1
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Moreira-Gomes T, Nóbrega C. From the disruption of RNA metabolism to the targeting of RNA-binding proteins: The case of polyglutamine spinocerebellar ataxias. J Neurochem 2024; 168:1442-1459. [PMID: 37990934 DOI: 10.1111/jnc.16010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/04/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023]
Abstract
Polyglutamine spinocerebellar ataxias (PolyQ SCAs) represent a group of monogenetic diseases in which the expanded polyglutamine repeats give rise to a mutated protein. The abnormally expanded polyglutamine protein produces aggregates and toxic species, causing neuronal dysfunction and neuronal death. The main symptoms of these disorders include progressive ataxia, motor dysfunction, oculomotor impairment, and swallowing problems. Nowadays, the current treatments are restricted to symptomatic alleviation, and no existing therapeutic strategies can reduce or stop the disease progression. Even though the origin of these disorders has been associated with polyglutamine-induced toxicity, RNA toxicity has recently gained relevance in polyQ SCAs molecular pathogenesis. Therefore, the research's focus on RNA metabolism has been increasing, especially on RNA-binding proteins (RBPs). The present review summarizes RNA metabolism, exposing the different processes and the main RBPs involved. We also explore the mechanisms by which RBPs are dysregulated in PolyQ SCAs. Finally, possible therapies targeting the RNA metabolism are presented as strategies to reverse neuropathological anomalies and mitigate physical symptoms.
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Affiliation(s)
- Tiago Moreira-Gomes
- ABC-RI, Algarve Biomedical Center Research Institute, Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, Faro, Portugal
- Doctoral Program in Biomedical Sciences, Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, Faro, Portugal
| | - Clévio Nóbrega
- ABC-RI, Algarve Biomedical Center Research Institute, Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, Faro, Portugal
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2
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Zhang H, Wang X. The Role of Protein Quantity Control in Polyglutamine Spinocerebellar Ataxias. CEREBELLUM (LONDON, ENGLAND) 2024:10.1007/s12311-024-01722-w. [PMID: 39052145 DOI: 10.1007/s12311-024-01722-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/15/2024] [Indexed: 07/27/2024]
Abstract
Polyglutamine spinocerebellar ataxias (polyQ SCAs) represent the most prevalent subtype of SCAs. The primary pathogenic mechanism is believed to be the gain-of-function neurotoxicity of polyQ proteins. Strategies such as enhancing the degradation or inhibiting the accumulation of these mutant proteins are pivotal for reducing their toxicity and slowing disease progression. The protein quality control (PQC) system, comprising primarily molecular chaperones and the ubiquitin‒proteasome system (UPS), is essential for maintaining protein homeostasis by regulating protein folding, trafficking, and degradation. Notably, polyQ proteins can disrupt the PQC system by sequestering its critical components and impairing its proteasomal functions. Therefore, restoring the PQC system through genetic or pharmacological interventions could potentially offer beneficial effects and alleviate the symptoms of the disease. Here, we will provide a review on the distribution, expression, and genetic or pharmacological intervention of protein quality control system in cellular or animal models of PolyQ SCAs.
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Affiliation(s)
- Hongfeng Zhang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, Department of Neurology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, 361005, Fujian, China.
- Shenzhen Research Institute of Xiamen University, Shenzhen, 518057, Guangdong, China.
| | - Xin Wang
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Neurodegenerative Disease and Aging Research, Institute of Neuroscience, Department of Neurology, School of Medicine, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen, 361005, Fujian, China.
- Shenzhen Research Institute of Xiamen University, Shenzhen, 518057, Guangdong, China.
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3
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Haugen RJ, Barnier C, Elrod ND, Luo H, Jensen MK, Ji P, Smibert CA, Lipshitz HD, Wagner EJ, Freddolino PL, Goldstrohm AC. Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex. RNA (NEW YORK, N.Y.) 2024; 30:866-890. [PMID: 38627019 PMCID: PMC11182014 DOI: 10.1261/rna.079813.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/04/2024] [Indexed: 05/07/2024]
Abstract
The sequence-specific RNA-binding protein Pumilio (Pum) controls Drosophila development; however, the network of mRNAs that it regulates remains incompletely characterized. In this study, we use knockdown and knockout approaches coupled with RNA-seq to measure the impact of Pum on the transcriptome of Drosophila cells in culture. We also use an improved RNA coimmunoprecipitation method to identify Pum-bound mRNAs in Drosophila embryos. Integration of these data sets with the locations of Pum-binding motifs across the transcriptome reveals novel direct Pum target genes involved in neural, muscle, wing, and germ cell development and in cellular proliferation. These genes include components of Wnt, TGF-β, MAPK/ERK, and Notch signaling pathways, DNA replication, and lipid metabolism. We identify the mRNAs regulated by the CCR4-NOT deadenylase complex, a key factor in Pum-mediated repression, and observe concordant regulation of Pum:CCR4-NOT target mRNAs. Computational modeling reveals that Pum binding, binding site number, clustering, and sequence context are important determinants of regulation. In contrast, we show that the responses of direct mRNA targets to Pum-mediated repression are not influenced by the content of optimal synonymous codons. Moreover, contrary to a prevailing model, we do not detect a role for CCR4-NOT in the degradation of mRNAs with low codon optimality. Together, the results of this work provide new insights into the Pum regulatory network and mechanisms and the parameters that influence the efficacy of Pum-mediated regulation.
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Affiliation(s)
- Rebecca J Haugen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Catherine Barnier
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Nathan D Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77550, USA
| | - Hua Luo
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Madeline K Jensen
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Ping Ji
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Craig A Smibert
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Howard D Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Eric J Wagner
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - P Lydia Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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4
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Cui ZT, Mao ZT, Yang R, Li JJ, Jia SS, Zhao JL, Zhong FT, Yu P, Dong M. Spinocerebellar ataxias: from pathogenesis to recent therapeutic advances. Front Neurosci 2024; 18:1422442. [PMID: 38894941 PMCID: PMC11185097 DOI: 10.3389/fnins.2024.1422442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 05/08/2024] [Indexed: 06/21/2024] Open
Abstract
Spinocerebellar ataxia is a phenotypically and genetically heterogeneous group of autosomal dominant-inherited degenerative disorders. The gene mutation spectrum includes dynamic expansions, point mutations, duplications, insertions, and deletions of varying lengths. Dynamic expansion is the most common form of mutation. Mutations often result in indistinguishable clinical phenotypes, thus requiring validation using multiple genetic testing techniques. Depending on the type of mutation, the pathogenesis may involve proteotoxicity, RNA toxicity, or protein loss-of-function. All of which may disrupt a range of cellular processes, such as impaired protein quality control pathways, ion channel dysfunction, mitochondrial dysfunction, transcriptional dysregulation, DNA damage, loss of nuclear integrity, and ultimately, impairment of neuronal function and integrity which causes diseases. Many disease-modifying therapies, such as gene editing technology, RNA interference, antisense oligonucleotides, stem cell technology, and pharmacological therapies are currently under clinical trials. However, the development of curative approaches for genetic diseases remains a global challenge, beset by technical, ethical, and other challenges. Therefore, the study of the pathogenesis of spinocerebellar ataxia is of great importance for the sustained development of disease-modifying molecular therapies.
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Affiliation(s)
- Zi-Ting Cui
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Zong-Tao Mao
- Department of Plastic and Reconstructive Surgery, The First Hospital of Jilin University, Changchun, China
| | - Rong Yang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Jia-Jia Li
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Shan-Shan Jia
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Jian-Li Zhao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Fang-Tian Zhong
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
| | - Peng Yu
- Department of Ophthalmology, the Second Hospital of Jilin University, Changchun, China
| | - Ming Dong
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun, China
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5
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Carrick BH, Crittenden SL, Chen F, Linsley M, Woodworth J, Kroll-Conner P, Ferdous AS, Keleş S, Wickens M, Kimble J. PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans. Dev Cell 2024; 59:661-675.e7. [PMID: 38290520 PMCID: PMC11253550 DOI: 10.1016/j.devcel.2024.01.005] [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: 07/31/2023] [Revised: 11/10/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Protein-RNA regulatory networks underpin much of biology. C. elegans FBF-2, a PUF-RNA-binding protein, binds over 1,000 RNAs to govern stem cells and differentiation. FBF-2 interacts with multiple protein partners via a key tyrosine, Y479. Here, we investigate the in vivo significance of partnerships using a Y479A mutant. Occupancy of the Y479A mutant protein increases or decreases at specific sites across the transcriptome, varying with RNAs. Germline development also changes in a specific fashion: Y479A abolishes one FBF-2 function-the sperm-to-oocyte cell fate switch. Y479A's effects on the regulation of one mRNA, gld-1, are critical to this fate change, though other network changes are also important. FBF-2 switches from repression to activation of gld-1 RNA, likely by distinct FBF-2 partnerships. The role of RNA-binding protein partnerships in governing RNA regulatory networks will likely extend broadly, as such partnerships pervade RNA controls in virtually all metazoan tissues and species.
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Affiliation(s)
- Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fan Chen
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - MaryGrace Linsley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer Woodworth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peggy Kroll-Conner
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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6
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Gkekas I, Vagiona AC, Pechlivanis N, Kastrinaki G, Pliatsika K, Iben S, Xanthopoulos K, Psomopoulos FE, Andrade-Navarro MA, Petrakis S. Intranuclear inclusions of polyQ-expanded ATXN1 sequester RNA molecules. Front Mol Neurosci 2023; 16:1280546. [PMID: 38125008 PMCID: PMC10730666 DOI: 10.3389/fnmol.2023.1280546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant neurodegenerative disease caused by a trinucleotide (CAG) repeat expansion in the ATXN1 gene. It is characterized by the presence of polyglutamine (polyQ) intranuclear inclusion bodies (IIBs) within affected neurons. In order to investigate the impact of polyQ IIBs in SCA1 pathogenesis, we generated a novel protein aggregation model by inducible overexpression of the mutant ATXN1(Q82) isoform in human neuroblastoma SH-SY5Y cells. Moreover, we developed a simple and reproducible protocol for the efficient isolation of insoluble IIBs. Biophysical characterization showed that polyQ IIBs are enriched in RNA molecules which were further identified by next-generation sequencing. Finally, a protein interaction network analysis indicated that sequestration of essential RNA transcripts within ATXN1(Q82) IIBs may affect the ribosome resulting in error-prone protein synthesis and global proteome instability. These findings provide novel insights into the molecular pathogenesis of SCA1, highlighting the role of polyQ IIBs and their impact on critical cellular processes.
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Affiliation(s)
- Ioannis Gkekas
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Nikolaos Pechlivanis
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
| | - Georgia Kastrinaki
- Aerosol and Particle Technology Laboratory, Centre for Research and Technology Hellas, Chemical Process and Energy Resources Institute, Thessaloniki, Greece
| | - Katerina Pliatsika
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sebastian Iben
- Department of Dermatology and Allergic Diseases, University of Ulm, Ulm, Germany
| | - Konstantinos Xanthopoulos
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
- Laboratory of Pharmacology, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Fotis E. Psomopoulos
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
| | | | - Spyros Petrakis
- Centre for Research and Technology Hellas, Institute of Applied Biosciences, Thessaloniki, Greece
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7
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Haugen RJ, Barnier C, Elrod ND, Luo H, Jensen MK, Ji P, Smibert CA, Lipshitz HD, Wagner EJ, Lydia Freddolino P, Goldstrohm AC. Regulation of the Drosophila transcriptome by Pumilio and CCR4-NOT deadenylase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.29.555372. [PMID: 37693497 PMCID: PMC10491259 DOI: 10.1101/2023.08.29.555372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The sequence-specific RNA-binding protein Pumilio controls development of Drosophila; however, the network of mRNAs that it regulates remains incompletely characterized. In this study, we utilize knockdown and knockout approaches coupled with RNA-Seq to measure the impact of Pumilio on the transcriptome of Drosophila cells. We also used an improved RNA co-immunoprecipitation method to identify Pumilio bound mRNAs in Drosophila embryos. Integration of these datasets with the content of Pumilio binding motifs across the transcriptome revealed novel direct Pumilio target genes involved in neural, muscle, wing, and germ cell development, and cellular proliferation. These genes include components of Wnt, TGF-beta, MAPK/ERK, and Notch signaling pathways, DNA replication, and lipid metabolism. Additionally, we identified the mRNAs regulated by the CCR4-NOT deadenylase complex, a key factor in Pumilio-mediated repression, and observed concordant regulation of Pumilio:CCR4-NOT target mRNAs. Computational modeling revealed that Pumilio binding, binding site number, density, and sequence context are important determinants of regulation. Moreover, the content of optimal synonymous codons in target mRNAs exhibits a striking functional relationship to Pumilio and CCR4-NOT regulation, indicating that the inherent translation efficiency and stability of the mRNA modulates their response to these trans-acting regulatory factors. Together, the results of this work provide new insights into the Pumilio regulatory network and mechanisms, and the parameters that influence the efficacy of Pumilio-mediated regulation.
