified the miR-30-5p family as a novel factor regulating TIA-1 expression. Augmented expression of the miR-30-5p family was responsible for driving mitochondrial elongation and promoting cellular senescence in response to IR. Taken together, our findings underscore the significance of the miR-30-5p/TIA-1 axis in governing mitochondrial dynamics and cellular senescence.
Collapse
Affiliation(s)
- Hyosun Tak
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
- INSERM U1052, CNRS UMR-5286, Cancer Research Center of Lyon (CRCL), Lyon, 69008, France
| | - Seongho Cha
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Youlim Hong
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Myeongwoo Jung
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Seungyeon Ryu
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Sukyoung Han
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Seung Min Jeong
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, 06591, South Korea
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Wook Kim
- Department of Molecular Science & Technology, Ajou University, Suwon, 16499, South Korea
| | - Eun Kyung Lee
- Department of Biochemistry, The Catholic University of Korea, Seoul, 06591, South Korea.
- Department of Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, 06591, South Korea.
- Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea.
| |
Collapse
|
2
|
Zhang L, Kwack KH, Thiyagarajan R, Mullaney KK, Lamb NA, Bard JE, Sohn J, Seldeen KL, Arao Y, Blackshear PJ, Abrams SI, Troen BR, Kirkwood KL. Tristetraprolin regulates the skeletal phenotype and osteoclastogenic potential through monocytic myeloid-derived suppressor cells. FASEB J 2024; 38:e23338. [PMID: 38038723 PMCID: PMC11128769 DOI: 10.1096/fj.202301703r] [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: 08/23/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 12/02/2023]
Abstract
Tristetraprolin (TTP; also known as NUP475, GOS24, or TIS11), encoded by Zfp36, is an RNA-binding protein that regulates target gene expression by promoting mRNA decay and preventing translation. Although previous studies have indicated that TTP deficiency is associated with systemic inflammation and a catabolic-like skeletal phenotype, the mechanistic underpinnings remain unclear. Here, using both TTP-deficient (TTPKO) and myeloid-specific TTPKO (cTTPKO) mice, we reveal that global absence or loss of TTP in the myeloid compartment results in a reduced bone microarchitecture, whereas gain-of-function TTP knock-in (TTPKI) mice exhibit no significant loss of bone microarchitecture. Flow cytometry analysis revealed a significant immunosuppressive immune cell phenotype with increased monocytic myeloid-derived suppressor cells (M-MDSCs) in TTPKO and cTTPKO mice, whereas no significant changes were observed in TTPKI mice. Single-cell transcriptomic analyses of bone marrow myeloid progenitor cell populations indicated a dramatic increase in early MDSC marker genes for both cTTPKO and TTPKO bone marrow populations. Consistent with these phenotypic and transcriptomic data, in vitro osteoclastogenesis analysis of bone marrow M-MDSCs from cTTPKO and TTPKO displayed enhanced osteoclast differentiation and functional capacity. Focused transcriptomic analyses of differentiated M-MDSCs showed increased osteoclast-specific transcription factors and cell fusion gene expression. Finally, functional data showed that M-MDSCs from TTP loss-of-function mice were capable of osteoclastogenesis and bone resorption in a context-dependent manner. Collectively, these findings indicate that TTP plays a central role in regulating osteoclastogenesis through multiple mechanisms, including induction of M-MDSCs that appear to regulate skeletal phenotype.
Collapse
Affiliation(s)
| | - Kyu Hwan Kwack
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul, Republic of Korea
| | - Ramkumar Thiyagarajan
- Departments of Medicine, University at Buffalo, Buffalo, NY, USA
- Division of Geriatrics and Palliative Medicine, University at Buffalo, Buffalo, NY, USA
- Research Service, Veterans Affairs Western New York Healthcare Service, Buffalo, NY, USA
| | - Kylie K. Mullaney
- Departments of Oral Biology, University at Buffalo, Buffalo, NY, USA
| | - Natalie A. Lamb
- Departments of Biochemistry, University at Buffalo, Buffalo, NY, USA
- Genomics and Bioinformatics Core, New York State Center of Excellence for Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Jonathan E. Bard
- Departments of Biochemistry, University at Buffalo, Buffalo, NY, USA
- Genomics and Bioinformatics Core, New York State Center of Excellence for Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | - Jiho Sohn
- Departments of Oral Biology, University at Buffalo, Buffalo, NY, USA
- Departments of Medicine, University at Buffalo, Buffalo, NY, USA
| | - Kenneth L. Seldeen
- Departments of Medicine, University at Buffalo, Buffalo, NY, USA
- Division of Geriatrics and Palliative Medicine, University at Buffalo, Buffalo, NY, USA
- Research Service, Veterans Affairs Western New York Healthcare Service, Buffalo, NY, USA
| | - Yukitomo Arao
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Perry J. Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
- Departments of Biochemistry & Medicine, Duke University Medical Center, Durham, NC, USA
| | - Scott I. Abrams
- Departments of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Bruce R. Troen
- Departments of Medicine, University at Buffalo, Buffalo, NY, USA
- Departments of Biochemistry, University at Buffalo, Buffalo, NY, USA
- Research Service, Veterans Affairs Western New York Healthcare Service, Buffalo, NY, USA
| | - Keith L. Kirkwood
- Departments of Oral Biology, University at Buffalo, Buffalo, NY, USA
- Head & Neck/Plastic & Reconstructive Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| |
Collapse
|
3
|
Hieber C, Grabbe S, Bros M. Counteracting Immunosenescence-Which Therapeutic Strategies Are Promising? Biomolecules 2023; 13:1085. [PMID: 37509121 PMCID: PMC10377144 DOI: 10.3390/biom13071085] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Aging attenuates the overall responsiveness of the immune system to eradicate pathogens. The increased production of pro-inflammatory cytokines by innate immune cells under basal conditions, termed inflammaging, contributes to impaired innate immune responsiveness towards pathogen-mediated stimulation and limits antigen-presenting activity. Adaptive immune responses are attenuated as well due to lowered numbers of naïve lymphocytes and their impaired responsiveness towards antigen-specific stimulation. Additionally, the numbers of immunoregulatory cell types, comprising regulatory T cells and myeloid-derived suppressor cells, that inhibit the activity of innate and adaptive immune cells are elevated. This review aims to summarize our knowledge on the cellular and molecular causes of immunosenescence while also taking into account senescence effects that constitute immune evasion mechanisms in the case of chronic viral infections and cancer. For tumor therapy numerous nanoformulated drugs have been developed to overcome poor solubility of compounds and to enable cell-directed delivery in order to restore immune functions, e.g., by addressing dysregulated signaling pathways. Further, nanovaccines which efficiently address antigen-presenting cells to mount sustained anti-tumor immune responses have been clinically evaluated. Further, senolytics that selectively deplete senescent cells are being tested in a number of clinical trials. Here we discuss the potential use of such drugs to improve anti-aging therapy.
Collapse
Affiliation(s)
- Christoph Hieber
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Stephan Grabbe
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Matthias Bros
- Department of Dermatology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstraße 1, 55131 Mainz, Germany
| |
Collapse
|
4
|
Varesi A, Campagnoli LIM, Barbieri A, Rossi L, Ricevuti G, Esposito C, Chirumbolo S, Marchesi N, Pascale A. RNA binding proteins in senescence: A potential common linker for age-related diseases? Ageing Res Rev 2023; 88:101958. [PMID: 37211318 DOI: 10.1016/j.arr.2023.101958] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/09/2023] [Accepted: 05/18/2023] [Indexed: 05/23/2023]
Abstract
Aging represents the major risk factor for the onset and/or progression of various disorders including neurodegenerative diseases, metabolic disorders, and bone-related defects. As the average age of the population is predicted to exponentially increase in the coming years, understanding the molecular mechanisms underlying the development of aging-related diseases and the discovery of new therapeutic approaches remain pivotal. Well-reported hallmarks of aging are cellular senescence, genome instability, autophagy impairment, mitochondria dysfunction, dysbiosis, telomere attrition, metabolic dysregulation, epigenetic alterations, low-grade chronic inflammation, stem cell exhaustion, altered cell-to-cell communication and impaired proteostasis. With few exceptions, however, many of the molecular players implicated within these processes as well as their role in disease development remain largely unknown. RNA binding proteins (RBPs) are known to regulate gene expression by dictating at post-transcriptional level the fate of nascent transcripts. Their activity ranges from directing primary mRNA maturation and trafficking to modulation of transcript stability and/or translation. Accumulating evidence has shown that RBPs are emerging as key regulators of aging and aging-related diseases, with the potential to become new diagnostic and therapeutic tools to prevent or delay aging processes. In this review, we summarize the role of RBPs in promoting cellular senescence and we highlight their dysregulation in the pathogenesis and progression of the main aging-related diseases, with the aim of encouraging further investigations that will help to better disclose this novel and captivating molecular scenario.
Collapse
Affiliation(s)
- Angelica Varesi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
| | | | - Annalisa Barbieri
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy
| | - Lorenzo Rossi
- Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | | | - Ciro Esposito
- Department of Internal Medicine and Therapeutics, University of Pavia, Italy; Nephrology and dialysis unit, ICS S. Maugeri SPA SB Hospital, Pavia, Italy; High School in Geriatrics, University of Pavia, Italy
| | | | - Nicoletta Marchesi
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy
| | - Alessia Pascale
- Department of Drug Sciences, Section of Pharmacology, University of Pavia, Pavia, Italy.
| |
Collapse
|
5
|
García-Ruiz S, Zhang D, Gustavsson EK, Rocamora-Perez G, Grant-Peters M, Fairbrother-Browne A, Reynolds RH, Brenton JW, Gil-Martínez AL, Chen Z, Rio DC, Botia JA, Guelfi S, Collado-Torres L, Ryten M. Splicing accuracy varies across human introns, tissues and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534370. [PMID: 37034741 PMCID: PMC10081249 DOI: 10.1101/2023.03.29.534370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Alternative splicing impacts most multi-exonic human genes. Inaccuracies during this process may have an important role in ageing and disease. Here, we investigated mis-splicing using RNA-sequencing data from ~14K control samples and 42 human body sites, focusing on split reads partially mapping to known transcripts in annotation. We show that mis-splicing occurs at different rates across introns and tissues and that these splicing inaccuracies are primarily affected by the abundance of core components of the spliceosome assembly and its regulators. Using publicly available data on short-hairpin RNA-knockdowns of numerous spliceosomal components and related regulators, we found support for the importance of RNA-binding proteins in mis-splicing. We also demonstrated that age is positively correlated with mis-splicing, and it affects genes implicated in neurodegenerative diseases. This in-depth characterisation of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.
