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Chang N, Wei Wei, Wang S, Hou S, Sui Y, Taoyang, He J, Ren Y, Chen G, Bu C. The metabolomics analysis of cecal contents elucidates significant metabolites involved in the therapeutic effects of total flavonoids derived from Sonchus arvensis L. in male C57BL/6 mice with ulcerative colitis. Heliyon 2024; 10:e32790. [PMID: 39005925 PMCID: PMC11239596 DOI: 10.1016/j.heliyon.2024.e32790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 07/16/2024] Open
Abstract
Ulcerative colitis (UC), an inflammatory disease affecting the colon and rectal mucosa, is characterized by chronic and heterogeneous behavior of unknown origin. The primary cause of UC is chronic inflammation, which is closely linked to the development of colorectal cancer. Sonchus arvensis L. (SAL), a plant consumed worldwide for its nutritional and medicinal properties, holds significance in this context. In this study, we employed the total flavone in SAL as a treatment for male C57BL/6 mice with UC. The cecal contents metabolic profile of C57BL/6 mice in different groups, including UC (group ML; n = 5), UC treated with aspirin (group AN; n = 5), UC treated with the total flavone in SAL (group FE; n = 5), and healthy male C57BL/6 mice (group CL; n = 5), was examined using UHPLC-Triple-TOF-MS. Through the identification of variations in key metabolites associated with UC and the exploration of their underlying biological mechanisms, our understanding of the pathological processes underlying this condition has been enhanced. This study identified a total of seventy-three metabolites that have a significant impact on UC. Notably, the composition of total flavone in SAL, a medication used for UC treatment, differs from that of aspirin due to the presence of four distinct metabolites (13,14-Dihydro-15-keto-PGE2, Prostaglandin I2 (PGI2), (20R,22R)-20,22-dihydroxycholesterol, and PS (18:1(9Z)/0:0)). These metabolites possess unique characteristics that set them apart. Moreover, the study identified a total of eleven pathways that were significantly enriched in mice with UC, including Aminoacyl-tRNA biosynthesis, Valine, leucine and isoleucine biosynthesis, Linoleic acid metabolism, PPAR signaling pathway, mTOR signaling pathway, Valine, leucine and isoleucine degradation, Lysine degradation, VEGF signaling pathway, Melanogenesis, Endocrine and other factor-regulated calcium reabsorption, and Cocaine addiction. These findings contribute to a better understanding of the metabolic variations in UC following total flavonoids of SAL therapy and provide valuable insights for the treatment of UC.Keywords: Ulcerative colitis; Total flavonoids of Sonchus arvensis L.; Key metabolites; Metabonomics; Cecal contents of male C57BL/6 mice.
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Affiliation(s)
| | - Wei Wei
- Daqing Oilfield Genaral Hospital, Daqing, 163319, China
| | | | | | - Yilei Sui
- Harbin Medical University 163319, China
| | - Taoyang
- Harbin Medical University 163319, China
| | - Jing He
- Harbin Medical University 163319, China
| | - Yachao Ren
- Harbin Medical University 163319, China
- School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin, 300000, China
| | | | - Chunlei Bu
- Harbin Medical University 163319, China
- Fifth Affiliated Hospital, Harbin Medical University, Daqing, 163319, China
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2
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Moreno N, Sabater-Arcis M, Sevilla T, Alonso MP, Ohana J, Bargiela A, Artero R. Therapeutic potential of oleic acid supplementation in myotonic dystrophy muscle cell models. Biol Res 2024; 57:29. [PMID: 38760841 PMCID: PMC11100173 DOI: 10.1186/s40659-024-00496-z] [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: 06/14/2023] [Accepted: 04/05/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND We recently reported that upregulation of Musashi 2 (MSI2) protein in the rare neuromuscular disease myotonic dystrophy type 1 contributes to the hyperactivation of the muscle catabolic processes autophagy and UPS through a reduction in miR-7 levels. Because oleic acid (OA) is a known allosteric regulator of MSI2 activity in the biogenesis of miR-7, here we sought to evaluate endogenous levels of this fatty acid and its therapeutic potential in rescuing cell differentiation phenotypes in vitro. In this work, four muscle cell lines derived from DM1 patients were treated with OA for 24 h, and autophagy and muscle differentiation parameters were analyzed. RESULTS We demonstrate a reduction of OA levels in different cell models of the disease. OA supplementation rescued disease-related phenotypes such as fusion index, myotube diameter, and repressed autophagy. This involved inhibiting MSI2 regulation of direct molecular target miR-7 since OA isoschizomer, elaidic acid (EA) could not cause the same rescues. Reduction of OA levels seems to stem from impaired biogenesis since levels of the enzyme stearoyl-CoA desaturase 1 (SCD1), responsible for converting stearic acid to oleic acid, are decreased in DM1 and correlate with OA amounts. CONCLUSIONS For the first time in DM1, we describe a fatty acid metabolism impairment that originated, at least in part, from a decrease in SCD1. Because OA allosterically inhibits MSI2 binding to molecular targets, reduced OA levels synergize with the overexpression of MSI2 and contribute to the MSI2 > miR-7 > autophagy axis that we proposed to explain the muscle atrophy phenotype.