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Affiliation(s)
- Rebecca J. Haugen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Catherine Barnier
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109
| | - Nathan D. Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77550, USA
| | - Hua Luo
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Madeline K. Jensen
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642
| | - Ping Ji
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642
| | - Craig A. Smibert
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Howard D. Lipshitz
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Eric J. Wagner
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642
| | - P. Lydia Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Aaron C. Goldstrohm
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Botta S, de Prisco N, Chemiakine A, Brandt V, Cabaj M, Patel P, Doron‐Mandel E, Treadway CJ, Jovanovic M, Brown NG, Soni RK, Gennarino VA. Dosage sensitivity to Pumilio1 variants in the mouse brain reflects distinct molecular mechanisms. EMBO J 2023; 42:e112721. [PMID: 37070548 PMCID: PMC10233381 DOI: 10.15252/embj.2022112721] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 04/19/2023] Open
Abstract
Different mutations in the RNA-binding protein Pumilio1 (PUM1) cause divergent phenotypes whose severity tracks with dosage: a mutation that reduces PUM1 levels by 25% causes late-onset ataxia, whereas haploinsufficiency causes developmental delay and seizures. Yet PUM1 targets are derepressed to equal degrees in both cases, and the more severe mutation does not hinder PUM1's RNA-binding ability. We therefore considered the possibility that the severe mutation might disrupt PUM1 interactions, and identified PUM1 interactors in the murine brain. We find that mild PUM1 loss derepresses PUM1-specific targets, but the severe mutation disrupts interactions with several RNA-binding proteins and the regulation of their targets. In patient-derived cell lines, restoring PUM1 levels restores these interactors and their targets to normal levels. Our results demonstrate that dosage sensitivity does not always signify a linear relationship with protein abundance but can involve distinct mechanisms. We propose that to understand the functions of RNA-binding proteins in a physiological context will require studying their interactions as well as their targets.
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Affiliation(s)
- Salvatore Botta
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
- Department of Translational Medical ScienceUniversity of Campania Luigi VanvitelliCasertaItaly
| | - Nicola de Prisco
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
| | - Alexei Chemiakine
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
| | - Vicky Brandt
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
| | - Maximilian Cabaj
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
| | - Purvi Patel
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | | | - Colton J Treadway
- Department of Pharmacology and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Marko Jovanovic
- Department of Biological SciencesColumbia UniversityNew YorkNYUSA
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Vincenzo A Gennarino
- Department of Genetics and DevelopmentColumbia University Irving Medical CenterNew YorkNYUSA
- Departments of NeurologyColumbia University Irving Medical CenterNew YorkNYUSA
- Columbia Stem Cell InitiativeColumbia University Irving Medical CenterNew YorkNYUSA
- Initiative for Columbia Ataxia and TremorColumbia University Irving Medical CenterNew YorkNYUSA
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9
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Sousa A, Rocha S, Vieira J, Reboiro-Jato M, López-Fernández H, Vieira CP. On the identification of potential novel therapeutic targets for spinocerebellar ataxia type 1 (SCA1) neurodegenerative disease using EvoPPI3. J Integr Bioinform 2023; 20:jib-2022-0056. [PMID: 36848492 PMCID: PMC10561075 DOI: 10.1515/jib-2022-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 11/26/2022] [Indexed: 03/01/2023] Open
Abstract
EvoPPI (http://evoppi.i3s.up.pt), a meta-database for protein-protein interactions (PPI), has been upgraded (EvoPPI3) to accept new types of data, namely, PPI from patients, cell lines, and animal models, as well as data from gene modifier experiments, for nine neurodegenerative polyglutamine (polyQ) diseases caused by an abnormal expansion of the polyQ tract. The integration of the different types of data allows users to easily compare them, as here shown for Ataxin-1, the polyQ protein involved in spinocerebellar ataxia type 1 (SCA1) disease. Using all available datasets and the data here obtained for Drosophila melanogaster wt and exp Ataxin-1 mutants (also available at EvoPPI3), we show that, in humans, the Ataxin-1 network is much larger than previously thought (380 interactors), with at least 909 interactors. The functional profiling of the newly identified interactors is similar to the ones already reported in the main PPI databases. 16 out of 909 interactors are putative novel SCA1 therapeutic targets, and all but one are already being studied in the context of this disease. The 16 proteins are mainly involved in binding and catalytic activity (mainly kinase activity), functional features already thought to be important in the SCA1 disease.
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Affiliation(s)
- André Sousa
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135Porto, Portugal
| | - Sara Rocha
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135Porto, Portugal
| | - Jorge Vieira
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135Porto, Portugal
| | - Miguel Reboiro-Jato
- Department of Computer Science, CINBIO, Universidade de Vigo, ESEI – Escuela Superior de Ingeniería Informática, 32004Ourense, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
| | - Hugo López-Fernández
- Department of Computer Science, CINBIO, Universidade de Vigo, ESEI – Escuela Superior de Ingeniería Informática, 32004Ourense, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain
| | - Cristina P. Vieira
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135Porto, Portugal
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135Porto, Portugal
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10
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Liu QZ, Yu HR, Wang LP, Zhou MJ, Chen Z, Zhou DH, Chen JY, Zhang N, Huang ZX, Xie YX, Gu FF, Li K, Tu XH. Up-regulation of PUM1 by miR-218-5p promotes colorectal tumor-initiating cell properties and tumorigenesis by regulating the PI3K/AKT axis. J Gastrointest Oncol 2023; 14:233-244. [PMID: 36915463 PMCID: PMC10007912 DOI: 10.21037/jgo-23-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/10/2023] [Indexed: 03/02/2023] Open
Abstract
Background Colorectal cancer (CRC) is the third most common cancer and the fourth most common cause of cancer-related death worldwide. Advanced stage CRC, during the recent past, had a dismal prognosis and only a few available treatments. Pumilio homologous protein 1 (PUM1) is reportedly aberrant in human malignancies, including CRC. However, the role of PUM1 in the regulation of tumor-initiating cells (T-ICs) remains unknown. Methods The levels of messenger RNAs (mRNAs) were determined by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and immunoblot analyses. Statistical analyses were performed to determine the associations between the levels of PUM1 and tumor features and patient outcomes. Whether PUM1 is a downstream target of miR-218-5p was verified by bioinformatics target gene prediction and qRT-PCR. Results Herein, it was found that T-ICs, chemoresistance, and recurrent CRC samples all manifest increased PUM1 expression. Functional investigations have shown that PUM1 increased the self-renewal, tumorigenicity, malignant proliferation, and chemoresistance of colorectal cells. PUM1 activates the phosphatidylinositol-3-kinase (PI3K)/protein kinase B (AKT) signaling pathway biochemically. Furthermore, it was discovered that miR-218-5p specifically targets T-ICs' PUM1 3'-untranslated region (3'-UTR). More importantly, the PUM1/PI3K/AKT axis regulates CRC cells' responses to treatment with cetuximab, and PUM1 overexpression increased cetuximab resistance. More evidence points to the possibility that low PUM1 may predict cetuximab benefits in CRC patients after analysis of the patient cohort, patient-derived tumor organoids, and patient-derived xenografts (PDXs). Conclusions Taken together, the result of this work points to the critical function of the miR-218-5p/PUM1/PI3K/AKT regulatory circuit in regulating T-ICs characteristics and thus suggests possible therapeutic targets for CRC.
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Affiliation(s)
- Qi-Zhi Liu
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hai-Rong Yu
- Department of Traditional Chinese Medicine, First Clinical Medical College, Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Li-Ping Wang
- Department of Breast Surgery/Plastic Surgery, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Min-Jun Zhou
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhuo Chen
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - De-Hua Zhou
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jun-Yi Chen
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Nan Zhang
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Zhen-Xing Huang
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yu-Xiang Xie
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fang-Fang Gu
- Department of Oncology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Kun Li
- Medicine School, Dalian University, Dalian, China
| | - Xiao-Huang Tu
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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11
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Mammalian pumilio proteins control cellular morphology, migration, and adhesion. Sci Rep 2023; 13:3002. [PMID: 36810759 PMCID: PMC9944931 DOI: 10.1038/s41598-023-30004-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/14/2023] [Indexed: 02/24/2023] Open
Abstract
Pumilio proteins are RNA-binding proteins that control mRNA translation and stability by binding to the 3' UTR of target mRNAs. Mammals have two canonical Pumilio proteins, PUM1 and PUM2, which are known to act in many biological processes, including embryonic development, neurogenesis, cell cycle regulation and genomic stability. Here, we characterized a new role of both PUM1 and PUM2 in regulating cell morphology, migration, and adhesion in T-REx-293 cells, in addition to previously known defects in growth rate. Gene ontology analysis of differentially expressed genes in PUM double knockout (PDKO) cells for both cellular component and biological process showed enrichment in categories related to adhesion and migration. PDKO cells had a collective cell migration rate significantly lower than that of WT cells and displayed changes in actin morphology. In addition, during growth, PDKO cells aggregated into clusters (clumps) due to an inability to escape cell-cell contacts. Addition of extracellular matrix (Matrigel) alleviated the clumping phenotype. Collagen IV (ColIV), a major component of Matrigel, was shown to be the driving force in allowing PDKO cells to monolayer appropriately, however, ColIV protein levels remained unperturbed in PDKO cells. This study characterizes a novel cellular phenotype associated with cellular morphology, migration, and adhesion which can aid in developing better models for PUM function in both developmental processes and disease.
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12
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Coffin SL, Durham MA, Nitschke L, Xhako E, Brown AM, Revelli JP, Villavicencio Gonzalez E, Lin T, Handler HP, Dai Y, Trostle AJ, Wan YW, Liu Z, Sillitoe RV, Orr HT, Zoghbi HY. Disruption of the ATXN1-CIC complex reveals the role of additional nuclear ATXN1 interactors in spinocerebellar ataxia type 1. Neuron 2023; 111:481-492.e8. [PMID: 36577402 PMCID: PMC9957872 DOI: 10.1016/j.neuron.2022.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/26/2022] [Accepted: 11/28/2022] [Indexed: 12/28/2022]
Abstract
Spinocerebellar ataxia type 1 (SCA1) is a paradigmatic neurodegenerative disease in that it is caused by a mutation in a broadly expressed protein, ATXN1; however, only select populations of cells degenerate. The interaction of polyglutamine-expanded ATXN1 with the transcriptional repressor CIC drives cerebellar Purkinje cell pathogenesis; however, the importance of this interaction in other vulnerable cells remains unknown. Here, we mutated the 154Q knockin allele of Atxn1154Q/2Q mice to prevent the ATXN1-CIC interaction globally. This normalized genome-wide CIC binding; however, it only partially corrected transcriptional and behavioral phenotypes, suggesting the involvement of additional factors in disease pathogenesis. Using unbiased proteomics, we identified three ATXN1-interacting transcription factors: RFX1, ZBTB5, and ZKSCAN1. We observed altered expression of RFX1 and ZKSCAN1 target genes in SCA1 mice and patient-derived iNeurons, highlighting their potential contributions to disease. Together, these data underscore the complexity of mechanisms driving cellular vulnerability in SCA1.