Collapse
Affiliation(s)
- S García-Ruiz
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - D Zhang
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
| | - E K Gustavsson
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - G Rocamora-Perez
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
| | - M Grant-Peters
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - A Fairbrother-Browne
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - R H Reynolds
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - J W Brenton
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| | - A L Gil-Martínez
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - Z Chen
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, UCL, London, UK
| | - D C Rio
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - J A Botia
- Departamento de Ingeniería de la Información y las Comunicaciones, Universidad de Murcia, Murcia, Spain
| | - S Guelfi
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- Verge Genomics, South San Francisco, CA, 94080, USA
| | - L Collado-Torres
- Lieber Institute for Brain Development, Baltimore, MD, USA , 21205
| | - M Ryten
- Department of Genetics and Genomic Medicine Research & Teaching, UCL GOS Institute of Child Health, London, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815
| |
Collapse
|
6
|
Kwack KH, Zhang L, Kramer ED, Thiyagarajan R, Lamb NA, Arao Y, Bard JE, Seldeen KL, Troen BR, Blackshear PJ, Abrams SI, Kirkwood KL. Tristetraprolin limits age-related expansion of myeloid-derived suppressor cells. Front Immunol 2022; 13:1002163. [PMID: 36263047 PMCID: PMC9573970 DOI: 10.3389/fimmu.2022.1002163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Aging results in enhanced myelopoiesis, which is associated with an increased prevalence of myeloid leukemias and the production of myeloid-derived suppressor cells (MDSCs). Tristetraprolin (TTP) is an RNA binding protein that regulates immune-related cytokines and chemokines by destabilizing target mRNAs. As TTP expression is known to decrease with age in myeloid cells, we used TTP-deficient (TTPKO) mice to model aged mice to study TTP regulation in age-related myelopoiesis. Both TTPKO and myeloid-specific TTPKO (cTTPKO) mice had significant increases in both MDSC subpopulations M-MDSCs (CD11b+Ly6ChiLy6G-) and PMN-MDSCs (CD11b+Ly6CloLy6G+), as well as macrophages (CD11b+F4/80+) in the spleen and mesenteric lymph nodes; however, no quantitative changes in MDSCs were observed in the bone marrow. In contrast, gain-of-function TTP knock-in (TTPKI) mice had no change in MDSCs compared with control mice. Within the bone marrow, total granulocyte-monocyte progenitors (GMPs) and monocyte progenitors (MPs), direct antecedents of M-MDSCs, were significantly increased in both cTTPKO and TTPKO mice, but granulocyte progenitors (GPs) were significantly increased only in TTPKO mice. Transcriptomic analysis of the bone marrow myeloid cell populations revealed that the expression of CC chemokine receptor 2 (CCR2), which plays a key role in monocyte mobilization to inflammatory sites, was dramatically increased in both cTTPKO and TTPKO mice. Concurrently, the concentration of CC chemokine ligand 2 (CCL2), a major ligand of CCR2, was high in the serum of cTTPKO and TTPKO mice, suggesting that TTP impacts the mobilization of M-MDSCs from the bone marrow to inflammatory sites during aging via regulation of the CCR2-CCL2 axis. Collectively, these studies demonstrate a previously unrecognized role for TTP in regulating age-associated myelopoiesis through the expansion of specific myeloid progenitors and M-MDSCs and their recruitment to sites of injury, inflammation, or other pathologic perturbations.
Collapse
Affiliation(s)
- Kyu Hwan Kwack
- Department of Oral Biology, University at Buffalo, Buffalo, NY, United States
- Department of Oral Microbiology, College of Dentistry, Kyung Hee University, Seoul, South Korea
| | - Lixia Zhang
- Department of Oral Biology, University at Buffalo, Buffalo, NY, United States
| | - Elliot D. Kramer
- Department of Medicine, University at Buffalo, Buffalo, NY, United States
- Departments of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Ramkumar Thiyagarajan
- Department of Medicine, University at Buffalo, Buffalo, NY, United States
- Division of Geriatrics and Palliative Medicine, University at Buffalo, Buffalo, NY, United States
- Research Service, Veterans Affairs Western New York Healthcare Service, Buffalo, NY, United States
| | - Natalie A. Lamb
- Department of Biochemistry, University at Buffalo, Buffalo, NY, United States
- Genomics and Bioinformatics Core, New York State Center of Excellence for Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Yukitomo Arao
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
| | - Jonathan E. Bard
- Department of Biochemistry, University at Buffalo, Buffalo, NY, United States
- Genomics and Bioinformatics Core, New York State Center of Excellence for Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Kenneth L. Seldeen
- Department of Medicine, University at Buffalo, Buffalo, NY, United States
- Division of Geriatrics and Palliative Medicine, University at Buffalo, Buffalo, NY, United States
- Research Service, Veterans Affairs Western New York Healthcare Service, Buffalo, NY, United States
| | - Bruce R. Troen
- Department of Medicine, University at Buffalo, Buffalo, NY, United States
- Division of Geriatrics and Palliative Medicine, University at Buffalo, Buffalo, NY, United States
- Research Service, Veterans Affairs Western New York Healthcare Service, Buffalo, NY, United States
| | - Perry J. Blackshear
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, United States
- Departments of Biochemistry & Medicine, Duke University Medical Center, Durham, NC, United States
| | - Scott I. Abrams
- Departments of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Keith L. Kirkwood
- Department of Oral Biology, University at Buffalo, Buffalo, NY, United States
- Head & Neck/Plastic & Reconstructive Surgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| |
Collapse
|
7
|
Chen M, Wang L, Li M, Budai MM, Wang J. Mitochondrion-Mediated Cell Death through Erk1-Alox5 Independent of Caspase-9 Signaling. Cells 2022; 11:cells11193053. [PMID: 36231015 PMCID: PMC9564198 DOI: 10.3390/cells11193053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/22/2022] [Accepted: 09/25/2022] [Indexed: 02/02/2023] Open
Abstract
Mitochondrial disruption leads to the release of cytochrome c to activate caspase-9 and the downstream caspase cascade for the execution of apoptosis. However, cell death can proceed efficiently in the absence of caspase-9 following mitochondrial disruption, suggesting the existence of caspase-9-independent cell death mechanisms. Through a genome-wide siRNA library screening, we identified a network of genes that mediate caspase-9-independent cell death, through ROS production and Alox5-dependent membrane lipid peroxidation. Erk1-dependent phosphorylation of Alox5 is critical for targeting Alox5 to the nuclear membrane to mediate lipid peroxidation, resulting in nuclear translocation of cytolytic molecules to induce DNA damage and cell death. Consistently, double knockouts of caspase-9 and Alox5 in mice, but not deletion of either gene alone, led to significant T cell expansion with inhibited cell death, indicating that caspase-9- and Alox5-dependent pathways function in parallel to regulate T cell death in vivo. This unbiased whole-genome screening reveals an Erk1-Alox5-mediated pathway that promotes membrane lipid peroxidation and nuclear translocation of cytolytic molecules, leading to the execution of cell death in parallel to the caspase-9 signaling cascade.
Collapse
Affiliation(s)
- Min Chen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: (M.C.); (J.W.)
| | - Lei Wang
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Min Li
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Marietta M. Budai
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Jin Wang
- Immunobiology and Transplant Science Center, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Surgery, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
- Correspondence: (M.C.); (J.W.)
| |
Collapse
|
8
|
Velasco BR, Izquierdo JM. T-Cell Intracellular Antigen 1-Like Protein in Physiology and Pathology. Int J Mol Sci 2022; 23:ijms23147836. [PMID: 35887183 PMCID: PMC9318959 DOI: 10.3390/ijms23147836] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
T-cell intracellular antigen 1 (TIA1)-related/like (TIAR/TIAL1) protein is a multifunctional RNA-binding protein (RBP) involved in regulating many aspects of gene expression, independently or in combination with its paralog TIA1. TIAR was first described in 1992 by Paul Anderson’s lab in relation to the development of a cell death phenotype in immune system cells, as it possesses nucleolytic activity against cytotoxic lymphocyte target cells. Similar to TIA1, it is characterized by a subcellular nucleo-cytoplasmic localization and ubiquitous expression in the cells of different tissues of higher organisms. In this paper, we review the relevant structural and functional information available about TIAR from a triple perspective (molecular, cellular and pathophysiological), paying special attention to its expression and regulation in cellular events and processes linked to human pathophysiology.
Collapse
|
9
|
Machine learning predicts translation initiation sites in neurologic diseases with nucleotide repeat expansions. PLoS One 2022; 17:e0256411. [PMID: 35648796 PMCID: PMC9159584 DOI: 10.1371/journal.pone.0256411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
A number of neurologic diseases associated with expanded nucleotide repeats, including an inherited form of amyotrophic lateral sclerosis, have an unconventional form of translation called repeat-associated non-AUG (RAN) translation. It has been speculated that the repeat regions in the RNA fold into secondary structures in a length-dependent manner, promoting RAN translation. Repeat protein products are translated, accumulate, and may contribute to disease pathogenesis. Nucleotides that flank the repeat region, especially ones closest to the initiation site, are believed to enhance translation initiation. A machine learning model has been published to help identify ATG and near-cognate translation initiation sites; however, this model has diminished predictive power due to its extensive feature selection and limited training data. Here, we overcome this limitation and increase prediction accuracy by the following: a) capture the effect of nucleotides most critical for translation initiation via feature reduction, b) implement an alternative machine learning algorithm better suited for limited data, c) build comprehensive and balanced training data (via sampling without replacement) that includes previously unavailable sequences, and d) split ATG and near-cognate translation initiation codon data to train two separate models. We also design a supplementary scoring system to provide an additional prognostic assessment of model predictions. The resultant models have high performance, with ~85-88% accuracy, exceeding that of the previously published model by >18%. The models presented here are used to identify translation initiation sites in genes associated with a number of neurologic repeat expansion disorders. The results confirm a number of sites of translation initiation upstream of the expanded repeats that have been found experimentally, and predict sites that are not yet established.
Collapse
|
10
|
Krohannon A, Srivastava M, Rauch S, Srivastava R, Dickinson BC, Janga SC. CASowary: CRISPR-Cas13 guide RNA predictor for transcript depletion. BMC Genomics 2022; 23:172. [PMID: 35236300 PMCID: PMC8889671 DOI: 10.1186/s12864-022-08366-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 02/03/2022] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Recent discovery of the gene editing system - CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) associated proteins (Cas), has resulted in its widespread use for improved understanding of a variety of biological systems. Cas13, a lesser studied Cas protein, has been repurposed to allow for efficient and precise editing of RNA molecules. The Cas13 system utilizes base complementarity between a crRNA/sgRNA (crispr RNA or single guide RNA) and a target RNA transcript, to preferentially bind to only the target transcript. Unlike targeting the upstream regulatory regions of protein coding genes on the genome, the transcriptome is significantly more redundant, leading to many transcripts having wide stretches of identical nucleotide sequences. Transcripts also exhibit complex three-dimensional structures and interact with an array of RBPs (RNA Binding Proteins), both of which may impact the effectiveness of transcript depletion of target sequences. However, our understanding of the features and corresponding methods which can predict whether a specific sgRNA will effectively knockdown a transcript is very limited. RESULTS Here we present a novel machine learning and computational tool, CASowary, to predict the efficacy of a sgRNA. We used publicly available RNA knockdown data from Cas13 characterization experiments for 555 sgRNAs targeting the transcriptome in HEK293 cells, in conjunction with transcriptome-wide protein occupancy information. Our model utilizes a Decision Tree architecture with a set of 112 sequence and target availability features, to classify sgRNA efficacy into one of four classes, based upon expected level of target transcript knockdown. After accounting for noise in the training data set, the noise-normalized accuracy exceeds 70%. Additionally, highly effective sgRNA predictions have been experimentally validated using an independent RNA targeting Cas system - CIRTS, confirming the robustness and reproducibility of our model's sgRNA predictions. Utilizing transcriptome wide protein occupancy map generated using POP-seq in HeLa cells against publicly available protein-RNA interaction map in Hek293 cells, we show that CASowary can predict high quality guides for numerous transcripts in a cell line specific manner. CONCLUSIONS Application of CASowary to whole transcriptomes should enable rapid deployment of CRISPR/Cas13 systems, facilitating the development of therapeutic interventions linked with aberrations in RNA regulatory processes.
Collapse
Affiliation(s)
- Alexander Krohannon
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), 535 West Michigan St, Indianapolis, IN, 46202, USA
| | - Mansi Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), 535 West Michigan St, Indianapolis, IN, 46202, USA
| | - Simone Rauch
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637, USA
| | - Rajneesh Srivastava
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), 535 West Michigan St, Indianapolis, IN, 46202, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Sarath Chandra Janga
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University Indianapolis (IUPUI), 535 West Michigan St, Indianapolis, IN, 46202, USA.