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Affiliation(s)
- Nerea Moreno
- Human Translational Genomics Group, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- CIBERER, IISCIII, Madrid, Spain
| | - Maria Sabater-Arcis
- Human Translational Genomics Group, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- CIBERER, IISCIII, Madrid, Spain
| | - Teresa Sevilla
- CIBERER, IISCIII, Madrid, Spain
- Neuromuscular and Ataxias Research Group, Health Research Institute Hospital, La Fe (IIS La Fe), Valencia, Spain
- Department of Medicine, University of Valencia, Valencia, Spain
| | - Manuel Perez Alonso
- Human Translational Genomics Group, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- CIBERER, IISCIII, Madrid, Spain
| | - Jessica Ohana
- Centre de Recherche en Myologie, Sorbonne Université, Inserm, Institut de Myologie, Paris, F-75013, France
| | - Ariadna Bargiela
- CIBERER, IISCIII, Madrid, Spain.
- Neuromuscular and Ataxias Research Group, Health Research Institute Hospital, La Fe (IIS La Fe), Valencia, Spain.
| | - Ruben Artero
- Human Translational Genomics Group, University Institute for Biotechnology and Biomedicine (BIOTECMED), University of Valencia, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- CIBERER, IISCIII, Madrid, Spain
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3
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Dolcemascolo R, Heras-Hernández M, Goiriz L, Montagud-Martínez R, Requena-Menéndez A, Ruiz R, Pérez-Ràfols A, Higuera-Rodríguez RA, Pérez-Ropero G, Vranken WF, Martelli T, Kaiser W, Buijs J, Rodrigo G. Repurposing the mammalian RNA-binding protein Musashi-1 as an allosteric translation repressor in bacteria. eLife 2024; 12:RP91777. [PMID: 38363283 PMCID: PMC10942595 DOI: 10.7554/elife.91777] [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] [Indexed: 02/17/2024] Open
Abstract
The RNA recognition motif (RRM) is the most common RNA-binding protein domain identified in nature. However, RRM-containing proteins are only prevalent in eukaryotic phyla, in which they play central regulatory roles. Here, we engineered an orthogonal post-transcriptional control system of gene expression in the bacterium Escherichia coli with the mammalian RNA-binding protein Musashi-1, which is a stem cell marker with neurodevelopmental role that contains two canonical RRMs. In the circuit, Musashi-1 is regulated transcriptionally and works as an allosteric translation repressor thanks to a specific interaction with the N-terminal coding region of a messenger RNA and its structural plasticity to respond to fatty acids. We fully characterized the genetic system at the population and single-cell levels showing a significant fold change in reporter expression, and the underlying molecular mechanism by assessing the in vitro binding kinetics and in vivo functionality of a series of RNA mutants. The dynamic response of the system was well recapitulated by a bottom-up mathematical model. Moreover, we applied the post-transcriptional mechanism engineered with Musashi-1 to specifically regulate a gene within an operon, implement combinatorial regulation, and reduce protein expression noise. This work illustrates how RRM-based regulation can be adapted to simple organisms, thereby adding a new regulatory layer in prokaryotes for translation control.