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Affiliation(s)
- Stephanie L Coffin
- Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Mark A Durham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Larissa Nitschke
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eder Xhako
- Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Amanda M Brown
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean-Pierre Revelli
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Esmeralda Villavicencio Gonzalez
- Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Tao Lin
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hillary P Handler
- Department of Laboratory Medicine and Pathology, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yanwan Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Alexander J Trostle
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ying-Wooi Wan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Zhandong Liu
- Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Roy V Sillitoe
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harry T Orr
- Department of Laboratory Medicine and Pathology, Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Huda Y Zoghbi
- Program in Genetics and Genomics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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13
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The Role of Epigenetics in Neuroinflammatory-Driven Diseases. Int J Mol Sci 2022; 23:ijms232315218. [PMID: 36499544 PMCID: PMC9740629 DOI: 10.3390/ijms232315218] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative disorders are characterized by the progressive loss of central and/or peripheral nervous system neurons. Within this context, neuroinflammation comes up as one of the main factors linked to neurodegeneration progression. In fact, neuroinflammation has been recognized as an outstanding factor for Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), Parkinson's disease (PD), and multiple sclerosis (MS). Interestingly, neuroinflammatory diseases are characterized by dramatic changes in the epigenetic profile, which might provide novel prognostic and therapeutic factors towards neuroinflammatory treatment. Deep changes in DNA and histone methylation, along with histone acetylation and altered non-coding RNA expression, have been reported at the onset of inflammatory diseases. The aim of this work is to review the current knowledge on this field.
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14
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Snoderly-Foster LJ, Olivas WM. Regulation of Parkinson's disease-associated genes by Pumilio proteins and microRNAs in SH-SY5Y neuronal cells. PLoS One 2022; 17:e0275235. [PMID: 36174040 PMCID: PMC9522289 DOI: 10.1371/journal.pone.0275235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Parkinson's disease is the second most common age-related, neurodegenerative disease. A small collection of genes has been linked to Parkinson's disease including LRRK2, SAT1, and SNCA, the latter of which encodes the protein alpha-synuclein that aggregates in Lewy bodies as a hallmark of the disease. Overexpression of even wild-type versions of these genes can lead to pathogenesis, yet the regulatory mechanisms that control protein production of the genes are not fully understood. Pumilio proteins belong to the highly conserved PUF family of eukaryotic RNA-binding proteins that post-transcriptionally regulate gene expression through binding conserved motifs in the 3' untranslated region (UTR) of mRNA targets known as PUF Recognition Elements (PREs). The 3'UTRs of LRRK2, SNCA and SAT1 each contain multiple putative PREs. Knockdown (KD) of the two human Pumilio homologs (Pumilio 1 and Pumilio 2) in a neurodegenerative model cell line, SH-SY5Y, resulted in increased SNCA and LRRK2 mRNA, as well as alpha-synuclein levels, suggesting these genes are normally repressed by the Pumilio proteins. Some studies have indicated a relationship between Pumilio and microRNA activities on the same target, especially when their binding sites are close together. LRRK2, SNCA, and SAT1 each contain several putative microRNA-binding sites within the 3'UTR, some of which reside near PREs. Small RNA-seq and microRNA qPCR assays were performed in both wild type and Pumilio KD SH-SY5Y cells to analyze global and differential microRNA expression. One thousand four hundred and four microRNAs were detected across wild type and Pumilio KD cells. Twenty-one microRNAs were differentially expressed between treatments, six of which were previously established to be altered in Parkinson's disease patient samples or research models. Expression of ten miRs predicted to target LRRK2 and SNCA was verified by RT-qPCR. Collectively, our results demonstrate that Pumilios and microRNAs play a multi-faceted role in regulating Parkinson's disease-associated genes.
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Affiliation(s)
- Lisa J. Snoderly-Foster
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, United States of America
| | - Wendy M. Olivas
- Department of Biology, University of Missouri-St. Louis, St. Louis, Missouri, United States of America
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15
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Liu Z, Lv C. RNA binding protein PUM2 promotes hepatocellular carcinoma proliferation and apoptosis via binding to the 3'UTR of BTG3. Oncol Lett 2022; 24:346. [PMID: 36072004 PMCID: PMC9434726 DOI: 10.3892/ol.2022.13466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/27/2022] [Indexed: 12/09/2022] Open
Affiliation(s)
- Zhenhua Liu
- Department of General Surgery, The First People's Hospital of Lin Ping District, Hangzhou, Zhejiang 311100, P.R. China
| | - Chunye Lv
- Department of General Surgery, The Affiliated Jiangning Hospital with Nanjing Medical University, Nanjing, Jiangsu 211100, P.R. China
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16
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Ma Q, Oksenberg JR, Didonna A. Epigenetic control of ataxin-1 in multiple sclerosis. Ann Clin Transl Neurol 2022; 9:1186-1194. [PMID: 35903875 PMCID: PMC9380165 DOI: 10.1002/acn3.51618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/09/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE ATXN1 encodes the polyglutamine protein ataxin-1, which we have demonstrated exerting an immunomodulatory function in the context of central nervous system (CNS) autoimmunity, in addition to its classical role in the neurodegenerative disorder spinocerebellar ataxia type 1 (SCA1). In this study, we dissected the contribution of DNA methylation to the regulation of ATXN1 in multiple sclerosis (MS). METHODS We interrogated a DNA methylation dataset previously generated via bisulfate DNA sequencing (BS-seq) in sorted peripheral immune cytotypes (CD4+ and CD8+ T cells, CD19+ B cells, and CD14+ monocytes) isolated from untreated MS patients at symptoms onset. RESULTS Here, we report that ATXN1 undergoes hypo-methylation at four distinct regions upon MS, exclusively in B cells. We also highlight how these differentially methylated sites overlap with other regulatory epigenetic marks and MS risk variants. Lastly, we employ luciferase assays to assess the functionality of these regions, showing that the loss of methylation leads to an increase in ATXN1 expression. INTERPRETATION Altogether, these findings provide biological insights into ataxin-1 regulation in the immune system as well as into the molecular mechanisms underlying MS risk.
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Affiliation(s)
- Qin Ma
- Weill Institute for Neurosciences, Department of NeurologyUniversity of CaliforniaSan FranciscoCalifornia94158USA
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences, Department of NeurologyUniversity of CaliforniaSan FranciscoCalifornia94158USA
| | - Alessandro Didonna
- Weill Institute for Neurosciences, Department of NeurologyUniversity of CaliforniaSan FranciscoCalifornia94158USA
- Department of Anatomy and Cell BiologyEast Carolina UniversityGreenvilleNorth Carolina27834USA
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17
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Rajasekaran S, Khan E, Ching SR, Khan M, Siddiqui J, Gradia DF, Lin C, Bouley SJ, Mercadante D, Manning AL, Gerber AP, Walker J, Miles W. PUMILIO competes with AUF1 to control DICER1 RNA levels and miRNA processing. Nucleic Acids Res 2022; 50:7048-7066. [PMID: 35736218 PMCID: PMC9262620 DOI: 10.1093/nar/gkac499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
DICER1 syndrome is a cancer pre-disposition disorder caused by mutations that disrupt the function of DICER1 in miRNA processing. Studying the molecular, cellular and oncogenic effects of these mutations can reveal novel mechanisms that control cell homeostasis and tumor biology. Here, we conduct the first analysis of pathogenic DICER1 syndrome allele from the DICER1 3'UTR. We find that the DICER1 syndrome allele, rs1252940486, abolishes interaction with the PUMILIO RNA binding protein with the DICER1 3'UTR, resulting in the degradation of the DICER1 mRNA by AUF1. This single mutational event leads to diminished DICER1 mRNA and protein levels, and widespread reprogramming of miRNA networks. The in-depth characterization of the rs1252940486 DICER1 allele, reveals important post-transcriptional regulatory events that control DICER1 levels.
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Affiliation(s)
- Swetha Rajasekaran
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Samuel R Ching
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Misbah Khan
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Jalal K Siddiqui
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Daniela F Gradia
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
| | - Chenyu Lin
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Stephanie J Bouley
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dayna L Mercadante
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Amity L Manning
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - André P Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - James A Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wayne O Miles
- To whom correspondence should be addressed. Tel: +1 614 366 2869;
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18
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Yoon DS, Lee KM, Choi Y, Ko EA, Lee NH, Cho S, Park KH, Lee JH, Kim HW, Lee JW. TLR4 downregulation by the RNA-binding protein PUM1 alleviates cellular aging and osteoarthritis. Cell Death Differ 2022; 29:1364-1378. [PMID: 35034101 DOI: 10.1038/s41418-021-00925-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/04/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022] Open
Abstract
Dysfunction of mRNA or RNA-binding proteins (RBPs) causes cellular aging and age-related degenerative diseases; however, information regarding the mechanism through which RBP-mediated posttranscriptional regulation affects cellular aging and related disease processes is limited. In this study, PUM1 was found to be associated with the self-renewal capacity and aging process of human mesenchymal stem cells (MSC). PUM1 interacted with the 3'-untranslated region of Toll-like receptor 4 (TLR4) to suppress TLR4 mRNA translation and regulate the activity of nuclear factor-κB (NF-κB), a master regulator of the aging process in MSCs. PUM1 overexpression protected MSCs against H2O2-induced cellular senescence by suppressing TLR4-mediated NF-κB activity. TLR4-mediated NF-κB activation is a key regulator in osteoarthritis (OA) pathogenesis. PUM1 overexpression enhanced the chondrogenic potential of MSCs even under the influence of inflammation-inducing factors, such as lipopolysaccharide (LPS) or interleukin-1β (IL-1β), whereas the chondrogenic potential was reduced following the PUM1 knockdown-mediated TLR4 activation. PUM1 levels decreased under inflammatory conditions in vitro and during OA progression in human and mouse disease models. PUM1 knockdown in human chondrocytes promoted chondrogenic phenotype loss, whereas PUM1 overexpression protected the cells from inflammation-mediated disruption of the chondrogenic phenotype. Gene therapy using a lentiviral vector encoding mouse PUM1 showed promise in preserving articular cartilage integrity in OA mouse models. In conclusion, PUM1 is a novel suppressor of MSC aging, and the PUM1-TLR4 regulatory axis represents a potential therapeutic target for OA.
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Affiliation(s)
- Dong Suk Yoon
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Kyoung-Mi Lee
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea.,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Yoorim Choi
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Eun Ae Ko
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Na-Hyun Lee
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, 31116, South Korea.,Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, South Korea
| | - Sehee Cho
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Kwang Hwan Park
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Jung-Hwan Lee
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, 31116, South Korea.,Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, South Korea.,Department of Biomaterials Science, School of Dentistry, Dankook University, Cheonan, 31116, South Korea.,UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan, 31116, South Korea
| | - Hae-Won Kim
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, 31116, South Korea. .,Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, South Korea. .,Department of Biomaterials Science, School of Dentistry, Dankook University, Cheonan, 31116, South Korea. .,UCL Eastman-Korea Dental Medicine Innovation Centre, Dankook University, Cheonan, 31116, South Korea.
| | - Jin Woo Lee
- Department of Orthopaedic Surgery, Yonsei University College of Medicine, Seoul, 03722, South Korea. .,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, 03722, South Korea. .,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea.
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19
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Botta S, Chemiakine A, Gennarino VA. Dual antibody strategy for high-resolution imaging of murine Purkinje cells and their dendrites across multiple layers. STAR Protoc 2022; 3:101427. [PMID: 35707684 PMCID: PMC9189630 DOI: 10.1016/j.xpro.2022.101427] [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] [Indexed: 12/02/2022] Open
Abstract
Despite being among the largest neurons in the mammalian brain, Purkinje cells are difficult to visualize and trace via immunofluorescence because their dendritic arbors extend through several cerebellar layers. This protocol describes a two-antibody strategy we developed to study Purkinje cell morphology in mice. With it, one can reconstruct three-dimensional images of Purkinje cells at single-neuron resolution across multiple layers. The substantially improved image quality reveals subtle defects, enabling more meaningful morphological analysis. For complete details on the use and execution of this protocol, please refer to Gennarino et al. (2015).