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translation Sciences (HITS), 410 West 10th Street, Indianapolis, IN, 46202, USA.
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN, 46202, USA.
| |
Collapse
|
11
|
The Multifunctional Faces of T-Cell Intracellular Antigen 1 in Health and Disease. Int J Mol Sci 2022; 23:ijms23031400. [PMID: 35163320 PMCID: PMC8836218 DOI: 10.3390/ijms23031400] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/13/2022] [Accepted: 01/22/2022] [Indexed: 02/06/2023] Open
Abstract
T-cell intracellular antigen 1 (TIA1) is an RNA-binding protein that is expressed in many tissues and in the vast majority of species, although it was first discovered as a component of human cytotoxic T lymphocytes. TIA1 has a dual localization in the nucleus and cytoplasm, where it plays an important role as a regulator of gene-expression flux. As a multifunctional master modulator, TIA1 controls biological processes relevant to the physiological functioning of the organism and the development and/or progression of several human pathologies. This review summarizes our current knowledge of the molecular aspects and cellular processes involving TIA1, with relevance for human pathophysiology.
Collapse
|
12
|
Abbadi D, Andrews JJ, Katsara O, Schneider RJ. AUF1 gene transfer increases exercise performance and improves skeletal muscle deficit in adult mice. Mol Ther Methods Clin Dev 2021; 22:222-236. [PMID: 34485607 PMCID: PMC8399044 DOI: 10.1016/j.omtm.2021.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022]
Abstract
Muscle function and mass begin declining in adults long before evidence of sarcopenia and include reduced mitochondrial function, although much remains to be characterized. We found that mRNA decay factor AU-rich mRNA binding factor 1 (AUF1), which stimulates myogenesis, is strongly reduced in skeletal muscle of adult and older mice in the absence of evidence of sarcopenia. Muscle-specific adeno-associated virus (AAV)8-AUF1 gene therapy increased expression of AUF1, muscle function, and mass. AAV8 AUF1 muscle gene transfer in 12-month-old mice increased the levels of activated muscle stem (satellite) cells, increased muscle mass, reduced markers of muscle atrophy, increased markers of mitochondrial content and muscle fiber oxidative capacity, and enhanced exercise performance to levels of 3-month-old mice. With wild-type and AUF1 knockout mice and cultured myoblasts, AUF1 supplementation of muscle fibers was found to increase expression of Peroxisome Proliferator-activated Receptor Gamma Co-activator 1-alpha (PGC1α), a major effector of skeletal muscle mitochondrial oxidative metabolism. AUF1 stabilized and increased translation of the pgc1α mRNA, which is strongly reduced in adult muscle in the absence of AUF1 supplementation. Skeletal muscle-specific gene transfer of AUF1 therefore restores muscle mass, increases exercise endurance, and may provide a therapeutic strategy for age-related muscle loss.
Collapse
Affiliation(s)
- Dounia Abbadi
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - John J. Andrews
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Olga Katsara
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Robert J. Schneider
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| |
Collapse
|
13
|
Narayan V, McMahon M, O'Brien JJ, McAllister F, Buffenstein R. Insights into the Molecular Basis of Genome Stability and Pristine Proteostasis in Naked Mole-Rats. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1319:287-314. [PMID: 34424521 DOI: 10.1007/978-3-030-65943-1_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The naked mole-rat (Heterocephalus glaber) is the longest-lived rodent, with a maximal reported lifespan of 37 years. In addition to its long lifespan - which is much greater than predicted based on its small body size (longevity quotient of ~4.2) - naked mole-rats are also remarkably healthy well into old age. This is reflected in a striking resistance to tumorigenesis and minimal declines in cardiovascular, neurological and reproductive function in older animals. Over the past two decades, researchers have been investigating the molecular mechanisms regulating the extended life- and health- span of this animal, and since the sequencing and assembly of the naked mole-rat genome in 2011, progress has been rapid. Here, we summarize findings from published studies exploring the unique molecular biology of the naked mole-rat, with a focus on mechanisms and pathways contributing to genome stability and maintenance of proteostasis during aging. We also present new data from our laboratory relevant to the topic and discuss our findings in the context of the published literature.
Collapse
Affiliation(s)
| | - Mary McMahon
- Calico Life Sciences, LLC, South San Francisco, CA, USA
| | | | | | - Rochelle Buffenstein
- Calico Life Sciences, LLC, South San Francisco, CA, USA. .,Department of Pharmacology, University of Texas Health at San Antonio, San Antonio, TX, USA.
| |
Collapse
|
14
|
Marcelo A, Koppenol R, de Almeida LP, Matos CA, Nóbrega C. Stress granules, RNA-binding proteins and polyglutamine diseases: too much aggregation? Cell Death Dis 2021; 12:592. [PMID: 34103467 PMCID: PMC8187637 DOI: 10.1038/s41419-021-03873-8] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 02/05/2023]
Abstract
Stress granules (SGs) are membraneless cell compartments formed in response to different stress stimuli, wherein translation factors, mRNAs, RNA-binding proteins (RBPs) and other proteins coalesce together. SGs assembly is crucial for cell survival, since SGs are implicated in the regulation of translation, mRNA storage and stabilization and cell signalling, during stress. One defining feature of SGs is their dynamism, as they are quickly assembled upon stress and then rapidly dispersed after the stress source is no longer present. Recently, SGs dynamics, their components and their functions have begun to be studied in the context of human diseases. Interestingly, the regulated protein self-assembly that mediates SG formation contrasts with the pathological protein aggregation that is a feature of several neurodegenerative diseases. In particular, aberrant protein coalescence is a key feature of polyglutamine (PolyQ) diseases, a group of nine disorders that are caused by an abnormal expansion of PolyQ tract-bearing proteins, which increases the propensity of those proteins to aggregate. Available data concerning the abnormal properties of the mutant PolyQ disease-causing proteins and their involvement in stress response dysregulation strongly suggests an important role for SGs in the pathogenesis of PolyQ disorders. This review aims at discussing the evidence supporting the existence of a link between SGs functionality and PolyQ disorders, by focusing on the biology of SGs and on the way it can be altered in a PolyQ disease context.
Collapse
Affiliation(s)
- Adriana Marcelo
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal
- PhD Program in Biomedial Sciences, Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, Portugal
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, Portugal
| | - Rebekah Koppenol
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal
- PhD Program in Biomedial Sciences, Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, Portugal
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, Portugal
| | - Luís Pereira de Almeida
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Carlos A Matos
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, Portugal
| | - Clévio Nóbrega
- Algarve Biomedical Center Research Institute (ABC-RI), Faro, Portugal.
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal.
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, Portugal.
- Champalimaud Research Program, Champalimaud Center for the Unknown, Lisbon, Portugal.
| |
Collapse
|
15
|
Deficiency of Tristetraprolin Triggers Hyperthermia through Enhancing Hypothalamic Inflammation. Int J Mol Sci 2021; 22:ijms22073328. [PMID: 33805094 PMCID: PMC8037390 DOI: 10.3390/ijms22073328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 11/17/2022] Open
Abstract
Tristetraprolin (TTP), an RNA-binding protein, controls the stability of RNA by capturing AU-rich elements on their target genes. It has recently been identified that TTP serves as an anti-inflammatory protein by guiding the unstable mRNAs of pro-inflammatory proteins in multiple cells. However, it has not yet been investigated whether TTP affects the inflammatory responses in the hypothalamus. Since hypothalamic inflammation is tightly coupled to the disturbance of energy homeostasis, we designed the current study to investigate whether TTP regulates hypothalamic inflammation and thereby affects energy metabolism by utilizing TTP-deficient mice. We observed that deficiency of TTP led to enhanced hypothalamic inflammation via stimulation of a variety of pro-inflammatory genes. In addition, microglial activation occurred in the hypothalamus, which was accompanied by an enhanced inflammatory response. In line with these molecular and cellular observations, we finally confirmed that deficiency of TTP results in elevated core body temperature and energy expenditure. Taken together, our findings unmask novel roles of hypothalamic TTP on energy metabolism, which is linked to inflammatory responses in hypothalamic microglial cells.
Collapse
|
16
|
Bakshi A, Rai U. Reproductive phase-dependent variation, sexually dimorphic expression and sex steroids-mediated transcriptional regulation of lep and lepr in lymphoid organs of Channa punctata. Sci Rep 2020; 10:999. [PMID: 31969648 PMCID: PMC6976713 DOI: 10.1038/s41598-020-57922-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 12/07/2019] [Indexed: 01/08/2023] Open
Abstract
The reproductive phase-dependent and sex-related differential expression of leptin (lep) and its receptor (lepr) in primary and secondary lymphoid organs of a highly nutritive economically important Channa punctata preempts the involvement of sex steroids in modulating intra-immuno-leptin system. This hypothesis was strengthened when plasma testosterone (T) and estradiol (E2) levels in male and female fish of reproductively active spawning and quiescent phases were correlated with lep and lepr expression in their immune organs. Splenic lep and lepr showed a negative correlation with T in both male and female, while with E2 there was a positive correlation in male and negative in female C. punctata. In head kidney, a contrasting correlation was observed as compared to spleen. To validate the implication of sex steroids in regulating leptin system in immune organs, in vivo and in vitro experiments were performed with DHT and E2. Upon administration, lep and lepr expression in tissues of either sex was downregulated. In addition, in vitro results with either of the sex steroids exemplified their direct involvement. Overall, this study, for the first time, reports correlation between sex steroids and transcript expression of leptin system in immune organs of a seasonally breeding vertebrate.
Collapse
Affiliation(s)
- Amrita Bakshi
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Umesh Rai
- Department of Zoology, University of Delhi, Delhi, 110007, India.
| |
Collapse
|
17
|
Nunes C, Mestre I, Marcelo A, Koppenol R, Matos CA, Nóbrega C. MSGP: the first database of the protein components of the mammalian stress granules. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5367298. [PMID: 30820574 PMCID: PMC6395795 DOI: 10.1093/database/baz031] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/14/2019] [Accepted: 02/11/2019] [Indexed: 01/09/2023]
Abstract
In response to different stress stimuli, cells transiently form stress granules (SGs) in order to protect themselves and re-establish homeostasis. Besides these important cellular functions, SGs are now being implicated in different human diseases, such as neurodegenerative disorders and cancer. SGs are ribonucleoprotein granules, constituted by a variety of different types of proteins, RNAs, factors involved in translation and signaling molecules, being capable of regulating mRNA translation to facilitate stress response. However, until now a complete list of the SG components has not been available. Therefore, we aimer at identifying and linting in an open access database all the proteins described so far as components of SGs. The identification was made through an exhaustive search of studies listed in PubMed and double checked. Moreover, for each identified protein several details were also gathered from public databases, such as the molecular function, the cell types in which they were detected, the type of stress stimuli used to induce SG formation and the reference of the study describing the recruitment of the component to SGs. Expression levels in the context of different neurodegenerative diseases were also obtained and are also described in the database. The Mammalian Stress Granules Proteome is available at https://msgp.pt/, being a new and unique open access online database, the first to list all the protein components of the SGs identified so far. The database constitutes an important and valuable tool for researchers in this research area of growing interest.