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Affiliation(s)
- Roswitha Dolcemascolo
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
- Department of Biotechnology, Polytechnic University of ValenciaValenciaSpain
| | - María Heras-Hernández
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
| | - Lucas Goiriz
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
- Department of Applied Mathematics, Polytechnic University of ValenciaValenciaSpain
| | - Roser Montagud-Martínez
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
- Department of Biotechnology, Polytechnic University of ValenciaValenciaSpain
| | | | - Raúl Ruiz
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
| | - Anna Pérez-Ràfols
- Giotto Biotech SRLSesto FiorentinoItaly
- Magnetic Resonance Center (CERM), Department of Chemistry Ugo Schiff, Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), University of FlorenceSesto FiorentinoItaly
| | - R Anahí Higuera-Rodríguez
- Dynamic Biosensors GmbHPlaneggGermany
- Department of Physics, Technical University of MunichGarchingGermany
| | - Guillermo Pérez-Ropero
- Ridgeview Instruments ABUppsalaSweden
- Department of Chemistry – BMC, Uppsala UniversityUppsalaSweden
| | - Wim F Vranken
- Structural Biology Brussels, Vrije Universiteit BrusselBrusselsBelgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles – Vrije Universiteit BrusselBrusselsBelgium
| | | | | | - Jos Buijs
- Ridgeview Instruments ABUppsalaSweden
- Department of Immunology, Genetics, and Pathology, Uppsala UniversityUppsalaSweden
| | - Guillermo Rodrigo
- Institute for Integrative Systems Biology (I2SysBio), CSIC – University of ValenciaPaternaSpain
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Salvato I, Ricciardi L, Nucera F, Nigro A, Dal Col J, Monaco F, Caramori G, Stellato C. RNA-Binding Proteins as a Molecular Link between COPD and Lung Cancer. COPD 2023; 20:18-30. [PMID: 36655862 DOI: 10.1080/15412555.2022.2107500] [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: 01/20/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) represents an independent risk factor for lung cancer development. Accelerated cell senescence, induced by oxidative stress and inflammation, is a common pathogenic determinant of both COPD and lung cancer. The post transcriptional regulation of genes involved in these processes is finely regulated by RNA-binding proteins (RBPs), which regulate mRNA turnover, subcellular localization, splicing and translation. Multiple pro-inflammatory mediators (including cytokines, chemokines, proteins, growth factors and others), responsible of lung microenvironment alteration, are regulated by RBPs. Several mouse models have shown the implication of RBPs in multiple mechanisms that sustain chronic inflammation and neoplastic transformation. However, further studies are required to clarify the role of RBPs in the pathogenic mechanisms shared by lung cancer and COPD, in order to identify novel biomarkers and therapeutic targets. This review will therefore focus on the studies collectively indicating the role of RBPs in oxidative stress and chronic inflammation as common pathogenic mechanisms shared by lung cancer and COPD.
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Affiliation(s)
- Ilaria Salvato
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Luca Ricciardi
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Francesco Nucera
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Francesco Monaco
- Chirurgia Toracica, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
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5
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Walters K, Sajek MP, Murphy E, Issaian A, Baldwin A, Harrison E, Daniels M, Reisz JA, Hansen K, D'Alessandro A, Mukherjee N. Small-molecule Ro-08-2750 interacts with many RNA-binding proteins and elicits MUSASHI2-independent phenotypes. RNA (NEW YORK, N.Y.) 2023; 29:1458-1470. [PMID: 37369529 PMCID: PMC10578479 DOI: 10.1261/rna.079605.123] [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: 01/20/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
RNA-binding proteins (RBPs) are key regulators of gene expression. Small molecules targeting these RBP-RNA interactions are a rapidly emerging class of therapeutics for treating a variety of diseases. Ro-08-2750 (Ro) is a small molecule identified as a competitive inhibitor of Musashi (MSI)-RNA interactions. Here, we show that multiple Ro-dependent cellular phenotypes, specifically adrenocortical steroid production and cell viability, are Musashi-2 (MSI2)-independent. Using an unbiased proteome-wide approach, we discovered Ro broadly interacts with RBPs, many containing RRM domains. To confirm this finding, we leveraged the large-scale ENCODE data to identify a subset of RBPs whose depletion phenocopies Ro inhibition, indicating Ro is a promiscuous inhibitor of multiple RBPs. Consistent with broad disruption of ribonucleoprotein complexes, Ro treatment leads to stress granule formation. This strategy represents a generalizable framework for validating the specificity and identifying targets of RBP inhibitors in a cellular context.