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Affiliation(s)
- Salvatore Botta
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, 80131 Napoli, Italy
| | - Alexei Chemiakine
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vincenzo A. Gennarino
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Departments of Pediatrics and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
- Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, NY 10032, USA
- Corresponding author
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20
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Li X, Zhu M, Zang M, Cao D, Xie Z, Liang H, Bian Z, Zhao T, Hu Z, Xu EY. PUMILIO-mediated translational control of somatic cell cycle program promotes folliculogenesis and contributes to ovarian cancer progression. Cell Mol Life Sci 2022; 79:279. [PMID: 35507203 PMCID: PMC11072887 DOI: 10.1007/s00018-022-04254-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 02/06/2023]
Abstract
Translational control is a fundamental mechanism regulating animal germ cell development. Gonadal somatic cells provide support and microenvironment for germ cell development to ensure fertility, yet the roles of translational control in gonadal somatic compartment remain largely undefined. We found that mouse homolog of conserved fly germline stem cell factor Pumilio, PUM1, is absent in oocytes of all growing follicles after the primordial follicle stage, instead, it is highly expressed in somatic compartments of ovaries. Global loss of Pum1, not oocyte-specific loss of Pum1, led to a significant reduction in follicular number and size as well as fertility. Whole-genome identification of PUM1 targets in ovarian somatic cells revealed an enrichment of cell proliferation pathway, including 48 key regulators of cell phase transition. Consistently granulosa cells proliferation is reduced and the protein expression of the PUM-bound Cell Cycle Regulators (PCCR) were altered accordingly in mutant ovaries, and specifically in granulosa cells. Increase in negative regulator expression and decrease in positive regulators in the mutant ovaries support a coordinated translational control of somatic cell cycle program via PUM proteins. Furthermore, postnatal knockdown, but not postnatal oocyte-specific loss, of Pum1 in Pum2 knockout mice reduced follicular growth and led to similar expression alteration of PCCR genes, supporting a critical role of PUM-mediated translational control in ovarian somatic cells for mammalian female fertility. Finally, expression of human PUM protein and its regulated cell cycle targets exhibited significant correlation with ovarian cancer and prognosis for cancer survival. Hence, PUMILIO-mediated cell cycle regulation represents an important mechanism in mammalian female reproduction and human cancer biology.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Reproductive Medicine (Suzhou Centre), The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
| | - Mengyi Zhu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Min Zang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Dandan Cao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zhengyao Xie
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Haibo Liang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zexin Bian
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Tingting Zhao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine (Suzhou Centre), The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, Jiangsu, China
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Eugene Yujun Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.
- Department of Neurology, Center for Reproductive Science, Feinberg School of Medicine, Northwestern University Feinberg School of Medicine, Chicago, USA.
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21
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Lee WS, Al-Ramahi I, Jeong HH, Jang Y, Lin T, Adamski CJ, Lavery LA, Rath S, Richman R, Bondar VV, Alcala E, Revelli JP, Orr HT, Liu Z, Botas J, Zoghbi HY. Cross-species genetic screens identify transglutaminase 5 as a regulator of polyglutamine-expanded ataxin-1. J Clin Invest 2022; 132:e156616. [PMID: 35499073 PMCID: PMC9057624 DOI: 10.1172/jci156616] [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: 11/10/2021] [Accepted: 03/08/2022] [Indexed: 12/31/2022] Open
Abstract
Many neurodegenerative disorders are caused by abnormal accumulation of misfolded proteins. In spinocerebellar ataxia type 1 (SCA1), accumulation of polyglutamine-expanded (polyQ-expanded) ataxin-1 (ATXN1) causes neuronal toxicity. Lowering total ATXN1, especially the polyQ-expanded form, alleviates disease phenotypes in mice, but the molecular mechanism by which the mutant ATXN1 is specifically modulated is not understood. Here, we identified 22 mutant ATXN1 regulators by performing a cross-species screen of 7787 and 2144 genes in human cells and Drosophila eyes, respectively. Among them, transglutaminase 5 (TG5) preferentially regulated mutant ATXN1 over the WT protein. TG enzymes catalyzed cross-linking of ATXN1 in a polyQ-length-dependent manner, thereby preferentially modulating mutant ATXN1 stability and oligomerization. Perturbing Tg in Drosophila SCA1 models modulated mutant ATXN1 toxicity. Moreover, TG5 was enriched in the nuclei of SCA1-affected neurons and colocalized with nuclear ATXN1 inclusions in brain tissue from patients with SCA1. Our work provides a molecular insight into SCA1 pathogenesis and an opportunity for allele-specific targeting for neurodegenerative disorders.
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Affiliation(s)
- Won-Seok Lee
- Integrative Molecular and Biomedical Science Program, and
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
| | - Ismael Al-Ramahi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
| | - Hyun-Hwan Jeong
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
- Department of Pediatrics-Neurology, and
| | - Youjin Jang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
| | - Tao Lin
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Carolyn J. Adamski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
- Howard Hughes Medical Institute, Houston, Texas, USA
| | - Laura A. Lavery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
| | - Smruti Rath
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
| | - Ronald Richman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
- Howard Hughes Medical Institute, Houston, Texas, USA
| | - Vitaliy V. Bondar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
| | - Elizabeth Alcala
- Exceptional Research Opportunities Program, Howard Hughes Medical Institute, Houston, Texas, USA
| | - Jean-Pierre Revelli
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
| | - Harry T. Orr
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, Minnesota, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
- Department of Pediatrics-Neurology, and
| | - Juan Botas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
| | - Huda Y. Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Houston, Texas, USA
- Department of Pediatrics-Neurology, and
- Howard Hughes Medical Institute, Houston, Texas, USA
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22
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Ko CF, Chang YC, Cho HC, Yu J. The Puf-A Protein Is Required for Primordial Germ Cell Development. Cells 2022; 11:cells11091476. [PMID: 35563782 PMCID: PMC9105799 DOI: 10.3390/cells11091476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 11/16/2022] Open
Abstract
Puf-A, a nucleolar Puf domain protein, is required for ribosome biogenesis. A study of Puf-A in zebrafish has shown that Puf-A is highly expressed in primordial germ cells (PGCs) and participates in PGC development. However, it remains unclear how Puf-A governs PGC development in mammals. Here, we generated transgenic mice carrying inducible Puf-A shRNA and obtained double heterozygous mice with Puf-A shRNA and Oct4-EGFP to examine the behavior of PGCs. It was found that the knockdown of Puf-A led to the loss of a considerable number of PGCs and a slowdown of the movement of the remaining PGCs. Puf-A and NPM1 colocalized in clusters in the nuclei of the PGCs. The silencing of Puf-A resulted in the translocation of NPM1 from nucleolus to nucleoplasm and the hyperactivation of p53 in the PGCs. The PGCs in Puf-A knockdown embryos showed a significant increase in subpopulations of PGCs at G1 arrest and apoptosis. Moreover, the expression of essential genes associated with PGC maintenance was decreased in the Puf-A knockdown PGCs. Our study showed that Puf-A governed PGC development by regulating the growth, survival, and maintenance of PGCs. We also observed the alterations of NPM1 and p53 upon Puf-A knockdown to be consistent with the previous study in cancer cells, which might explain the molecular mechanism for the role of Puf-A in PGC development.
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23
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Cairrão F, Santos CC, Le Thomas A, Marsters S, Ashkenazi A, Domingos PM. Pumilio protects Xbp1 mRNA from regulated Ire1-dependent decay. Nat Commun 2022; 13:1587. [PMID: 35332141 PMCID: PMC8948244 DOI: 10.1038/s41467-022-29105-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 02/17/2022] [Indexed: 12/12/2022] Open
Abstract
The unfolded protein response (UPR) maintains homeostasis of the endoplasmic reticulum (ER). Residing in the ER membrane, the UPR mediator Ire1 deploys its cytoplasmic kinase-endoribonuclease domain to activate the key UPR transcription factor Xbp1 through non-conventional splicing of Xbp1 mRNA. Ire1 also degrades diverse ER-targeted mRNAs through regulated Ire1-dependent decay (RIDD), but how it spares Xbp1 mRNA from this decay is unknown. Here, we identify binding sites for the RNA-binding protein Pumilio in the 3'UTR Drosophila Xbp1. In the developing Drosophila eye, Pumilio binds both the Xbp1unspliced and Xbp1spliced mRNAs, but only Xbp1spliced is stabilized by Pumilio. Furthermore, Pumilio displays Ire1 kinase-dependent phosphorylation during ER stress, which is required for its stabilization of Xbp1spliced. hIRE1 can phosphorylate Pumilio directly, and phosphorylated Pumilio protects Xbp1spliced mRNA against RIDD. Thus, Ire1-mediated phosphorylation enables Pumilio to shield Xbp1spliced from RIDD. These results uncover an unexpected regulatory link between an RNA-binding protein and the UPR.
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Affiliation(s)
- Fátima Cairrão
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
| | - Cristiana C Santos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | - Adrien Le Thomas
- Cancer Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Scot Marsters
- Cancer Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Avi Ashkenazi
- Cancer Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Pedro M Domingos
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
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24
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Lee W, de Prisco N, Gennarino VA. Identifying patients and assessing variant pathogenicity for an autosomal dominant disease-driving gene. STAR Protoc 2022; 3:101150. [PMID: 35146449 PMCID: PMC8819039 DOI: 10.1016/j.xpro.2022.101150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Identifying a disease gene and determining its causality in patients can be challenging. Here, we present an approach to predicting the pathogenicity of deletions and missense variants for an autosomal dominant gene. We provide online resources for identifying patients and determining constraint metrics to isolate the causal gene among several candidates encompassed in a shared region of deletion. We also provide instructions for optimizing functional annotation programs that may be otherwise inaccessible to a nonexpert or novice in computational approaches. For complete details on the use and execution of this protocol, please refer to Gennarino et al. (2018).
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Affiliation(s)
- Winston Lee
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nicola de Prisco
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vincenzo A. Gennarino
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Departments of Pediatrics and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
- Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, NY 10032, USA
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25
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Yang Y, Su X, Shen K, Zhang C, Dai H, Ma H, Jiang Y, Shuai L, Liu Z, You J, Min K, Chen Z. PUM1 is upregulated by DNA methylation to suppress antitumor immunity and results in poor prognosis in pancreatic cancer. Transl Cancer Res 2022; 10:2153-2168. [PMID: 35116535 PMCID: PMC8798770 DOI: 10.21037/tcr-20-3295] [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: 11/19/2020] [Accepted: 02/26/2021] [Indexed: 12/24/2022]
Abstract
Background Pancreatic carcinoma (PAAD) is a highly malignant cancer with a poor prognosis and high mortality rate. Pumilio homologous protein 1 (PUM1) promotes cell growth, invasion, and metastasis and suppresses apoptosis in many different kinds of cancers, such as non-small-cell lung carcinoma (NSCLC), ovarian cancer and lymphocyte leukemia. However, the underlying mechanism and potential role of PUM1 in PAAD have not been investigated. Methods Bioinformatics analysis was performed using multiple databases [The Cancer Genome Atlas (TCGA), Gene Expression Profiling Interactive Analysis (GEPIA), BBCancer, Human Protein Atlas (HPA), MethSurv, cBioPortal, The Cancer Imaging Archive (TCIA), xCell, Gene Expression Omnibus (GEO)] to explore the diagnostic and prognostic role of PUM1, and the relationship between expression of PUM1 and prognosis of patients with PAAD. The analysis was further validated using the Kaplan-Meier plotter. Results PUM1 plays a role in both diagnostic and prognostic prediction. The PUM1 mRNA expression level correlates with both the prognosis and incidence of pancreatic cancer. PUM1 can serve as a potential diagnostic indicator for pancreatic cancer. Furthermore, the DNA methylation levels of PUM1 affects its oncogene function in pancreatic cancer. PUM1 can also inhibit the immune microenvironment by altering immune cell infiltration, which affects immunotherapy response in pancreatic cancer. Conclusions PUM1 takes a crucial part in the immune microenvironment and immunotherapy response of PAAD and is potentially useful for the development of novel diagnostic and treatment strategies.