Collapse
Affiliation(s)
- Catarina Nunes
- Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal.,Centre for Biomedical Research, University of Algarve, Faro, Portugal
| | - Isa Mestre
- Centre for Biomedical Research, University of Algarve, Faro, Portugal
| | - Adriana Marcelo
- Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal.,Centre for Biomedical Research, University of Algarve, Faro, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Rebekah Koppenol
- Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal
| | - Carlos A Matos
- Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal.,Centre for Biomedical Research, University of Algarve, Faro, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Clévio Nóbrega
- Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal.,Centre for Biomedical Research, University of Algarve, Faro, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Algarve Biomedical Center, University of Algarve, Faro, Portugal
| |
Collapse
|
18
|
Kotagama K, Schorr AL, Steber HS, Mangone M. ALG-1 Influences Accurate mRNA Splicing Patterns in the Caenorhabditis elegans Intestine and Body Muscle Tissues by Modulating Splicing Factor Activities. Genetics 2019; 212:931-951. [PMID: 31073019 PMCID: PMC6614907 DOI: 10.1534/genetics.119.302223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023] Open
Abstract
MicroRNAs (miRNAs) are known to modulate gene expression, but their activity at the tissue-specific level remains largely uncharacterized. To study their contribution to tissue-specific gene expression, we developed novel tools to profile putative miRNA targets in the Caenorhabditis elegans intestine and body muscle. We validated many previously described interactions and identified ∼3500 novel targets. Many of the candidate miRNA targets curated are known to modulate the functions of their respective tissues. Within our data sets we observed a disparity in the use of miRNA-based gene regulation between the intestine and body muscle. The intestine contained significantly more putative miRNA targets than the body muscle highlighting its transcriptional complexity. We detected an unexpected enrichment of RNA-binding proteins targeted by miRNA in both tissues, with a notable abundance of RNA splicing factors. We developed in vivo genetic tools to validate and further study three RNA splicing factors identified as putative miRNA targets in our study (asd-2, hrp-2, and smu-2), and show that these factors indeed contain functional miRNA regulatory elements in their 3'UTRs that are able to repress their expression in the intestine. In addition, the alternative splicing pattern of their respective downstream targets (unc-60, unc-52, lin-10, and ret-1) is dysregulated when the miRNA pathway is disrupted. A reannotation of the transcriptome data in C. elegans strains that are deficient in the miRNA pathway from past studies supports and expands on our results. This study highlights an unexpected role for miRNAs in modulating tissue-specific gene isoforms, where post-transcriptional regulation of RNA splicing factors associates with tissue-specific alternative splicing.
Collapse
Affiliation(s)
- Kasuen Kotagama
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, Arizona 85287
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona
| | - Anna L Schorr
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, Arizona 85287
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona
| | - Hannah S Steber
- Barrett, The Honors College, Arizona State University, Tempe, Arizona 85281
| | - Marco Mangone
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, Arizona State University, Tempe, Arizona 85287
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, Arizona
| |
Collapse
|
19
|
Van Pelt DW, Hettinger ZR, Vanderklish PW. RNA-binding proteins: The next step in translating skeletal muscle adaptations? J Appl Physiol (1985) 2019; 127:654-660. [PMID: 31120811 DOI: 10.1152/japplphysiol.00076.2019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The decline of skeletal muscle mass during illness, injury, disuse, and aging is associated with poor health outcomes. Therefore, it is important to pursue a greater understanding of the mechanisms that dictate skeletal muscle adaptation. In this review, we propose that RNA-binding proteins (RBPs) comprise a critical regulatory node in the orchestration of adaptive responses in skeletal muscle. While RBPs have broadly pleiotropic molecular functions, our discussion is constrained at the outset by observations from hibernating animals, which suggest that RBP regulation of RNA stability and its impact on translational reprogramming is a key component of skeletal muscle response to anabolic and catabolic stimuli. We discuss the limited data available on the expression and functions of RBPs in adult skeletal muscle in response to disuse, aging, and exercise. A model is proposed in which dynamic changes in RBPs play a central role in muscle adaptive processes through their differential effects on mRNA stability. While limited, the currently available data suggest that understanding how adaptive (and maladaptive) changes in the expression of RBPs regulate mRNA stability in skeletal muscle could be an informative and productive research area for finding new strategies to limit atrophy and promote hypertrophy.
Collapse
Affiliation(s)
- Douglas W Van Pelt
- College of Health Sciences, Department of Rehabilitation Sciences, University of Kentucky, Lexington, Kentucky.,Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - Zachary R Hettinger
- College of Health Sciences, Department of Rehabilitation Sciences, University of Kentucky, Lexington, Kentucky.,Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - Peter W Vanderklish
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California
| |
Collapse
|
20
|
Li X, Ding D, Yao J, Zhou B, Shen T, Qi Y, Ni T, Wei G. Chromatin remodeling factor BAZ1A regulates cellular senescence in both cancer and normal cells. Life Sci 2019; 229:225-232. [PMID: 31085244 DOI: 10.1016/j.lfs.2019.05.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/06/2019] [Accepted: 05/10/2019] [Indexed: 12/13/2022]
Abstract
AIMS Cellular senescence is a well-known cancer prevention mechanism, inducing cancer cells to senescence can enhance cancer immunotherapy. However, how cellular senescence is regulated is not fully understood. Dynamic chromatin changes have been discovered during cellular senescence, while the causality remains elusive. BAZ1A, a gene coding the accessory subunit of ATP-dependent chromatin remodeling complex, showed decreased expression in multiple cellular senescence models. We aim to investigate the functional role of BAZ1A in regulating senescence in cancer and normal cells. MATERIALS AND METHODS Knockdown of BAZ1A was performed via lentivirus mediated short hairpin RNA (shRNA) in various cancer cell lines (A549 and U2OS) and normal cells (HUVEC, NIH3T3 and MEF). A series of senescence-associated phenotypes were quantified by CCK-8 assay, SA-β-Gal staining and EdU incorporation assay, etc. KEY FINDINGS: Knockdown (KD) of BAZ1A induced series of senescence-associated phenotypes in both cancer and normal cells. BAZ1A-KD caused the upregulated expression of SMAD3, which in turn activated the transcription of p21 coding gene CDKN1A and resulted in senescence-associated phenotypes in human cancer cells (A549 and U2OS). SIGNIFICANCE Our results revealed chromatin remodeling modulator BAZ1A acting as a novel regulator of cellular senescence in both normal and cancer cells, indicating a new target for potential cancer treatment.
Collapse
Affiliation(s)
- Xueping Li
- Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Dong Ding
- Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jun Yao
- Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Bin Zhou
- Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ting Shen
- Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yun Qi
- The State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ting Ni
- Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Gang Wei
- Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai 200438, China.
| |
Collapse
|
21
|
D'Amico D, Mottis A, Potenza F, Sorrentino V, Li H, Romani M, Lemos V, Schoonjans K, Zamboni N, Knott G, Schneider BL, Auwerx J. The RNA-Binding Protein PUM2 Impairs Mitochondrial Dynamics and Mitophagy During Aging. Mol Cell 2019; 73:775-787.e10. [PMID: 30642763 DOI: 10.1016/j.molcel.2018.11.034] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/23/2018] [Accepted: 11/27/2018] [Indexed: 12/11/2022]
Abstract
Little information is available about how post-transcriptional mechanisms regulate the aging process. Here, we show that the RNA-binding protein Pumilio2 (PUM2), which is a translation repressor, is induced upon aging and acts as a negative regulator of lifespan and mitochondrial homeostasis. Multi-omics and cross-species analyses of PUM2 function show that it inhibits the translation of the mRNA encoding for the mitochondrial fission factor (Mff), thereby impairing mitochondrial fission and mitophagy. This mechanism is conserved in C. elegans by the PUM2 ortholog PUF-8. puf-8 knock-down in old nematodes and Pum2 CRISPR/Cas9-mediated knockout in the muscles of elderly mice enhances mitochondrial fission and mitophagy in both models, hence improving mitochondrial quality control and tissue homeostasis. Our data reveal how a PUM2-mediated layer of post-transcriptional regulation links altered Mff translation to mitochondrial dynamics and mitophagy, thereby mediating age-related mitochondrial dysfunctions.
Collapse
Affiliation(s)
- Davide D'Amico
- Laboratory for Integrative and Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Adrienne Mottis
- Laboratory for Integrative and Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Francesca Potenza
- Laboratory for Integrative and Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Vincenzo Sorrentino
- Laboratory for Integrative and Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Hao Li
- Laboratory for Integrative and Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Mario Romani
- Laboratory for Integrative and Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Vera Lemos
- Laboratory of Metabolic Signaling, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Kristina Schoonjans
- Laboratory of Metabolic Signaling, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Nicola Zamboni
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich (ETHZ), CH-8093, Zurich, Switzerland
| | - Graham Knott
- BioEM Facility, Faculty of Life Sciences Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Bernard L Schneider
- Brain Mind Insitute, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory for Integrative and Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
| |
Collapse
|
22
|
RNA Granules and Their Role in Neurodegenerative Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:195-245. [DOI: 10.1007/978-3-030-31434-7_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
23
|
Carrascoso I, Alcalde J, Tabas-Madrid D, Oliveros JC, Izquierdo JM. Transcriptome-wide analysis links the short-term expression of the b isoforms of TIA proteins to protective proteostasis-mediated cell quiescence response. PLoS One 2018; 13:e0208526. [PMID: 30533021 PMCID: PMC6289441 DOI: 10.1371/journal.pone.0208526] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/19/2018] [Indexed: 12/20/2022] Open
Abstract
Control of gene expression depends on genetics and environmental factors. The T-cell intracellular antigens T-cell intracellular antigen 1 (TIA1), TIA1-like/related protein (TIAL1/TIAR) and human antigen R (HuR/ELAVL1) are RNA-binding proteins that play crucial roles in regulating gene expression in both situations. This study used massive sequencing analysis to uncover molecular and functional mechanisms resulting from the short-time expression of the b isoforms of TIA1 and TIAR, and of HuR in HEK293 cells. Our gene profiling analysis identified several hundred differentially expressed genes (DEGs) and tens of alternative splicing events associated with TIA1b, TIARb and HuR overexpression. Gene ontology analysis revealed that the controlled expression of these proteins strongly influences the patterns of DEGs and RNA variants preferentially associated with development, reproduction, cell cycle, metabolism, autophagy and apoptosis. Mechanistically, TIA1b and TIARb isoforms display both common and differential effects on the regulation of gene expression, involving systematic perturbations of cell biosynthetic machineries (splicing and translation). The transcriptome outputs were validated using functional assays of the targeted cellular processes as well as expression analysis for selected genes. Collectively, our observations suggest that early TIA1b and TIARb expression operates to connect the regulatory crossroads to protective proteostasis responses associated with a survival quiescence phenotype.
Collapse
Affiliation(s)
- Isabel Carrascoso
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera, Madrid, Spain
| | - José Alcalde
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera, Madrid, Spain
| | - Daniel Tabas-Madrid
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, C/ Darwin, Madrid, Spain
| | - Juan Carlos Oliveros
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, C/ Darwin, Madrid, Spain
| | - José M. Izquierdo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC/UAM), C/ Nicolás Cabrera, Madrid, Spain
- * E-mail:
| |
Collapse
|
24
|
A Heterologous Cell Model for Studying the Role of T-Cell Intracellular Antigen 1 in Welander Distal Myopathy. Mol Cell Biol 2018; 39:MCB.00299-18. [PMID: 30348840 DOI: 10.1128/mcb.00299-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/09/2018] [Indexed: 11/20/2022] Open
Abstract
Welander distal myopathy (WDM) is a muscle dystrophy characterized by adult-onset distal muscle weakness, prevalently impacting the distal long extensors of the hands and feet. WDM is an autosomal dominant disorder caused by a missense mutation (c.1362G>A; p.E384K) in the TIA1 (T-cell intracellular antigen 1) gene, which encodes an RNA-binding protein basically required for the posttranscriptional regulation of RNAs. We have developed a heterologous cell model of WDM to study the molecular and cellular events associated with mutated TIA1 expression. Specifically, we analyzed how this mutation affects three regulatory functions mediated by TIA1: (i) control of alternative SMN2 (survival motor neuron 2) splicing; (ii) formation, assembly, and disassembly of stress granules; and (iii) mitochondrial dynamics and its consequences for mitophagy, autophagy, and apoptosis. Our results show that whereas WDM-associated TIA1 expression had only a mild effect on SMN2 splicing, it led to suboptimal adaptation to environmental stress, with exacerbated stress granule formation that was accompanied by mitochondrial dysfunction and autophagy. Overall, our observations indicate that some aspects of the cell phenotype seen in muscle of patients with WDM can be recapitulated by ectopic expression of WDM-TIA1 in embryonic kidney cells, highlighting the potential of this model to investigate the pathogenesis of this degenerative disease and possible therapeutics.