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Affiliation(s)
- Yishi Yang
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Xingxing Su
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Kaicheng Shen
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Chengcheng Zhang
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Haisu Dai
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Hongbo Ma
- Department of Oncology, The Fuling Central Hospital of Chongqing City, Chongqing, China
| | - Yan Jiang
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Ling Shuai
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Zhipeng Liu
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Jinshan You
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Ke Min
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
| | - Zhiyu Chen
- Department of Hepatobiliary Surgery, Southwest Hospital, First Affiliated Hospital of the Army Medical University, Chongqing, China
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26
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Ye Y, Hu Z, Mai J, Chen L, Cao D, Liao J, Duan J. A de novo PUM1 Variant in a Girl With a Dravet-Like Syndrome: Case Report and Literature Review. Front Pediatr 2022; 10:759889. [PMID: 35386260 PMCID: PMC8978559 DOI: 10.3389/fped.2022.759889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/07/2022] [Indexed: 02/05/2023] Open
Abstract
In the recent 3 years, subjects with Pumilio1-associated developmental disability, ataxia, and seizure syndrome have been identified as harboring Pumilio homolog 1 (PUM1) mutations. However, the characteristics of the seizure phenotype remain to be elucidated. We herein described a 3-year-old female proband who was diagnosed with developmental and epileptic encephalopathy presenting with some features suggestive of a Dravet-like syndrome. For genetic analyses, trio-based whole-exome sequencing and array comparative genomic hybridization were performed. Consequently, a de novo heterozygous missense variant was identified in exon 22 of the PUM1 gene: NM_001020658: c.3439C > T (p.Arg1147Trp). Upon thoroughly reviewing the existing literature, nine cases of PUM1 mutation-related epilepsy were identified, and their clinical features were summarized. A relationship between PUM1 mutation and clinical manifestations characteristic of a Dravet-like syndrome was proposed. To our knowledge, this is the first report of a patient with PUM1 mutation presenting with a Dravet-like syndrome.
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27
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Elevated endogenous GDNF induces altered dopamine signalling in mice and correlates with clinical severity in schizophrenia. Mol Psychiatry 2022; 27:3247-3261. [PMID: 35618883 PMCID: PMC9708553 DOI: 10.1038/s41380-022-01554-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/08/2022]
Abstract
Presynaptic increase in striatal dopamine is the primary dopaminergic abnormality in schizophrenia, but the underlying mechanisms are not understood. Here, we hypothesized that increased expression of endogenous GDNF could induce dopaminergic abnormalities that resemble those seen in schizophrenia. To test the impact of GDNF elevation, without inducing adverse effects caused by ectopic overexpression, we developed a novel in vivo approach to conditionally increase endogenous GDNF expression. We found that a 2-3-fold increase in endogenous GDNF in the brain was sufficient to induce molecular, cellular, and functional changes in dopamine signalling in the striatum and prefrontal cortex, including increased striatal presynaptic dopamine levels and reduction of dopamine in prefrontal cortex. Mechanistically, we identified adenosine A2a receptor (A2AR), a G-protein coupled receptor that modulates dopaminergic signalling, as a possible mediator of GDNF-driven dopaminergic abnormalities. We further showed that pharmacological inhibition of A2AR with istradefylline partially normalised striatal GDNF and striatal and cortical dopamine levels in mice. Lastly, we found that GDNF levels are increased in the cerebrospinal fluid of first episode psychosis patients, and in post-mortem striatum of schizophrenia patients. Our results reveal a possible contributor for increased striatal dopamine signalling in a subgroup of schizophrenia patients and suggest that GDNF-A2AR crosstalk may regulate dopamine function in a therapeutically targetable manner.
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28
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RNA-binding protein dysfunction in neurodegeneration. Essays Biochem 2021; 65:975-986. [PMID: 34927200 DOI: 10.1042/ebc20210024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 11/17/2022]
Abstract
Protein homeostasis (proteostasis) is a prerequisite for cellular viability and plasticity. In particular, post-mitotic cells such as neurons rely on a tightly regulated safeguard system that allows for regulated protein expression. Previous investigations have identified RNA-binding proteins (RBPs) as crucial regulators of protein expression in nerve cells. However, during neurodegeneration, their ability to control the proteome is progressively disrupted. In this review, we examine the malfunction of key RBPs such as TAR DNA-binding protein 43 (TDP-43), Fused in Sarcoma (FUS), Staufen, Pumilio and fragile-X mental retardation protein (FMRP). Therefore, we focus on two key aspects of RBP dysfunctions in neurodegeneration: protein aggregation and dysregulation of their target RNAs. Moreover, we discuss how the chaperone system responds to changes in the RBP-controlled transcriptome. Based on recent findings, we propose a two-hit model in which both, harmful RBP deposits and target mRNA mistranslation contribute to neurodegeneration observed in RBPathologies.
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29
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Landínez-Macías M, Urwyler O. The Fine Art of Writing a Message: RNA Metabolism in the Shaping and Remodeling of the Nervous System. Front Mol Neurosci 2021; 14:755686. [PMID: 34916907 PMCID: PMC8670310 DOI: 10.3389/fnmol.2021.755686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/18/2021] [Indexed: 01/25/2023] Open
Abstract
Neuronal morphogenesis, integration into circuits, and remodeling of synaptic connections occur in temporally and spatially defined steps. Accordingly, the expression of proteins and specific protein isoforms that contribute to these processes must be controlled quantitatively in time and space. A wide variety of post-transcriptional regulatory mechanisms, which act on pre-mRNA and mRNA molecules contribute to this control. They are thereby critically involved in physiological and pathophysiological nervous system development, function, and maintenance. Here, we review recent findings on how mRNA metabolism contributes to neuronal development, from neural stem cell maintenance to synapse specification, with a particular focus on axon growth, guidance, branching, and synapse formation. We emphasize the role of RNA-binding proteins, and highlight their emerging roles in the poorly understood molecular processes of RNA editing, alternative polyadenylation, and temporal control of splicing, while also discussing alternative splicing, RNA localization, and local translation. We illustrate with the example of the evolutionary conserved Musashi protein family how individual RNA-binding proteins are, on the one hand, acting in different processes of RNA metabolism, and, on the other hand, impacting multiple steps in neuronal development and circuit formation. Finally, we provide links to diseases that have been associated with the malfunction of RNA-binding proteins and disrupted post-transcriptional regulation.
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Affiliation(s)
- María Landínez-Macías
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Molecular Life Sciences Program, Life Science Zurich Graduate School, University of Zurich and Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Olivier Urwyler
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.,Molecular Life Sciences Program, Life Science Zurich Graduate School, University of Zurich and Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.,Neuroscience Center Zurich (ZNZ), University of Zurich, Zurich, Switzerland
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30
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Behbahanipour M, García-Pardo J, Ventura S. Decoding the role of coiled-coil motifs in human prion-like proteins. Prion 2021; 15:143-154. [PMID: 34428113 PMCID: PMC8386614 DOI: 10.1080/19336896.2021.1961569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 11/28/2022] Open
Abstract
Prions are self-propagating proteins that cause fatal neurodegenerative diseases in humans. However, increasing evidence suggests that eukaryotic cells exploit prion conformational conversion for functional purposes. A recent study delineated a group of twenty prion-like proteins in humans, characterized by the presence of low-complexity glutamine-rich sequences with overlapping coiled-coil (CCs) motifs. This is the case of Mediator complex subunit 15 (MED15), which is overexpressed in a wide range of human cancers. Biophysical studies demonstrated that the prion-like domain (PrLD) of MED15 forms homodimers in solution, sustained by CCs interactions. Furthermore, the same coiled-coil (CC) region plays a crucial role in the PrLD structural transition to a transmissible β-sheet amyloid state. In this review, we discuss the role of CCs motifs and their contribution to amyloid transitions in human prion-like domains (PrLDs), while providing a comprehensive overview of six predicted human prion-like proteins involved in transcription, gene expression, or DNA damage response and associated with human disease, whose PrLDs contain or overlap with CCs sequences. Finally, we try to rationalize how these molecular signatures might relate to both their function and involvement in disease.
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Affiliation(s)
- Molood Behbahanipour
- Institut De Biotecnologia I De Biomedicina (Ibb) and Departament De Bioquímica I Biologia Molecular, Universitat Autónoma De Barcelona, Barcelona, Spain
| | - Javier García-Pardo
- Institut De Biotecnologia I De Biomedicina (Ibb) and Departament De Bioquímica I Biologia Molecular, Universitat Autónoma De Barcelona, Barcelona, Spain
| | - Salvador Ventura
- Institut De Biotecnologia I De Biomedicina (Ibb) and Departament De Bioquímica I Biologia Molecular, Universitat Autónoma De Barcelona, Barcelona, Spain
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31
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Wang Y, Sun L, Wang L, Yu H, Yu X, Zou Y. PUM1 modulates trophoblast cell proliferation and migration through LRP6. Biochem Cell Biol 2021; 99:735-740. [PMID: 34734756 DOI: 10.1139/bcb-2021-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Preeclampsia is a severe pregnancy complication characterized by hypertension and may cause maternal morbidity and mortality. A better understanding of the essential genes involved in preeclampsia pathophysiology is urgently needed. This study investigated the function and molecular mechanisms of pumilio RNA binding family member 1 (PUM1) in extravillous trophoblast cells (EVTs). The interaction between protein and mRNA was verified by RNA pull-down assays, RNA immunoprecipitation assays, and luciferase reporter assays. The mRNA and protein levels of the genes involved were determined by RT-qPCR and western blot assays, respectively. Our results demonstrated that PUM1 could bind to the 3'-untranslated region of low-density lipoprotein receptor-related protein 6 (LRP6) mRNA, resulting in reduced expression of LRP6 mRNA and protein. Repression of PUM1 resulted in enhanced colony formation, cell proliferation, migration, and invasion of EVTs. The PUM1-depletion-mediated promotion effects on EVTs could be abrogated by LRP6 knockdown. PUM1 regulates the growth and mobility of EVTs by modulating LRP6 expression. Developing strategies to balance PUM1 and LRP6 levels may be beneficial for the management of preeclampsia patients.
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Affiliation(s)
- Yuping Wang
- Department of Obstetrics and Gynecology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangding East Road, Yantai, Shandong 264000, China.,Department of Obstetrics and Gynecology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangding East Road, Yantai, Shandong 264000, China
| | - Li Sun
- Department of Obstetrics and Gynecology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangding East Road, Yantai, Shandong 264000, China.,Department of Obstetrics and Gynecology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangding East Road, Yantai, Shandong 264000, China
| | - Lanlan Wang
- Department of Obstetrics and Gynecology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangding East Road, Yantai, Shandong 264000, China.,Department of Obstetrics and Gynecology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangding East Road, Yantai, Shandong 264000, China
| | - Hui Yu
- Department of Obstetrics and Gynecology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangding East Road, Yantai, Shandong 264000, China.,Department of Obstetrics and Gynecology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangding East Road, Yantai, Shandong 264000, China
| | - Xiaoyan Yu
- Department of Obstetrics and Gynecology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangding East Road, Yantai, Shandong 264000, China.,Department of Obstetrics and Gynecology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangding East Road, Yantai, Shandong 264000, China
| | - Yanfen Zou
- Department of Obstetrics and Gynecology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangding East Road, Yantai, Shandong 264000, China.,Department of Obstetrics and Gynecology, the Affiliated Yantai Yuhuangding Hospital of Qingdao University, No. 20 Yuhuangding East Road, Yantai, Shandong 264000, China
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32
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Abstract
The term SCA refers to a phenotypically and genetically heterogeneous group of autosomal dominant spinocerebellar ataxias. Phenotypically they present as gait ataxia frequently in combination with dysarthria and oculomotor problems. Additional signs and symptoms are common and can include various pyramidal and extrapyramidal signs and intellectual impairment. Genetic causes of SCAs are either repeat expansions within disease genes or common mutations (point mutations, deletions, insertions etc.). Frequently the two types of mutations cause indistinguishable phenotypes (locus heterogeneity). This article focuses on SCAs caused by common mutations. It describes phenotype and genotype of the presently 27 types known and discusses the molecular pathogenesis in those 21 types where the disease gene has been identified. Apart from the dominant types, the article also summarizes findings in a variant caused by mutations in a mitochondrial gene. Possible common disease mechanisms are considered based on findings in the various SCAs described.
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Affiliation(s)
- Ulrich Müller
- Institute of Human Genetics, JLU-Gießen, Schlangenzahl 14, 35392, Giessen, Germany.
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33
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Yin S, Liao Q, Wang Y, Shi Q, Xia P, Yi M, Huang J. Ccdc134 deficiency impairs cerebellar development and motor coordination. GENES, BRAIN, AND BEHAVIOR 2021; 20:e12763. [PMID: 34382738 DOI: 10.1111/gbb.12763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 11/28/2022]
Abstract
Coiled-coil domain containing 134 (CCDC134) has been shown to serve as an immune cytokine to exert antitumor effects and to act as a novel regulator of hADA2a to affect PCAF acetyltransferase activity. While Ccdc134 loss causes abnormal brain development in mice, the significance of CCDC134 in neuronal development in vivo is controversial. Here, we report that CCDC134 is highly expressed in Purkinje cells (PCs) at all developmental stages and regulates mammalian cerebellar development in a cell type-specific manner. Selective deletion of Ccdc134 in mouse neural stem cells (NSCs) caused defects in cerebellar morphogenesis, including a decrease in the number of PCs and impairment of PC dendritic growth, as well as abnormal granule cell development. Moreover, loss of Ccdc134 caused progressive motor dysfunction with deficits in motor coordination and motor learning. Finally, Ccdc134 deficiency inhibited Wnt signaling but increased Ataxin1 levels. Our findings provide evidence that CCDC134 plays an important role in cerebellar development, possibly through regulating Wnt signaling and Ataxin1 expression levels, and in controlling cerebellar function for motor coordination and motor learning, ultimately making it a potential contributor to cerebellar pathogenesis.
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Affiliation(s)
- Sha Yin
- Department of Immunology, School of Basic Medical Sciences, Peking University, and NHC Key Laboratory of Medical Immunology (Peking University), Beijing, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China
| | - Qinyuan Liao
- Department of Immunology, Guilin Medical University, Guilin, Guangxi province, China
| | - Yida Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University, and NHC Key Laboratory of Medical Immunology (Peking University), Beijing, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China
| | - Qianwen Shi
- Department of Immunology, School of Basic Medical Sciences, Peking University, and NHC Key Laboratory of Medical Immunology (Peking University), Beijing, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China
| | - Peng Xia
- Department of Immunology, School of Basic Medical Sciences, Peking University, and NHC Key Laboratory of Medical Immunology (Peking University), Beijing, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China
| | - Ming Yi
- Neuroscience Research Institute and Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, China
| | - Jing Huang
- Department of Immunology, School of Basic Medical Sciences, Peking University, and NHC Key Laboratory of Medical Immunology (Peking University), Beijing, China
- Key Laboratory of Molecular Immunology, Chinese Academy of Medical Sciences, Beijing, China
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34
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Rodrigues DC, Mufteev M, Ellis J. Regulation, diversity and function of MECP2 exon and 3'UTR isoforms. Hum Mol Genet 2021; 29:R89-R99. [PMID: 32681172 PMCID: PMC7530521 DOI: 10.1093/hmg/ddaa154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/12/2020] [Accepted: 07/14/2020] [Indexed: 12/11/2022] Open
Abstract
The methyl-CpG-binding protein 2 (MECP2) is a critical global regulator of gene expression. Mutations in MECP2 cause neurodevelopmental disorders including Rett syndrome (RTT). MECP2 exon 2 is spliced into two alternative messenger ribonucleic acid (mRNA) isoforms encoding MECP2-E1 or MECP2-E2 protein isoforms that differ in their N-termini. MECP2-E2, isolated first, was used to define the general roles of MECP2 in methyl-deoxyribonucleic acid (DNA) binding, targeting of transcriptional regulatory complexes, and its disease-causing impact in RTT. It was later found that MECP2-E1 is the most abundant isoform in the brain and its exon 1 is also mutated in RTT. MECP2 transcripts undergo alternative polyadenylation generating mRNAs with four possible 3'untranslated region (UTR) lengths ranging from 130 to 8600 nt. Together, the exon and 3'UTR isoforms display remarkable abundance disparity across cell types and tissues during development. These findings indicate discrete means of regulation and suggest that protein isoforms perform non-overlapping roles. Multiple regulatory programs have been explored to explain these disparities. DNA methylation patterns of the MECP2 promoter and first intron impact MECP2-E1 and E2 isoform levels. Networks of microRNAs and RNA-binding proteins also post-transcriptionally regulate the stability and translation efficiency of MECP2 3'UTR isoforms. Finally, distinctions in biophysical properties in the N-termini between MECP2-E1 and E2 lead to variable protein stabilities and DNA binding dynamics. This review describes the steps taken from the discovery of MECP2, the description of its key functions, and its association with RTT, to the emergence of evidence revealing how MECP2 isoforms are differentially regulated at the transcriptional, post-transcriptional and post-translational levels.
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Affiliation(s)
- Deivid Carvalho Rodrigues
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto ON M5G 0A4, Canada
| | - Marat Mufteev
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto ON M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto ON M5S 1A8, Canada
| | - James Ellis
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto ON M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto ON M5S 1A8, Canada
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35
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Li X, Yang J, Chen X, Cao D, Xu EY. PUM1 represses CDKN1B translation and contributes to prostate cancer progression. J Biomed Res 2021; 35:371-382. [PMID: 34531333 PMCID: PMC8502688 DOI: 10.7555/jbr.35.20210067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Posttranscriptional regulation of cancer gene expression programs plays a vital role in carcinogenesis; identifying the critical regulators of tumorigenesis and their molecular targets may provide novel strategies for cancer diagnosis and therapeutics. Highly conserved RNA-binding protein Pumilio-1 (PUM1) regulates mouse growth and cell proliferation, propelling us to examine its role in cancer. We found human PUM1 is highly expressed in a diverse group of cancer, including prostate cancer; enhanced PUM1 expression is also correlated with reduced survival among prostate cancer patients. Detailed expression analysis in twenty prostate cancer tissues showed enhanced expression of PUM1 at mRNA and protein levels. Knockdown of PUM1 reduced prostate cancer cell proliferation and colony formation, and subcutaneous injection of PUM1 knockdown cells led to reduced tumor size. Downregulation of PUM1 in prostate cancer cells consistently elevated cyclin-dependent kinase inhibitor 1B (CDKN1B) protein expression through increased translation but did not impact its mRNA level, while overexpression of PUM1 reduced CDKN1B protein level. Our finding established a critical role of PUM1 mediated translational control, particularly the PUM1-CDKN1B axis, in prostate cancer cell growth and tumorigenesis. We proposed that PUM1-CDKN1B regulatory axis may represent a novel mechanism for the loss of CDKN1B protein expression in diverse cancers and potential targets for therapeutics development.
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Affiliation(s)
- Xin Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jian Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Urology, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xia Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Dandan Cao
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Eugene Yujun Xu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China.,Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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36
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Lou MM, Tang XQ, Wang GM, He J, Luo F, Guan MF, Wang F, Zou H, Wang JY, Zhang Q, Xu MJ, Shi QL, Shen LB, Ma GM, Wu Y, Zhang YY, Liang AB, Wang TH, Xiong LL, Wang J, Xu J, Wang WY. Long noncoding RNA BS-DRL1 modulates the DNA damage response and genome stability by interacting with HMGB1 in neurons. Nat Commun 2021; 12:4075. [PMID: 34210972 PMCID: PMC8249382 DOI: 10.1038/s41467-021-24236-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/09/2021] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are known to regulate DNA damage response (DDR) and genome stability in proliferative cells. However, it remains unknown whether lncRNAs are involved in these vital biological processes in post-mitotic neurons. Here, we report and characterize a lncRNA, termed Brain Specific DNA-damage Related lncRNA1 (BS-DRL1), in the central nervous system. BS-DRL1 is a brain-specific lncRNA and depletion of BS-DRL1 in neurons leads to impaired DDR upon etoposide treatment in vitro. Mechanistically, BS-DRL1 interacts with HMGB1, a chromatin protein that is important for genome stability, and is essential for the assembly of HMGB1 on chromatin. BS-DRL1 mediated DDR exhibits cell-type specificity in the cortex and cerebellum in gamma-irradiated mice and BS-DRL1 knockout mice show impaired motor function and concomitant purkinje cell degeneration. Our study extends the understanding of lncRNAs in DDR and genome stability and implies a protective role of lncRNA against neurodegeneration.
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Affiliation(s)
- Min-Min Lou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Qiang Tang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guang-Ming Wang
- East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Hematology, Tongji Hospital of Tongji University School of Medicine, Shanghai, China
- Postdoctoral Station of Clinical Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jia He
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fang Luo
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
| | - Ming-Feng Guan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huan Zou
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Ying Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qun Zhang
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Ming-Jian Xu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
| | - Qi-Li Shi
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
| | - Li-Bing Shen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
| | - Guo-Ming Ma
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Wu
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yao-Yang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China
| | - Ai-Bin Liang
- Postdoctoral Station of Clinical Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ting-Hua Wang
- Animal Center of Zoology, Institute of Neuroscience, Kunming medical University, Kunming, China
| | - Liu-Lin Xiong
- Animal Center of Zoology, Institute of Neuroscience, Kunming medical University, Kunming, China
| | - Jian Wang
- Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Jing'an District, Shanghai, China.
| | - Jun Xu
- East Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Wen-Yuan Wang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese academy of Science, Shanghai, 200032, China.
- Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai, China.
- Animal Center of Zoology, Institute of Neuroscience, Kunming medical University, Kunming, China.
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37
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Huang R, Liu M, Gong G, Wu P, Patra B, Yuan L, Qin H, Wang X, Wang G, Liao H, Gao L, Yang C, Li H, Zhang S. The Pumilio RNA-binding protein APUM24 regulates seed maturation by fine-tuning the BPM-WRI1 module in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1240-1259. [PMID: 33729679 DOI: 10.1111/jipb.13092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/15/2021] [Indexed: 05/25/2023]
Abstract
Pumilio RNA-binding proteins participate in messenger RNA (mRNA) degradation and translational repression, but their roles in plant development are largely unclear. Here, we show that Arabidopsis PUMILIO PROTEIN24 (APUM24), an atypical Pumilio-homology domain-containing protein, plays an important part in regulating seed maturation, a major stage of plant development. APUM24 is strongly expressed in maturing seeds. Reducing APUM24 expression resulted in abnormal seed maturation, wrinkled seeds, and lower seed oil contents, and APUM24 knockdown resulted in lower levels of WRINKLED 1 (WRI1), a key transcription factor controlling seed oil accumulation, and lower expression of WRI1 target genes. APUM24 reduces the mRNA stability of BTB/POZMATH (BPM) family genes, thus decreasing BPM protein levels. BPM is responsible for the 26S proteasome-mediated degradation of WRI1 and has important functions in plant growth and development. The 3' untranslated regions of BPM family genes contain putative Pumilio response elements (PREs), which are bound by APUM24. Reduced BPM or increased WRI1 expression rescued the deficient seed maturation of apum24-2 knockdown mutants, and APUM24 overexpression resulted in increased seed size and weight. Therefore, APUM24 is crucial to seed maturation through its action as a positive regulator fine-tuning the BPM-WRI1 module, making APUM24 a promising target for breeding strategies to increase crop yields.