Collapse
|
25
|
Masuda K, Kuwano Y. Diverse roles of RNA-binding proteins in cancer traits and their implications in gastrointestinal cancers. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1520. [PMID: 30479000 DOI: 10.1002/wrna.1520] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023]
Abstract
Gene expression patterns in cancer cells are strongly influenced by posttranscriptional mechanisms. RNA-binding proteins (RBPs) play key roles in posttranscriptional gene regulation; they can interact with target mRNAs in a sequence- and structure-dependent manner, and determine cellular behavior by manipulating the processing of these mRNAs. Numerous RBPs are aberrantly deregulated in many human cancers and hence, affect the functioning of mRNAs that encode proteins, implicated in carcinogenesis. Here, we summarize the key roles of RBPs in posttranscriptional gene regulation, describe RBPs disrupted in cancer, and lastly focus on RBPs that are responsible for implementing cancer traits in the digestive tract. These evidences may reveal a potential link between changes in expression/function of RBPs and malignant transformation, and a framework for new insights and potential therapeutic applications. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
Collapse
Affiliation(s)
- Kiyoshi Masuda
- Kawasaki Medical School at Kurashiki-City, Okayama, Japan
| | - Yuki Kuwano
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School at Tokushima-City, Tokushima, Japan
| |
Collapse
|
26
|
Gong Q, Stump MR, Zhou Z. Regulation of Kv11.1 potassium channel C-terminal isoform expression by the RNA-binding proteins HuR and HuD. J Biol Chem 2018; 293:19624-19632. [PMID: 30377250 DOI: 10.1074/jbc.ra118.003720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 10/17/2018] [Indexed: 12/19/2022] Open
Abstract
The potassium voltage-gated channel subfamily H member 2 (KCNH2) gene encodes the Kv11.1 potassium channel, which conducts the rapidly activating delayed rectifier current in the heart. KCNH2 pre-mRNA undergoes alternative polyadenylation and forms a functional, full-length Kv11.1a isoform if exon 15 is polyadenylated or a nonfunctional, C-terminally truncated Kv11.1a-USO isoform if intron 9 is polyadenylated. The molecular mechanisms that regulate Kv11.1 isoform expression are poorly understood. In this study, using HEK293 cells and reporter gene expression, pulldown assays, and RNase protection assays, we identified the RNA-binding proteins Hu antigen R (HuR) and Hu antigen D (HuD) as regulators of Kv11.1 isoform expression. We show that HuR and HuD inhibit activity at the intron 9 polyadenylation site. When co-expressed with the KCNH2 gene, HuR and HuD increased levels of the Kv11.1a isoform and decreased the Kv11.1a-USO isoform in the RNase protection assays and immunoblot analyses. In patch clamp experiments, HuR and HuD significantly increased the Kv11.1 current. siRNA-mediated knockdown of HuR protein decreased levels of the Kv11.1a isoform and increased those of the Kv11.1a-USO isoform. Our findings suggest that the relative expression levels of Kv11.1 C-terminal isoforms are regulated by the RNA-binding HuR and HuD proteins.
Collapse
Affiliation(s)
- Qiuming Gong
- From the Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon 97239 and
| | - Matthew R Stump
- Department of Biology, George Fox University, Newberg, Oregon 97132
| | - Zhengfeng Zhou
- From the Knight Cardiovascular Institute, Oregon Health & Science University, Portland, Oregon 97239 and
| |
Collapse
|
27
|
Herman AB, Autieri MV. Cardiovascular disease, inflammation, and mRNA stability. Aging (Albany NY) 2018; 10:3046-3047. [PMID: 30365397 PMCID: PMC6286849 DOI: 10.18632/aging.101619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/25/2018] [Indexed: 12/05/2022]
Affiliation(s)
- Allison B. Herman
- Department of Physiology, Independence Blue Cross Cardiovascular Research Center, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Michael V. Autieri
- Department of Physiology, Independence Blue Cross Cardiovascular Research Center, Temple University School of Medicine, Philadelphia, PA 19140, USA
| |
Collapse
|
28
|
Kim C, Kang D, Lee EK, Lee JS. Long Noncoding RNAs and RNA-Binding Proteins in Oxidative Stress, Cellular Senescence, and Age-Related Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:2062384. [PMID: 28811863 PMCID: PMC5547732 DOI: 10.1155/2017/2062384] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/27/2017] [Accepted: 06/06/2017] [Indexed: 12/12/2022]
Abstract
Cellular senescence is a complex biological process that leads to irreversible cell-cycle arrest. Various extrinsic and intrinsic insults are associated with the onset of cellular senescence and frequently accompany genomic or epigenomic alterations. Cellular senescence is believed to contribute to tumor suppression, immune response, and tissue repair as well as aging and age-related diseases. Long noncoding RNAs (lncRNAs) are >200 nucleotides long, poorly conserved, and transcribed in a manner similar to that of mRNAs. They are tightly regulated during various cellular and physiological processes. Although many lncRNAs and their functional roles are still undescribed, the importance of lncRNAs in a variety of biological processes is widely recognized. RNA-binding proteins (RBPs) have a pivotal role in posttranscriptional regulation as well as in mRNA transport, storage, turnover, and translation. RBPs interact with mRNAs, other RBPs, and noncoding RNAs (ncRNAs) including lncRNAs, and they are involved in the regulation of a broad spectrum of cellular processes. Like other cell fate regulators, lncRNAs and RBPs, separately or cooperatively, are implicated in initiation and maintenance of cellular senescence, aging, and age-related diseases. Here, we review the current understanding of both lncRNAs and RBPs and their association with oxidative stress, senescence, and age-related diseases.
Collapse
Affiliation(s)
- Chongtae Kim
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, Republic of Korea
| | - Donghee Kang
- Department of Molecular Medicine and Hypoxia-Related Disease Research Center, Inha University College of Medicine, Incheon 22212, Republic of Korea
| | - Eun Kyung Lee
- Department of Biochemistry, The Catholic University of Korea College of Medicine, Seoul 06591, Republic of Korea
| | - Jae-Seon Lee
- Department of Molecular Medicine and Hypoxia-Related Disease Research Center, Inha University College of Medicine, Incheon 22212, Republic of Korea
| |
Collapse
|
29
|
Ghassemi F, Madadgar O, Roohvand F, Rasekhian M, Etemadzadeh MH, Boroujeni GRN, Langroudi AG, Azadmanesh K. Translational efficiency of BVDV IRES and EMCV IRES for T7 RNA polymerase driven cytoplasmic expression in mammalian cell lines. Mol Biol 2017. [DOI: 10.1134/s002689331702011x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
30
|
Marchese D, de Groot NS, Lorenzo Gotor N, Livi CM, Tartaglia GG. Advances in the characterization of RNA-binding proteins. WILEY INTERDISCIPLINARY REVIEWS. RNA 2016; 7:793-810. [PMID: 27503141 PMCID: PMC5113702 DOI: 10.1002/wrna.1378] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/14/2016] [Accepted: 06/23/2016] [Indexed: 12/14/2022]
Abstract
From transcription, to transport, storage, and translation, RNA depends on association with different RNA-binding proteins (RBPs). Methods based on next-generation sequencing and protein mass-spectrometry have started to unveil genome-wide interactions of RBPs but many aspects still remain out of sight. How many of the binding sites identified in high-throughput screenings are functional? A number of computational methods have been developed to analyze experimental data and to obtain insights into the specificity of protein-RNA interactions. How can theoretical models be exploited to identify RBPs? In addition to oligomeric complexes, protein and RNA molecules can associate into granular assemblies whose physical properties are still poorly understood. What protein features promote granule formation and what effects do these assemblies have on cell function? Here, we describe the newest in silico, in vitro, and in vivo advances in the field of protein-RNA interactions. We also present the challenges that experimental and computational approaches will have to face in future studies. WIREs RNA 2016, 7:793-810. doi: 10.1002/wrna.1378 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Domenica Marchese
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Natalia Sanchez de Groot
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Nieves Lorenzo Gotor
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carmen Maria Livi
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- IFOM Foundation, FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | - Gian G Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| |
Collapse
|
31
|
Abstract
T-cell intracellular antigen 1 (TIA1) and TIA1-related/like protein (TIAR/TIAL1) are 2 proteins discovered in 1991 as components of cytotoxic T lymphocyte granules. They act in the nucleus as regulators of transcription and pre-mRNA splicing. In the cytoplasm, TIA1 and TIAR regulate and/or modulate the location, stability and/or translation of mRNAs. As knowledge of the different genes regulated by these proteins and the cellular/biological programs in which they are involved increases, it is evident that these antigens are key players in human physiology and pathology. This review will discuss the latest developments in the field, with physiopathological relevance, that point to novel roles for these regulators in the molecular and cell biology of higher eukaryotes.
Collapse
Affiliation(s)
- Carmen Sánchez-Jiménez
- a Centro de Biología Molecular Severo Ochoa; Consejo Superior de Investigaciones Científicas; Universidad Autónoma de Madrid (CSIC/UAM); C/Nicolás Cabrera 1 ; Madrid , Spain
| | | |
Collapse
|
32
|
Cascajo MV, Abdelmohsen K, Noh JH, Fernández-Ayala DJM, Willers IM, Brea G, López-Lluch G, Valenzuela-Villatoro M, Cuezva JM, Gorospe M, Siendones E, Navas P. RNA-binding proteins regulate cell respiration and coenzyme Q biosynthesis by post-transcriptional regulation of COQ7. RNA Biol 2015; 13:622-34. [PMID: 26690054 PMCID: PMC7609068 DOI: 10.1080/15476286.2015.1119366] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Coenzyme Q (CoQ) is a key component of the mitochondrial respiratory chain carrying electrons from complexes I and II to complex III and it is an intrinsic component of the respirasome. CoQ concentration is highly regulated in cells in order to adapt the metabolism of the cell to challenges of nutrient availability and stress stimuli. At least 10 proteins have been shown to be required for CoQ biosynthesis in a multi-peptide complex and COQ7 is a central regulatory factor of this pathway. We found that the first 765 bp of the 3′-untranslated region (UTR) of COQ7 mRNA contains cis-acting elements of interaction with RNA-binding proteins (RBPs) HuR and hnRNP C1/C2. Binding of hnRNP C1/C2 to COQ7 mRNA was found to require the presence of HuR, and hnRNP C1/C2 silencing appeared to stabilize COQ7 mRNA modestly. By contrast, lowering HuR levels by silencing or depriving cells of serum destabilized and reduced the half-life of COQ7 mRNA, thereby reducing COQ7 protein and CoQ biosynthesis rate. Accordingly, HuR knockdown decreased oxygen consumption rate and mitochondrial production of ATP, and increased lactate levels. Taken together, our results indicate that a reduction in COQ7 mRNA levels by HuR depletion causes mitochondrial dysfunction and a switch toward an enhanced aerobic glycolysis, the characteristic phenotype exhibited by primary deficiency of CoQ10. Thus HuR contributes to efficient oxidative phosphorylation by regulating of CoQ10 biosynthesis.