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Affiliation(s)
- Ruihua Huang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Mengling Liu
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Guanping Gong
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Pingzhi Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Barunava Patra
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, 40546, USA
| | - Ling Yuan
- Department of Plant and Soil Sciences and Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, 40546, USA
| | - Hongting Qin
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xiaoxu Wang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Guohe Wang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Huimei Liao
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Lu Gao
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Chengwei Yang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Hongqing Li
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Shengchun Zhang
- Guangdong Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou, 510631, China
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38
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Zwaka TP, Skowronska M, Richman R, Dejosez M. Ronin overexpression induces cerebellar degeneration in a mouse model of ataxia. Dis Model Mech 2021; 14:269269. [PMID: 34165550 PMCID: PMC8246265 DOI: 10.1242/dmm.044834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/18/2021] [Indexed: 11/26/2022] Open
Abstract
Spinocerebellar ataxias (SCAs) are a group of genetically heterogeneous inherited neurodegenerative disorders characterized by progressive ataxia and cerebellar degeneration. Here, we used a mouse model to test a possible connection between SCA and Ronin (Thap11), a polyglutamine-containing transcriptional regulator encoded in a region of human chromosome 16q22.1 that has been genetically linked to SCA type 4. We report that transgenic expression of Ronin in mouse cerebellar Purkinje cells leads to detrimental loss of these cells and the development of severe ataxia as early as 10 weeks after birth. Mechanistically, we find that several SCA-causing genes harbor Ronin DNA-binding motifs and are transcriptionally deregulated in transgenic animals. In addition, ectopic expression of Ronin in embryonic stem cells significantly increases the protein level of Ataxin-1, the protein encoded by Atxn1, alterations of which cause SCA type 1. This increase is also seen in the cerebellum of transgenic animals, although the latter was not statistically significant. Hence, our data provide evidence for a link between Ronin and SCAs, and suggest that Ronin may be involved in the development of other neurodegenerative diseases. Summary: Ronin is a polyglutamine protein encoded in a region of human chromosome 16q22.1 linked to spinocerebellar ataxia type 4. Overexpression of Ronin in mouse cerebellar Purkinje cells leads to their loss and ataxia.
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Affiliation(s)
- Thomas P Zwaka
- Department for Cell, Regenerative and Developmental Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Huffington Center for Cell-Based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marta Skowronska
- Department for Cell, Regenerative and Developmental Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Huffington Center for Cell-Based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ronald Richman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.,Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marion Dejosez
- Department for Cell, Regenerative and Developmental Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Huffington Center for Cell-Based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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39
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NORAD-induced Pumilio phase separation is required for genome stability. Nature 2021; 595:303-308. [PMID: 34108682 DOI: 10.1038/s41586-021-03633-w] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/11/2021] [Indexed: 01/10/2023]
Abstract
Liquid-liquid phase separation is a major mechanism of subcellular compartmentalization1,2. Although the segregation of RNA into phase-separated condensates broadly affects RNA metabolism3,4, whether and how specific RNAs use phase separation to regulate interacting factors such as RNA-binding proteins (RBPs), and the phenotypic consequences of such regulatory interactions, are poorly understood. Here we show that RNA-driven phase separation is a key mechanism through which a long noncoding RNA (lncRNA) controls the activity of RBPs and maintains genomic stability in mammalian cells. The lncRNA NORAD prevents aberrant mitosis by inhibiting Pumilio (PUM) proteins5-8. We show that NORAD can out-compete thousands of other PUM-binding transcripts to inhibit PUM by nucleating the formation of phase-separated PUM condensates, termed NP bodies. Dual mechanisms of PUM recruitment, involving multivalent PUM-NORAD and PUM-PUM interactions, enable NORAD to competitively sequester a super-stoichiometric amount of PUM in NP bodies. Disruption of NORAD-driven PUM phase separation leads to PUM hyperactivity and genome instability that is rescued by synthetic RNAs that induce the formation of PUM condensates. These results reveal a mechanism by which RNA-driven phase separation can regulate RBP activity and identify an essential role for this process in genome maintenance. The repetitive sequence architecture of NORAD and other lncRNAs9-11 suggests that phase separation may be a widely used mechanism of lncRNA-mediated regulation.
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40
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Systematic Analysis of Targets of Pumilio-Mediated mRNA Decay Reveals that PUM1 Repression by DNA Damage Activates Translesion Synthesis. Cell Rep 2021; 31:107542. [PMID: 32375027 DOI: 10.1016/j.celrep.2020.107542] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 01/28/2020] [Accepted: 03/31/2020] [Indexed: 02/07/2023] Open
Abstract
RNA-binding proteins (RBPs) play a pivotal role in gene expression by modulating the stability of transcripts. However, the identification of degradation target mRNAs of RBPs remains difficult. By the combined analysis of transcriptome-wide mRNA stabilities and the binding of mRNAs to human Pumilio 1 (PUM1), we identify 48 mRNAs that both bind to PUM1 and exhibit PUM1-dependent degradation. Analysis of changes in the abundance of PUM1 and its degradation target mRNAs in RNA-seq data indicate that DNA-damaging agents negatively regulate PUM1-mediated mRNA decay. Cells exposed to cisplatin have reduced PUM1 abundance and increased PCNA and UBE2A mRNAs encoding proteins involved in DNA damage tolerance by translesion synthesis (TLS). Cells overexpressing PUM1 exhibit impaired DNA synthesis and TLS and increased sensitivity to the cytotoxic effect of cisplatin. Thus, our method identifies target mRNAs of PUM1-mediated decay and reveals that cells respond to DNA damage by inhibiting PUM1-mediated mRNA decay to activate TLS.
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41
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Xie M, Swanson MS. UTteR control through miRs: fine-tuning ATXN1 levels to prevent ataxia. Genes Dev 2021; 34:1107-1109. [PMID: 32873576 PMCID: PMC7462066 DOI: 10.1101/gad.343020.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This Outlook discusses the insights by Nitschke et al. into the multitiered posttranscriptional regulatory schemes required to fine-tune the levels of a dosage-sensitive gene implicated in multiple neurodegenerative diseases. Pathomechanistic studies of neurodegenerative diseases have documented the toxic effects of mutant protein expression, misfolding, and aggregation. However, alterations in the expression of the corresponding wild-type (WT) gene, due to either variations in copy number or transcriptional regulation, have also been linked to Alzheimer's and Parkinson's diseases. Another striking example of this mutant and WT duality is spinocerebellar ataxia type 1 (SCA1) caused by an ATXN1 polyglutamine protein, although subtle variations in WT AXTN1 levels also lead to ataxia. In this issue of Genes & Development, Nitschke and colleagues (pp. 1147–1160) delve into posttranscriptional events that fine-tune ATXN1 expression and uncover a key role for 5′ untranslated region (5′ UTR)–miR760 interactions. Thus, this study not only provides significant insights into the complexities of modulating the expression of a dosage-sensitive gene but also highlights the critical importance of identifying noncoding polymorphisms as disease risk factors.
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Affiliation(s)
- Mingyi Xie
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, the Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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42
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Enwerem III, Elrod ND, Chang CT, Lin A, Ji P, Bohn JA, Levdansky Y, Wagner EJ, Valkov E, Goldstrohm AC. Human Pumilio proteins directly bind the CCR4-NOT deadenylase complex to regulate the transcriptome. RNA (NEW YORK, N.Y.) 2021; 27:445-464. [PMID: 33397688 PMCID: PMC7962487 DOI: 10.1261/rna.078436.120] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/28/2020] [Indexed: 05/13/2023]
Abstract
Pumilio paralogs, PUM1 and PUM2, are sequence-specific RNA-binding proteins that are essential for vertebrate development and neurological functions. PUM1&2 negatively regulate gene expression by accelerating degradation of specific mRNAs. Here, we determined the repression mechanism and impact of human PUM1&2 on the transcriptome. We identified subunits of the CCR4-NOT (CNOT) deadenylase complex required for stable interaction with PUM1&2 and to elicit CNOT-dependent repression. Isoform-level RNA sequencing revealed broad coregulation of target mRNAs through the PUM-CNOT repression mechanism. Functional dissection of the domains of PUM1&2 identified a conserved amino-terminal region that confers the predominant repressive activity via direct interaction with CNOT. In addition, we show that the mRNA decapping enzyme, DCP2, has an important role in repression by PUM1&2 amino-terminal regions. Our results support a molecular model of repression by human PUM1&2 via direct recruitment of CNOT deadenylation machinery in a decapping-dependent mRNA decay pathway.
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Affiliation(s)
- Isioma I I Enwerem
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Nathan D Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77550, USA
| | - Chung-Te Chang
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ai Lin
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77550, USA
| | - Ping Ji
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77550, USA
| | - Jennifer A Bohn
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yevgen Levdansky
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77550, USA
| | - Eugene Valkov
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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43
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Pei J, Wang G, Feng L, Zhang J, Jiang T, Sun Q, Ouyang L. Targeting Lysosomal Degradation Pathways: New Strategies and Techniques for Drug Discovery. J Med Chem 2021; 64:3493-3507. [PMID: 33764774 DOI: 10.1021/acs.jmedchem.0c01689] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A series of tools for targeted protein degradation are inspiring scientists to develop new drugs with advantages over traditional small-molecule drugs. Among these tools, proteolysis-targeting chimeras (PROTACs) are most representative of the technology based on proteasomes. However, the proteasome has little degradation effect on certain macromolecular proteins or aggregates, extracellular proteins, and organelles, which limits the application of PROTACs. Additionally, lysosomes play an important role in protein degradation. Therefore, lysosome-induced protein degradation drugs can directly regulate protein levels in vivo, achieve the goal of treating diseases, and provide new strategies for drug discovery. Lysosome-based degradation technology has the potential for clinical translation. In this review, strategies targeting lysosomal pathways and lysosome-based degradation techniques are summarized. In addition, lysosome-based degrading drugs are described, and the advantages and challenges are listed. Our efforts will certainly promote the design, discovery, and clinical application of drugs associated with this technology.
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Affiliation(s)
- Junping Pei
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lu Feng
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Jifa Zhang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Tingting Jiang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Qiu Sun
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
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44
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Lee WS, Lavery L, Rousseaux MWC, Rutledge EB, Jang Y, Wan YW, Wu SR, Kim W, Al-Ramahi I, Rath S, Adamski CJ, Bondar VV, Tewari A, Soleimani S, Mota S, Yalamanchili HK, Orr HT, Liu Z, Botas J, Zoghbi HY. Dual targeting of brain region-specific kinases potentiates neurological rescue in Spinocerebellar ataxia type 1. EMBO J 2021; 40:e106106. [PMID: 33709453 DOI: 10.15252/embj.2020106106] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 02/01/2021] [Accepted: 02/10/2021] [Indexed: 12/26/2022] Open
Abstract
A critical question in neurodegeneration is why the accumulation of disease-driving proteins causes selective neuronal loss despite their brain-wide expression. In Spinocerebellar ataxia type 1 (SCA1), accumulation of polyglutamine-expanded Ataxin-1 (ATXN1) causes selective degeneration of cerebellar and brainstem neurons. Previous studies revealed that inhibiting Msk1 reduces phosphorylation of ATXN1 at S776 as well as its levels leading to improved cerebellar function. However, there are no regulators that modulate ATXN1 in the brainstem-the brain region whose pathology is most closely linked to premature death. To identify new regulators of ATXN1, we performed genetic screens and identified a transcription factor-kinase axis (ZBTB7B-RSK3) that regulates ATXN1 levels. Unlike MSK1, RSK3 is highly expressed in the human and mouse brainstems where it regulates Atxn1 by phosphorylating S776. Reducing Rsk3 rescues brainstem-associated pathologies and deficits, and lowering Rsk3 and Msk1 together improves cerebellar and brainstem function in an SCA1 mouse model. Our results demonstrate that selective vulnerability of brain regions in SCA1 is governed by region-specific regulators of ATXN1, and targeting multiple regulators could rescue multiple degenerating brain areas.