Collapse
Affiliation(s)
- María V Cascajo
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| | - Kotb Abdelmohsen
- b Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH , Baltimore , Maryland , USA
| | - Ji Heon Noh
- b Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH , Baltimore , Maryland , USA
| | - Daniel J M Fernández-Ayala
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| | - Imke M Willers
- c Departamento de Biología Molecular , Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM) and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Madrid , Spain
| | - Gloria Brea
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| | - Guillermo López-Lluch
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| | - Marina Valenzuela-Villatoro
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| | - José M Cuezva
- c Departamento de Biología Molecular , Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid (CSIC-UAM) and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Madrid , Spain
| | - Myriam Gorospe
- b Laboratory of Genetics, National Institute on Aging-Intramural Research Program, NIH , Baltimore , Maryland , USA
| | - Emilio Siendones
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| | - Plácido Navas
- a Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII , Sevilla , Spain
| |
Collapse
|
33
|
Protein synthesis as an integral quality control mechanism during ageing. Ageing Res Rev 2015; 23:75-89. [PMID: 25555680 DOI: 10.1016/j.arr.2014.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 12/18/2014] [Accepted: 12/22/2014] [Indexed: 01/17/2023]
Abstract
Ageing is manifested as functional and structural deterioration that affects cell and tissue physiology. mRNA translation is a central cellular process, supplying cells with newly synthesized proteins. Accumulating evidence suggests that alterations in protein synthesis are not merely a corollary but rather a critical factor for the progression of ageing. Here, we survey protein synthesis regulatory mechanisms and focus on the pre-translational regulation of the process exerted by non-coding RNA species, RNA binding proteins and alterations of intrinsic RNA properties. In addition, we discuss the tight relationship between mRNA translation and two central pathways that modulate ageing, namely the insulin/IGF-1 and TOR signalling cascades. A thorough understanding of the complex interplay between protein synthesis regulation and ageing will provide critical insights into the pathogenesis of age-related disorders, associated with impaired proteostasis and protein quality control.
Collapse
|
34
|
Kim J, Kim KM, Noh JH, Yoon JH, Abdelmohsen K, Gorospe M. Long noncoding RNAs in diseases of aging. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:209-21. [PMID: 26141605 DOI: 10.1016/j.bbagrm.2015.06.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/13/2015] [Accepted: 06/24/2015] [Indexed: 12/22/2022]
Abstract
Aging is a process during which progressive deteriorating of cells, tissues, and organs over time lead to loss of function, disease, and death. Towards the goal of extending human health span, there is escalating interest in understanding the mechanisms that govern aging-associated pathologies. Adequate regulation of expression of coding and noncoding genes is critical for maintaining organism homeostasis and preventing disease processes. Long noncoding RNAs (lncRNAs) are increasingly recognized as key regulators of gene expression at all levels--transcriptional, post-transcriptional and post-translational. In this review, we discuss our emerging understanding of lncRNAs implicated in aging illnesses. We focus on diseases arising from age-driven impairment in energy metabolism (obesity, diabetes), the declining capacity to respond homeostatically to proliferative and damaging stimuli (cancer, immune dysfunction), and neurodegeneration. We identify the lncRNAs involved in these ailments and discuss the rising interest in lncRNAs as diagnostic and therapeutic targets to ameliorate age-associated pathologies and prolong health. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
Collapse
Affiliation(s)
- Jiyoung Kim
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kyoung Mi Kim
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ji Heon Noh
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Je-Hyun Yoon
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
| |
Collapse
|
35
|
Brennan-Laun SE, Li XL, Ezelle HJ, Venkataraman T, Blackshear PJ, Wilson GM, Hassel BA. RNase L attenuates mitogen-stimulated gene expression via transcriptional and post-transcriptional mechanisms to limit the proliferative response. J Biol Chem 2014; 289:33629-43. [PMID: 25301952 DOI: 10.1074/jbc.m114.589556] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cellular response to mitogens is tightly regulated via transcriptional and post-transcriptional mechanisms to rapidly induce genes that promote proliferation and efficiently attenuate their expression to prevent malignant growth. RNase L is an endoribonuclease that mediates diverse antiproliferative activities, and tristetraprolin (TTP) is a mitogen-induced RNA-binding protein that directs the decay of proliferation-stimulatory mRNAs. In light of their roles as endogenous proliferative constraints, we examined the mechanisms and functional interactions of RNase L and TTP to attenuate a mitogenic response. Mitogen stimulation of RNase L-deficient cells significantly increased TTP transcription and the induction of other mitogen-induced mRNAs. This regulation corresponded with elevated expression of serum-response factor (SRF), a master regulator of mitogen-induced transcription. RNase L destabilized the SRF transcript and formed a complex with SRF mRNA in cells providing a mechanism by which RNase L down-regulates SRF-induced genes. TTP and RNase L proteins interacted in cells suggesting that RNase L is directed to cleave TTP-bound RNAs as a mechanism of substrate specificity. Consistent with their concerted function in RNA turnover, the absence of either RNase L or TTP stabilized SRF mRNA, and a subset of established TTP targets was also regulated by RNase L. RNase L deficiency enhanced mitogen-induced proliferation demonstrating its functional role in limiting the mitogenic response. Our findings support a model of feedback regulation in which RNase L and TTP target SRF mRNA and SRF-induced transcripts. Accordingly, meta-analysis revealed an enrichment of RNase L and TTP targets among SRF-regulated genes suggesting that the RNase L/TTP axis represents a viable target to inhibit SRF-driven proliferation in neoplastic diseases.
Collapse
Affiliation(s)
- Sarah E Brennan-Laun
- From the Marlene and Stewart Greenebaum Cancer Center, Departments of Microbiology and Immunology and
| | - Xiao-Ling Li
- the Genetics Branch, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Heather J Ezelle
- From the Marlene and Stewart Greenebaum Cancer Center, Departments of Microbiology and Immunology and the Research Services, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland 21201, and
| | | | - Perry J Blackshear
- the Laboratory of Signal Transduction, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Gerald M Wilson
- From the Marlene and Stewart Greenebaum Cancer Center, Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Bret A Hassel
- From the Marlene and Stewart Greenebaum Cancer Center, Departments of Microbiology and Immunology and the Research Services, Baltimore Veterans Affairs Medical Center, Baltimore, Maryland 21201, and
| |
Collapse
|
36
|
Mercken EM, Majounie E, Ding J, Guo R, Kim J, Bernier M, Mattison J, Cookson MR, Gorospe M, de Cabo R, Abdelmohsen K. Age-associated miRNA alterations in skeletal muscle from rhesus monkeys reversed by caloric restriction. Aging (Albany NY) 2014; 5:692-703. [PMID: 24036467 PMCID: PMC3808701 DOI: 10.18632/aging.100598] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The levels of microRNAs (miRNAs) are altered under different conditions such as cancer, senescence, and aging. Here, we have identified differentially expressed miRNAs in skeletal muscle from young and old rhesus monkeys using RNA sequencing. In old muscle, several miRNAs were upregulated, including miR-451, miR-144, miR-18a and miR-15a, while a few miRNAs were downregulated, including miR-181a and miR-181b. A number of novel miRNAs were also identified, particularly in old muscle. We also examined the impact of caloric restriction (CR) on miRNA abundance by reverse transcription (RT) followed by real-time, quantitative (q)PCR analysis and found that CR rescued the levels of miR-181b and chr1:205580546, and also dampened the age-induced increase in miR-451 and miR-144 levels. Our results reveal that there are changes in expression of known and novel miRNAs with skeletal muscle aging and that CR may reverse some of these changes to a younger phenotype.
Collapse
Affiliation(s)
- Evi M Mercken
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Ball CB, Rodriguez KF, Stumpo DJ, Ribeiro-Neto F, Korach KS, Blackshear PJ, Birnbaumer L, Ramos SBV. The RNA-binding protein, ZFP36L2, influences ovulation and oocyte maturation. PLoS One 2014; 9:e97324. [PMID: 24830504 PMCID: PMC4022657 DOI: 10.1371/journal.pone.0097324] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/17/2014] [Indexed: 02/01/2023] Open
Abstract
ZFP36L2 protein destabilizes AU-rich element-containing transcripts and has been implicated in female fertility. In the C57BL/6NTac mouse, a mutation in Zfp36l2 that results in the decreased expression of a form of ZFP36L2 in which the 29 N-terminal amino acid residues have been deleted, ΔN-ZFP36L2, leads to fertilized eggs that arrest at the two-cell stage. Interestingly, homozygous ΔN-Zfp36l2 females in the C57BL/6NTac strain release 40% fewer eggs than the WT littermates (Ramos et al., 2004), suggesting an additional defect in ovulation and/or oocyte maturation. Curiously, the same ΔN-Zfp36l2 mutation into the SV129 strain resulted in anovulation, prompting us to investigate a potential problem in ovulation and oocyte maturation. Remarkably, only 20% of ΔN-Zfp36l2 oocytes in the 129S6/SvEvTac strain matured ex vivo, suggesting a defect on the oocyte meiotic maturation process. Treatment of ΔN-Zfp36l2 oocytes with a PKA inhibitor partially rescued the meiotic arrested oocytes. Furthermore, cAMP levels were increased in ΔN-Zfp36l2 oocytes, linking the cAMP/PKA pathway and ΔN-Zfp36l2 with meiotic arrest. Since ovulation and oocyte maturation are both triggered by LHR signaling, the downstream pathway was investigated. Adenylyl cyclase activity was increased in ΔN-Zfp36l2 ovaries only upon LH stimulation. Moreover, we discovered that ZFP36L2 interacts with the 3′UTR of LHR mRNA and that decreased expression levels of Zfp36l2 correlates with higher levels of LHR mRNA in synchronized ovaries. Furthermore, overexpression of ZFP36L2 decreases the endogenous expression of LHR mRNA in a cell line. Therefore, we propose that lack of the physiological down regulation of LHR mRNA levels by ZFP36L2 in the ovaries is associated with anovulation and oocyte meiotic arrest.
Collapse
Affiliation(s)
- Christopher B. Ball
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Karina F. Rodriguez
- Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Deborah J. Stumpo
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Fernando Ribeiro-Neto
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Kenneth S. Korach
- Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Perry J. Blackshear
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
- Medicine and Biochemistry Departments, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Lutz Birnbaumer
- Laboratory of Neurobiology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Silvia B. V. Ramos
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
- * E-mail:
| |
Collapse
|
38
|
Moore AE, Chenette DM, Larkin LC, Schneider RJ. Physiological networks and disease functions of RNA-binding protein AUF1. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:549-64. [PMID: 24687816 DOI: 10.1002/wrna.1230] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/20/2014] [Accepted: 02/24/2014] [Indexed: 11/09/2022]
Abstract
Regulated messenger RNA (mRNA) decay is an essential mechanism that governs proper control of gene expression. In fact, many of the most physiologically potent proteins are encoded by short-lived mRNAs, many of which contain AU-rich elements (AREs) in their 3'-untranslated region (3'-UTR). AREs target mRNAs for post-transcriptional regulation, generally rapid decay, but also stabilization and translation inhibition. AREs control mRNA turnover and translation activities through association with trans-acting RNA-binding proteins that display high affinity for these AU-rich regulatory elements. AU-rich element RNA-binding protein (AUF1), also known as heterogeneous nuclear ribonucleoprotein D (HNRNPD), is an extensively studied AU-rich binding protein (AUBP). AUF1 has been shown to regulate ARE-mRNA turnover, primarily functioning to promote rapid ARE-mRNA degradation. In certain cellular contexts, AUF1 has also been shown to regulate gene expression at the translational and even the transcriptional level. AUF1 comprises a family of four related protein isoforms derived from a common pre-mRNA by differential exon splicing. AUF1 isoforms have been shown to display multiple and distinct functions that include the ability to target ARE-mRNA stability or decay, and transcriptional activation of certain genes that is controlled by their differential subcellular locations, expression levels, and post-translational modifications. AUF1 has been implicated in controlling a variety of physiological functions through its ability to regulate the expression of numerous mRNAs containing 3'-UTR AREs, thereby coordinating functionally related pathways. This review highlights the physiological functions of AUF1-mediated regulation of mRNA and gene expression, and the consequences of deficient AUF1 levels in different physiological settings.
Collapse
Affiliation(s)
- Ashleigh E Moore
- Alexandria Center for Life Sciences, New York University School of Medicine, New York, NY, USA
| | | | | | | |
Collapse
|
39
|
Rasekhian M, Roohvand F, Teimoori-Toolabi L, Amini S, Azadmanesh K. Application of the 3'-noncoding region of poliovirus RNA for cell-based regulation of mRNA stability: implication for biotechnological applications. Biotechnol Appl Biochem 2014; 61:699-706. [PMID: 24612228 DOI: 10.1002/bab.1218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 02/12/2014] [Indexed: 11/08/2022]
Abstract
Enrichment of production yield of therapeutic proteins in mammalian cell cultures by modulation of the mRNA stability of the target protein to increase its in vivo half-life is a new strategy in biotechnological applications. The present article describes one of the most novel approaches to modulate mRNA stability by application of 3'-noncoding region (3'NCR) from RNA viral genome in the expression constructs. Our data indicated that although utilizing the 3'NCR sequence form poliovirus (PV-3'NCR) downstream of the target gene might generally stabilize the secondary structure of RNA, it influenced the mRNA stability (and thereby the amount of protein production) in a cell type and time-dependent manner, thus indicating a central role of mRNA-stabilizing binding sites/cellular factors in this process. Our data might be of interest to the biotechnology community to improve recombinant protein production in mammalian cell cultures and RNA-based therapy/vaccination approaches.
Collapse
Affiliation(s)
- Mahsa Rasekhian
- Virology Department, Pasteur Institute of Iran, Tehran, Iran
| | | | | | | | | |
Collapse
|
40
|
Pullmann R, Rabb H. HuR and other turnover- and translation-regulatory RNA-binding proteins: implications for the kidney. Am J Physiol Renal Physiol 2014; 306:F569-76. [PMID: 24431206 DOI: 10.1152/ajprenal.00270.2013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The posttranscriptional regulation of gene expression occurs through cis RNA regulatory elements by the action of trans factors, which are represented by noncoding RNAs (especially microRNAs) and turnover- and translation-regulatory (TTR) RNA-binding proteins (RBPs). These multifactorial proteins are a group of heterogeneous RBPs primarily implicated in controlling the decay and translation rates of target mRNAs. TTR-RBPs usually shuttle between cellular compartments (the nucleus and cytoplasm) in response to various stimuli and undergo posttranslational modifications such as phosphorylation or methylation to ensure their proper subcellular localization and function. TTR-RBPs are emerging as key regulators of a wide variety of genes influencing kidney physiology and pathology. This review summarizes the current knowledge of TTR-RBPs that influence renal metabolism. We will discuss the role of TTR-RBPs as regulators of kidney ischemia, fibrosis and matrix remodeling, angiogenesis, membrane transport, immunity, vascular tone, hypertension, and acid-base balance as well as anemia, bone mineral disease, and vascular calcification.
Collapse
|
41
|
Vanderweyde T, Youmans K, Liu-Yesucevitz L, Wolozin B. Role of stress granules and RNA-binding proteins in neurodegeneration: a mini-review. Gerontology 2013; 59:524-33. [PMID: 24008580 DOI: 10.1159/000354170] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 07/03/2013] [Indexed: 12/13/2022] Open
Abstract
The eukaryotic stress response involves translational suppression of non-housekeeping proteins and the sequestration of unnecessary mRNA transcripts into stress granules (SGs). This process is dependent on mRNA-binding proteins (RBPs) that interact with capped mRNA transcripts through RNA recognition motifs, and exhibit reversible aggregation through hydrophobic polyglycine domains, some of which are homologous to yeast prion proteins. The activity and aggregation of RBPs appears to be important in the context of unfolded protein diseases. The discovery that mutations in these RBPs can cause familial motoneuron diseases and familial dementias indicates the importance of these genes to neuronal degeneration. Some disorders linked to mutations in RBPs include: amyotrophic lateral sclerosis, frontotemporal dementia and spinal muscular atrophy. These RBPs also associate with pathological structures in other neurodegenerative diseases, including Huntington's chorea, Creutzfeldt-Jakob disease, and Alzheimer's disease. Interestingly, protein levels of RBPs change across the aging spectrum and may be linked to other age-related disorders, such as type 2 diabetes. The link between SG pathways and proteins linked to neurodegenerative diseases suggests a potential role for common pathways in both processes, such as those involved in translational control, and highlights potentially novel targets for therapeutic intervention in neurodegenerative diseases.
Collapse
Affiliation(s)
- Tara Vanderweyde
- Department of Pharmacology, Boston University School of Medicine, Boston, Mass., USA
| | | | | | | |
Collapse
|
42
|
Blech-Hermoni Y, Ladd AN. RNA binding proteins in the regulation of heart development. Int J Biochem Cell Biol 2013; 45:2467-78. [PMID: 23973289 DOI: 10.1016/j.biocel.2013.08.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/09/2013] [Accepted: 08/13/2013] [Indexed: 11/28/2022]
Abstract
In vivo, RNA molecules are constantly accompanied by RNA binding proteins (RBPs), which are intimately involved in every step of RNA biology, including transcription, editing, splicing, transport and localization, stability, and translation. RBPs therefore have opportunities to shape gene expression at multiple levels. This capacity is particularly important during development, when dynamic chemical and physical changes give rise to complex organs and tissues. This review discusses RBPs in the context of heart development. Since the targets and functions of most RBPs--in the heart and at large--are not fully understood, this review focuses on the expression and roles of RBPs that have been implicated in specific stages of heart development or developmental pathology. RBPs are involved in nearly every stage of cardiogenesis, including the formation, morphogenesis, and maturation of the heart. A fuller understanding of the roles and substrates of these proteins could ultimately provide attractive targets for the design of therapies for congenital heart defects, cardiovascular disease, or cardiac tissue repair.
Collapse
Affiliation(s)
- Yotam Blech-Hermoni
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Program in Cell Biology, Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | | |
Collapse
|
43
|
Chen YJ, Chang LS. Hydroquinone-induced miR-122 down-regulation elicits ADAM17 up-regulation, leading to increased soluble TNF-α production in human leukemia cells with expressed Bcr/Abl. Biochem Pharmacol 2013; 86:620-31. [PMID: 23791922 DOI: 10.1016/j.bcp.2013.06.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Revised: 06/12/2013] [Accepted: 06/12/2013] [Indexed: 01/10/2023]
Abstract
Studies on HQ-treated human leukemia K562 (Bcr/Abl-positive) cells were conducted to address the hydroquinone (HQ) mechanism that promotes soluble TNF-α (sTNF-α) production. HQ post-translationally down-regulated cell surface TNF-α expression increases the release of sTNF-α into K562 cell culture medium. Meanwhile, HQ increased ADAM17 mRNA stability, leading to ADAM17 up-regulation in HQ-treated cells. Knock-down of ADAM17 abrogated HQ-induced sTNF-α secretion. HQ-evoked miR-122 down-regulation was proven to promote ADAM17 mRNA stability and up-regulate ADAM17 expression. HQ-induced p38 MAPK and JNK activation were responsible for suppression of miR-122 promoter luciferase activity and miR-122 expression. Activation of p38 MAPK and JNK elicited phosphorylation of c-Jun, ATF-2 and c-Fos, and knock-down of c-Jun, ATF-2 and c-Fos restored miR-122 expression in HQ-treated cells. Chromatin immunoprecipitating and DNA affinity purification assay revealed c-Jun, ATF-2 and c-Fos binding to the miR-122 gene promoter region. Moreover, HQ-induced sTNF-α production in Bcr/Abl-positive leukemia cell lines KU812 and MEG-01 was also connected with miR-122 down-regulation and ADAM17 up-regulation, while HQ was unable to affect miR-122 and ADAM-17 expression on Bcr/Abl-negative leukemia U937 cells. Taken together, our data indicate that HQ induces down-regulation of miR-122 expression, leading to ADAM17 up-regulation and ADAM17-mediated TNF-α shedding. Consequently, HQ treatment increases the production of sTNF-α in leukemia cells with expressed Bcr/Abl.
Collapse
Affiliation(s)
- Ying-Jung Chen
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | | |
Collapse
|
44
|
Wang K, Zhang J, Liu J, Tian J, Wu Y, Wang X, Quan L, Xu H, Wang W, Liu H. Variations in the protein level of Omi/HtrA2 in the heart of aged rats may contribute to the increased susceptibility of cardiomyocytes to ischemia/reperfusion injury and cell death : Omi/HtrA2 and aged heart injury. AGE (DORDRECHT, NETHERLANDS) 2013; 35:733-746. [PMID: 22535253 PMCID: PMC3636415 DOI: 10.1007/s11357-012-9406-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 03/26/2012] [Indexed: 05/31/2023]
Abstract
Survival after acute myocardial infarction is decreased in elderly patients. The enhanced rates of apoptosis in the aging heart exacerbate myocardial ischemia/reperfusion (MI/R) injury. We have recently demonstrated that the X-linked inhibitor of apoptosis protein (XIAP), the most potent endogenous inhibitor of apoptosis, was decreased in aging rats' hearts. XIAP was balanced by two mitochondria proteins, Omi/HtrA2 and Smac/DIABLO. However, the implicative role of XIAP, Omi/HtrA2, and Smac/DIABLO to aging-related MI/R injury has not been previously investigated. In our study, male aging rats (20-24 months) or young adult rats (4-6 months) were subjected to 30 min of myocardial ischemia followed by reperfusion. MI/R-induced cardiac injury was enhanced in aging rats, as evidenced by aggravated cardiac dysfunction, enlarged infarct size, and increased myocardial apoptosis (TUNEL and caspase-3 activity). Then, the XIAP, Omi/HtrA2, and Smac/DIABLO protein and mRNA expression was detected. XIAP protein and mRNA expression was decreased in both aging hearts and aging hearts subjected to MI/R. Meanwhile, myocardial XIAP protein expression was correlated to cardiac function after MI/R. However, Omi/HtrA2, but not Smac/DIABLO, expression was increased in aging hearts. Moreover, the translocation of Omi/HtrA2 from mitochondria to cytosol was increased in both aging hearts and aging hearts subjected to MI/R. Treatment with ucf-101 (a novel and specific Omi/HtrA2 inhibitor) attenuated XIAP degradation and caspase-3 activity and exerted cardioprotective effects. Taken together, these results demonstrated that increased expression and leakage of Omi/HtrA2 enhanced MI/R injury in aging hearts via degrading XIAP and promoting myocardial apoptosis.