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Affiliation(s)
- Won-Seok Lee
- Integrative Molecular and Biomedical Science Program, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Laura Lavery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Maxime W C Rousseaux
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Eric B Rutledge
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Youjin Jang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Ying-Wooi Wan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Sih-Rong Wu
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Wonho Kim
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Howard Hughes Medical Institute, Houston, TX, USA
| | - Ismael Al-Ramahi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Smruti Rath
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Carolyn J Adamski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Howard Hughes Medical Institute, Houston, TX, USA
| | - Vitaliy V Bondar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Ambika Tewari
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Shirin Soleimani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Samantha Mota
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Hari K Yalamanchili
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Harry T Orr
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Juan Botas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Huda Y Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA.,Howard Hughes Medical Institute, Houston, TX, USA
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45
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Liu Z, Sun H, Dai J, Xue X, Sun J, Wang X. ITPR1 Mutation Contributes to Hemifacial Microsomia Spectrum. Front Genet 2021; 12:616329. [PMID: 33747042 PMCID: PMC7971309 DOI: 10.3389/fgene.2021.616329] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/28/2021] [Indexed: 11/13/2022] Open
Abstract
Hemifacial microsomia (HM) is a craniofacial congenital defect involving the first and second branchial arch, mainly characterized by ocular, ear, maxilla-zygoma complex, mandible, and facial nerve malformation. HM follows autosomal dominant inheritance. Whole-exome sequencing of a family revealed a missense mutation in a highly conserved domain of ITPR1. ITPR1 is a calcium ion channel. By studying ITPR1's expression pattern, we found that ITPR1 participated in craniofacial development, especially the organs that corresponded to the phenotype of HM. In zebrafish, itpr1b, which is homologous to human ITPR1, is closely related to craniofacial bone formation. The knocking down of itpr1b in zebrafish could lead to a remarkable decrease in craniofacial skeleton formation. qRT-PCR suggested that knockdown of itpr1b could increase the expression of plcb4 while decreasing the mRNA level of Dlx5/6. Our findings highlighted ITPR1's role in craniofacial formation for the first time and suggested that ITPR1 mutation contributes to human HM.
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Affiliation(s)
- Zhixu Liu
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration, Ministry of Education, Tongji University, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Hao Sun
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jiewen Dai
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Xiaochen Xue
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jian Sun
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Xudong Wang
- Department of Oral and Cranio-Maxillofacial Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
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46
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Abstract
A new study shows that the pioneer transcription factor BLMP-1 governs the cyclic transcriptional output of hundreds of genes during Caenorhabditis elegans larval development. BLMP-1 is also critical for restarting the proper developmental dynamics of gene expression after nutritionally induced developmental arrest.
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Affiliation(s)
- Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA, USA.
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47
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Pan MK, Li YS, Wong SB, Ni CL, Wang YM, Liu WC, Lu LY, Lee JC, Cortes EP, Vonsattel JPG, Sun Q, Louis ED, Faust PL, Kuo SH. Cerebellar oscillations driven by synaptic pruning deficits of cerebellar climbing fibers contribute to tremor pathophysiology. Sci Transl Med 2021; 12:12/526/eaay1769. [PMID: 31941824 DOI: 10.1126/scitranslmed.aay1769] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
Abstract
Essential tremor (ET) is one of the most common movement disorders and the prototypical disorder for abnormal rhythmic movements. However, the pathophysiology of tremor generation in ET remains unclear. Here, we used autoptic cerebral tissue from patients with ET, clinical data, and mouse models to report that synaptic pruning deficits of climbing fiber (CF)-to-Purkinje cell (PC) synapses, which are related to glutamate receptor delta 2 (GluRδ2) protein insufficiency, cause excessive cerebellar oscillations and might be responsible for tremor. The CF-PC synaptic pruning deficits were correlated with the reduction in GluRδ2 expression in the postmortem ET cerebellum. Mice with GluRδ2 insufficiency and CF-PC synaptic pruning deficits develop ET-like tremor that can be suppressed with viral rescue of GluRδ2 protein. Step-by-step optogenetic or pharmacological inhibition of neuronal firing, axonal activity, or synaptic vesicle release confirmed that the activity of the excessive CF-to-PC synapses is required for tremor generation. In vivo electrophysiology in mice showed that excessive cerebellar oscillatory activity is CF dependent and necessary for tremor and optogenetic-driven PC synchronization was sufficient to generate tremor in wild-type animals. Human validation by cerebellar electroencephalography confirmed that excessive cerebellar oscillations also exist in patients with ET. Our findings identify a pathophysiologic contribution to tremor at molecular (GluRδ2), structural (CF-to-PC synapses), physiological (cerebellar oscillations), and behavioral levels (kinetic tremor) that might have clinical applications for treating ET.
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Affiliation(s)
- Ming-Kai Pan
- Department of Medical Research, National Taiwan University Hospital, Taipei City 10002, Taiwan. .,Institute of Pharmacology, College of Medicine, National Taiwan University Hospital, Taipei City 10051, Taiwan.,Neurobiology and Cognitive Science Center, National Taiwan University, Taipei City 10051, Taiwan.,Molecular Imaging Center, National Taiwan University, Taipei City 10051, Taiwan.,Department of Neurology, National Taiwan University Hospital, Yun-Lin Branch, Yun-Lin 64041, Taiwan
| | - Yong-Shi Li
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Shi-Bing Wong
- Department of Neurology, Columbia University, New York, NY 10032, USA.,Department of Pediatrics, Taipei Tzu Chi Hospital, Tzu Chi Medical Foundation, New Taipei City 23142, Taiwan
| | - Chun-Lun Ni
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Yi-Mei Wang
- Department of Neurology, National Taiwan University Hospital, Yun-Lin Branch, Yun-Lin 64041, Taiwan
| | - Wen-Chuan Liu
- Department of Medical Research, National Taiwan University Hospital, Taipei City 10002, Taiwan.,Institute of Pharmacology, College of Medicine, National Taiwan University Hospital, Taipei City 10051, Taiwan
| | - Liang-Yin Lu
- Neurobiology and Cognitive Science Center, National Taiwan University, Taipei City 10051, Taiwan
| | - Jye-Chang Lee
- Molecular Imaging Center, National Taiwan University, Taipei City 10051, Taiwan
| | - Etty P Cortes
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Jean-Paul G Vonsattel
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Qian Sun
- Department of Neuroscience, Columbia University, New York, NY 10032, USA.,Department of Neurosciences, Case Western Reserve University, Cleveland, OH 44016, USA
| | - Elan D Louis
- Department of Neurology, Yale School of Medicine, Yale University, New Haven, CT 06519, USA.,Department of Chronic Disease Epidemiology, Yale School of Public Health, Yale University, New Haven, CT 06510, USA
| | - Phyllis L Faust
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Sheng-Han Kuo
- Department of Neurology, Columbia University, New York, NY 10032, USA. .,Initiative of Columbia Ataxia and Tremor, New York, NY 10032, USA
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48
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Takei N, Takada Y, Kawamura S, Sato K, Saitoh A, Bormann J, Yuen WS, Carroll J, Kotani T. Changes in subcellular structures and states of pumilio 1 regulate the translation of target Mad2 and cyclin B1 mRNAs. J Cell Sci 2020; 133:jcs249128. [PMID: 33148609 DOI: 10.1242/jcs.249128] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Temporal and spatial control of mRNA translation has emerged as a major mechanism for promoting diverse biological processes. However, the molecular nature of temporal and spatial control of translation remains unclear. In oocytes, many mRNAs are deposited as a translationally repressed form and are translated at appropriate times to promote the progression of meiosis and development. Here, we show that changes in subcellular structures and states of the RNA-binding protein pumilio 1 (Pum1) regulate the translation of target mRNAs and progression of oocyte maturation. Pum1 was shown to bind to Mad2 (also known as Mad2l1) and cyclin B1 mRNAs, assemble highly clustered aggregates, and surround Mad2 and cyclin B1 RNA granules in mouse oocytes. These Pum1 aggregates were dissolved prior to the translational activation of target mRNAs, possibly through phosphorylation. Stabilization of Pum1 aggregates prevented the translational activation of target mRNAs and progression of oocyte maturation. Together, our results provide an aggregation-dissolution model for the temporal and spatial control of translation.
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Affiliation(s)
- Natsumi Takei
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Yuki Takada
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Shohei Kawamura
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Keisuke Sato
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Atsushi Saitoh
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Jenny Bormann
- Development and Stem Cells Program and Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Wai Shan Yuen
- Development and Stem Cells Program and Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - John Carroll
- Development and Stem Cells Program and Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria 3800, Australia
| | - Tomoya Kotani
- Biosystems Science Course, Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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49
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Wolfe MB, Schagat TL, Paulsen MT, Magnuson B, Ljungman M, Park D, Zhang C, Campbell ZT, Goldstrohm AC, Freddolino PL. Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis. RNA (NEW YORK, N.Y.) 2020; 26:1680-1703. [PMID: 32753408 PMCID: PMC7566576 DOI: 10.1261/rna.077362.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/30/2020] [Indexed: 05/27/2023]
Abstract
The human PUF-family proteins, PUM1 and PUM2, posttranscriptionally regulate gene expression by binding to a PUM recognition element (PRE) in the 3'-UTR of target mRNAs. Hundreds of PUM1/2 targets have been identified from changes in steady-state RNA levels; however, prior studies could not differentiate between the contributions of changes in transcription and RNA decay rates. We applied metabolic labeling to measure changes in RNA turnover in response to depletion of PUM1/2, showing that human PUM proteins regulate expression almost exclusively by changing RNA stability. We also applied an in vitro selection workflow to precisely identify the binding preferences of PUM1 and PUM2. By integrating our results with prior knowledge, we developed a "rulebook" of key contextual features that differentiate functional versus nonfunctional PREs, allowing us to train machine learning models that accurately predict the functional regulation of RNA targets by the human PUM proteins.
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Affiliation(s)
- Michael B Wolfe
- Department of Biological Chemistry and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | | | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Brian Magnuson
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Daeyoon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Chi Zhang
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Zachary T Campbell
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Peter L Freddolino
- Department of Biological Chemistry and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
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50
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Li L, Meng H, Zhang J, Liu Y, Zou Q, Gao Y, Yang H, Lai L. A tunable, rapid, and precise drug control of protein expression by combining transcriptional and post-translational regulation systems. J Genet Genomics 2020; 47:705-712. [PMID: 33549479 DOI: 10.1016/j.jgg.2020.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/10/2020] [Accepted: 07/20/2020] [Indexed: 10/23/2022]
Abstract
Rapid, precise, and tunable regulation of protein abundance would be significantly useful in a variety of biotechnologies and biomedical applications. Here, we describe a system that allows tunable and rapid drug control of gene expression for either gene activation or inactivation in mammalian cells. We construct the system by coupling Tet-on 3G and small molecule-assisted shutoff systems, which can respectively induce transcriptional activation and protein degradation in the presence of corresponding small molecules. This dual-input drug inducer regulation system facilitates a bidirectional control of gene expression. The gene of interest can be precisely controlled by dual small molecules in a broad dynamic range of expression from overexpression to complete silence, allowing gene function study in a comprehensive expression profile. Our results reveal that the bidirectional control system enables sensitive dosage- and time-dependent regulation for either turn-on or shutoff of gene expression. We also apply this system for inducible genome editing and gene activation mediated by clustered regularly interspaced short palindromic repeats. The system provides an integrated platform for studying multiple biological processes by manipulating gene expression in a more flexible way.
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Affiliation(s)
- Li Li
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Hongyi Meng
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Jianmin Zhang
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China
| | - Yang Liu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Qingjian Zou
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.
| | - Yi Gao
- Department of Hepatobiliary Surgery II, Guangdong Provincial Research Center for Artificial Organ and Tissue Engineering, Institute of Regenerative Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China.
| | - Huaqiang Yang
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Liangxue Lai
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.
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