Collapse
MESH Headings
- Aging/genetics
- Aging/metabolism
- Aging/pathology
- Animals
- Apoptosis Regulatory Proteins
- Blotting, Western
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Death/genetics
- Disease Models, Animal
- Gene Expression Regulation
- High-Temperature Requirement A Serine Peptidase 2
- In Situ Nick-End Labeling
- Male
- Mitochondria, Heart/genetics
- Mitochondria, Heart/metabolism
- Mitochondria, Heart/pathology
- Mitochondrial Proteins/biosynthesis
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Myocardial Reperfusion Injury/genetics
- Myocardial Reperfusion Injury/metabolism
- Myocardial Reperfusion Injury/pathology
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Nerve Tissue Proteins/biosynthesis
- Nerve Tissue Proteins/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA-Binding Proteins/biosynthesis
- RNA-Binding Proteins/genetics
- Rats
- Rats, Sprague-Dawley
- Real-Time Polymerase Chain Reaction
- Serine Endopeptidases/biosynthesis
- Serine Endopeptidases/genetics
- Serine-Arginine Splicing Factors
- X-Linked Inhibitor of Apoptosis Protein/genetics
- X-Linked Inhibitor of Apoptosis Protein/metabolism
Collapse
Affiliation(s)
- Ke Wang
- />Department of Pathophysiology, School of Basic Medical Sciences, Capital Medical University, 10 Xitoutiao, You An Men, P.O. Box 907, Beijing, 100069 People’s Republic of China
| | - Jie Zhang
- />Department of Physiology, Shanxi Medical University, Taiyuan, Shanxi 030001 People’s Republic of China
| | - Jingyi Liu
- />Department of Physiology, Shanxi Medical University, Taiyuan, Shanxi 030001 People’s Republic of China
| | - Jue Tian
- />Department of Pathophysiology, Ningxia Medical University, Yinchuan, Ningxia 750004 People’s Republic of China
| | - Ye Wu
- />Department of Physiology, Shanxi Medical University, Taiyuan, Shanxi 030001 People’s Republic of China
| | - Xiaoliang Wang
- />Department of Physiology, Shanxi Medical University, Taiyuan, Shanxi 030001 People’s Republic of China
| | - Lin Quan
- />Department of Pathophysiology, School of Basic Medical Sciences, Capital Medical University, 10 Xitoutiao, You An Men, P.O. Box 907, Beijing, 100069 People’s Republic of China
| | - Haibo Xu
- />Department of Pathophysiology, School of Basic Medical Sciences, Capital Medical University, 10 Xitoutiao, You An Men, P.O. Box 907, Beijing, 100069 People’s Republic of China
| | - Wen Wang
- />Department of Pathophysiology, School of Basic Medical Sciences, Capital Medical University, 10 Xitoutiao, You An Men, P.O. Box 907, Beijing, 100069 People’s Republic of China
| | - Huirong Liu
- />Department of Pathophysiology, School of Basic Medical Sciences, Capital Medical University, 10 Xitoutiao, You An Men, P.O. Box 907, Beijing, 100069 People’s Republic of China
- />The Key Laboratory of Remodeling-related Cardiovascular Diseases, Capital Medical University, Ministry of Education, Beijing, 100069 People’s Republic of China
| |
Collapse
|
45
|
The impact of mRNA turnover and translation on age-related muscle loss. Ageing Res Rev 2012; 11:432-41. [PMID: 22687959 DOI: 10.1016/j.arr.2012.05.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 05/25/2012] [Accepted: 05/31/2012] [Indexed: 12/21/2022]
Abstract
The deterioration of skeletal muscle that develops slowly with age, termed sarcopenia, often leads to disability and mortality in the elderly population. As the proportion of elderly citizens continues to increase due to the dramatic rise in life expectancy, there are rising concerns about the healthcare cost and social burden of caring for geriatric patients. Thus, there is a growing need to understand the underlying mechanisms of sarcopenic muscle loss so that more efficacious therapies may be developed. Building evidence suggests that the onset of age-related muscle loss is linked to the age-related changes in gene expression that occur during sarcopenia. In recent work, the posttranscriptional regulation of gene expression by RNA-binding proteins (RBPs) and microRNA (miRNA) involved in the turnover and translation of mRNA were shown as key players believed to be involved in the induction of muscle wasting. Furthermore, posttranscriptional regulation may also be linked to the reduced ability of muscle satellite cells to contribute to muscle mass during ageing, a key contributing factor to sarcopenic progression. Here we highlight how the activation of pathways such as the p38 MAPK and the phosphoinositide 3-kinase (PI3K) pathways alter the ability of RBPs to regulate the expression of their target mRNAs encoding proteins involved in cell cycle (p21 and p16), as well as myogenesis (Pax7, myogenin and MyoD). Further investigation into the role of RBPs and miRNA during sarcopenia may provide new insights into the development and progression of this disorder, which may lead to the development of new treatment options for elderly patients suffering from sarcopenia.
Collapse
|
46
|
Masuda K, Kuwano Y, Nishida K, Rokutan K. General RBP expression in human tissues as a function of age. Ageing Res Rev 2012; 11:423-31. [PMID: 22326651 DOI: 10.1016/j.arr.2012.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/09/2012] [Accepted: 01/19/2012] [Indexed: 10/14/2022]
Abstract
Gene expression patterns vary dramatically in a tissue-specific and age-dependent manner. RNA-binding proteins that regulate mRNA turnover and/or translation (TTR-RBPs) critically affect the subsets of expressed proteins. Although many proteins implicated in age-related processes are encoded by mRNAs that are targets of TTR-RBPs, very little is known regarding the tissue- and age-dependent expression of TTR-RBPs in humans. Recent analysis of TTR-RBPs expression using human tissue microarray has provided us interesting insight into their possibly physiologic roles as a function of age. This analysis has also revealed striking discrepancies between the levels of TTR-RBPs in senescent human diploid fibroblasts (HDFs), widely used as an in vitro model of aging, and the levels of TTR-RBPs in tissues from individuals of advancing age. In this article, we will review our knowledge of human TTR-RBP expression in different tissues as a function of age.
Collapse
|
47
|
Ross CR, Brennan-Laun SE, Wilson GM. Tristetraprolin: roles in cancer and senescence. Ageing Res Rev 2012; 11:473-84. [PMID: 22387927 DOI: 10.1016/j.arr.2012.02.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 02/09/2012] [Accepted: 02/10/2012] [Indexed: 12/17/2022]
Abstract
Cancer and senescence are both complex transformative processes that dramatically alter many features of cell physiology and their interactions with surrounding tissues. Developing the wide range of cellular features characteristic of these conditions requires profound alterations in global gene expression patterns, which can be achieved by suppressing, activating, or uncoupling cellular gene regulatory pathways. Many genes associated with the initiation and development of tumors are regulated at the level of mRNA decay, frequently through the activity of AU-rich mRNA-destabilizing elements (AREs) located in their 3'-untranslated regions. As such, cellular factors that recognize and control the decay of ARE-containing mRNAs can influence tumorigenic or senescent phenotypes mediated by products of these transcripts. In this review, we discuss evidence showing how suppressed expression and/or activity of the ARE-binding protein tristetraprolin (TTP) can contribute to these processes. Next, we outline current findings linking TTP suppression to exacerbation of individual tumorigenic phenotypes, and the roles of specific TTP substrate mRNAs in mediating these effects. Finally, we survey potential mechanisms that cells may employ to suppress TTP expression in cancer, and propose potential diagnostic and therapeutic strategies that may exploit the relationship between TTP expression and tumor progression or senescence.
Collapse
Affiliation(s)
- Christina R Ross
- Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | | |
Collapse
|
48
|
Wang W. Regulatory RNA-binding proteins in senescence. Ageing Res Rev 2012; 11:485-90. [PMID: 22414963 DOI: 10.1016/j.arr.2012.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 02/08/2012] [Accepted: 02/08/2012] [Indexed: 11/18/2022]
Abstract
The expression of senescence-associated genes, which governs the progression and the maintenance of senescence, is regulated at multiple levels. Apart from the transcriptional mechanisms that control cellular senescence, studies over the past decade have revealed that post-transcriptional gene regulation, especially through changes in mRNA turnover and translation, critically influences protein expression patterns in the senescent cell. Among the post-transcriptional regulatory factors, RNA-binding proteins (RBPs) are particularly influential in the establishment of senescence-associated protein profiles. In this review, I discuss the current knowledge of the role of RBPs in cellular senescence and the molecular mechanisms that regulate their function.
Collapse
Affiliation(s)
- Wengong Wang
- Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 38 Xueyuan Road, Beijing 100191, PR China.
| |
Collapse
|
49
|
D'souza D, Lai RYJ, Shuen M, Hood DA. mRNA stability as a function of striated muscle oxidative capacity. Am J Physiol Regul Integr Comp Physiol 2012; 303:R408-17. [DOI: 10.1152/ajpregu.00085.2012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
A change in mRNA stability alters the abundance of mRNA available for translation and is emerging as a critical pathway influencing gene expression. Variations in the stability of functional and regulatory mitochondrial proteins may contribute to the divergent mitochondrial densities observed in striated muscle. Thus we hypothesized that the stability of mRNAs encoding for regulatory nuclear and mitochondrial transcription factors would be inversely proportional to muscle oxidative capacity and would be facilitated by the activity of RNA binding proteins (RBPs). The stability of mitochondrial transcription factor A (Tfam), peroxisome proliferator-activated receptor gamma coactivator 1α (PGC-1α), and nuclear respiratory factor 2α (NRF-2α) mRNA was assessed in striated muscles with distinct oxidative capacities using in vitro decay assays. All three mitochondrial regulators were rapidly degraded in cardiac and slow-twitch red (STR) muscle, resulting in a ∼60–65% lower ( P < 0.05) mRNA half-life ( t1/2) compared with fast-twitch white (FTW) fibers. This accelerated rate of Tfam mRNA decay was matched by a 2.5-fold increase in Tfam transcription in slow- compared with fast-twitch muscle ( P = 0.05). Protein expression of four unique RBPs [AU-rich binding factor 1 (AUF1), human antigen R (HuR), KH-homology splicing regulatory protein (KSRP), and CUG binding protein 1 (CUGBP1)] believed to modulate mRNA stability was elevated in cardiac and STR muscles ( P < 0.05) and was moderately associated with the decay of Tfam, PGC-1α, and NRF-2α mRNA. Variable rates of transcript degradation were apparent when comparing all transcripts within the same muscle type. Thus the distribution of RBPs appears to follow a fiber-type specific pattern and subsequently functions to alter the stability of specific mitochondrial regulators in a transcript- and tissue-specific fashion.
Collapse
Affiliation(s)
- Donna D'souza
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada; and Muscle Health Research Centre, York University, Toronto, Ontario, Canada
| | - Ruanne Y. J. Lai
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada; and Muscle Health Research Centre, York University, Toronto, Ontario, Canada
| | - Michael Shuen
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada; and Muscle Health Research Centre, York University, Toronto, Ontario, Canada
| | - David A. Hood
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada; and Muscle Health Research Centre, York University, Toronto, Ontario, Canada
| |
Collapse
|
50
|
Pont AR, Sadri N, Hsiao SJ, Smith S, Schneider RJ. mRNA decay factor AUF1 maintains normal aging, telomere maintenance, and suppression of senescence by activation of telomerase transcription. Mol Cell 2012; 47:5-15. [PMID: 22633954 DOI: 10.1016/j.molcel.2012.04.019] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 03/07/2012] [Accepted: 04/12/2012] [Indexed: 01/31/2023]
Abstract
Inflammation is associated with DNA damage, cellular senescence, and aging. Cessation of the inflammatory cytokine response is mediated in part through cytokine mRNA degradation facilitated by RNA-binding proteins, including AUF1. We report a major function of AUF1-it activates telomerase expression, suppresses cellular senescence, and maintains normal aging. AUF1-deficient mice undergo striking telomere erosion, markedly increased DNA damage responses at telomere ends, pronounced cellular senescence, and rapid premature aging that increases with successive generations, which can be rescued in AUF1 knockout mice and their cultured cells by resupplying AUF1 expression. AUF1 binds and strongly activates the transcription promoter for telomerase catalytic subunit Tert. In addition to directing inflammatory cytokine mRNA decay, AUF1 destabilizes cell-cycle checkpoint mRNAs, preventing cellular senescence. Thus, a single gene, AUF1, links maintenance of telomere length and normal aging to attenuation of inflammatory cytokine expression and inhibition of cellular senescence.
Collapse
Affiliation(s)
- Adam R Pont
- Department of Microbiology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | | | | | | | | |
Collapse
|