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Affiliation(s)
- Kathryn Walters
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Marcin Piotr Sajek
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Elisabeth Murphy
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Aaron Issaian
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Amber Baldwin
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Evan Harrison
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Miles Daniels
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- Howard University Karsh STEM Scholars Program, Washington DC 20059, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Kirk Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Neelanjan Mukherjee
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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6
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Sicking M, Falke I, Löblein MT, Eich HT, Götte M, Greve B, Troschel FM. The Musashi RNA-binding proteins in female cancers: insights on molecular mechanisms and therapeutic relevance. Biomark Res 2023; 11:76. [PMID: 37620963 PMCID: PMC10463710 DOI: 10.1186/s40364-023-00516-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
RNA-binding proteins have increasingly been identified as important regulators of gene expression given their ability to bind distinct RNA sequences and regulate their fate. Mounting evidence suggests that RNA-binding proteins are involved in the onset and progression of multiple malignancies, prompting increasing interest in their potential for therapeutic intervention.The Musashi RNA binding proteins Musashi-1 and Musashi-2 were initially identified as developmental factors of the nervous system but have more recently been found to be ubiquitously expressed in physiological tissues and may be involved in pathological cell behavior. Both proteins are increasingly investigated in cancers given dysregulation in multiple tumor entities, including in female malignancies. Recent data suggest that the Musashi proteins serve as cancer stem cell markers as they contribute to cancer cell proliferation and therapy resistance, prompting efforts to identify mechanisms to target them. However, as the picture remains incomplete, continuous efforts to elucidate their role in different signaling pathways remain ongoing.In this review, we focus on the roles of Musashi proteins in tumors of the female - breast, endometrial, ovarian and cervical cancer - as we aim to summarize current knowledge and discuss future perspectives.
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Affiliation(s)
- Mark Sicking
- Department of Radiation Oncology, University Hospital Münster, Albert Schweitzer-Campus 1, 48149, Münster, Germany
| | - Isabel Falke
- Department of Radiation Oncology, University Hospital Münster, Albert Schweitzer-Campus 1, 48149, Münster, Germany
| | - Maria T Löblein
- Department of Radiation Oncology, University Hospital Münster, Albert Schweitzer-Campus 1, 48149, Münster, Germany
| | - Hans Th Eich
- Department of Radiation Oncology, University Hospital Münster, Albert Schweitzer-Campus 1, 48149, Münster, Germany
| | - Martin Götte
- Department of Gynecology and Obstetrics, University Hospital Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Burkhard Greve
- Department of Radiation Oncology, University Hospital Münster, Albert Schweitzer-Campus 1, 48149, Münster, Germany
| | - Fabian M Troschel
- Department of Radiation Oncology, University Hospital Münster, Albert Schweitzer-Campus 1, 48149, Münster, Germany.
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7
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Feng Y, Zhu S, Liu T, Zhi G, Shao B, Liu J, Li B, Jiang C, Feng Q, Wu P, Wang D. Surmounting Cancer Drug Resistance: New Perspective on RNA-Binding Proteins. Pharmaceuticals (Basel) 2023; 16:1114. [PMID: 37631029 PMCID: PMC10458901 DOI: 10.3390/ph16081114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
RNA-binding proteins (RBPs), being pivotal elements in both physiological and pathological processes, possess the ability to directly impact RNA, thereby exerting a profound influence on cellular life. Furthermore, the dysregulation of RBPs not only induces alterations in the expression levels of genes associated with cancer but also impairs the occurrence of post-transcriptional regulatory mechanisms. Consequently, these circumstances can give rise to aberrations in cellular processes, ultimately resulting in alterations within the proteome. An aberrant proteome can disrupt the equilibrium between oncogenes and tumor suppressor genes, promoting cancer progression. Given their significant role in modulating gene expression and post-transcriptional regulation, directing therapeutic interventions towards RBPs represents a viable strategy for combating drug resistance in cancer treatment. RBPs possess significant potential as diagnostic and prognostic markers for diverse cancer types. Gaining comprehensive insights into the structure and functionality of RBPs, along with delving deeper into the molecular mechanisms underlying RBPs in tumor drug resistance, can enhance cancer treatment strategies and augment the prognostic outcomes for individuals afflicted with cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Peijie Wu
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
| | - Dong Wang
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
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8
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Quentin D, Schuhmacher JS, Klink BU, Lauer J, Shaikh TR, Huis In 't Veld PJ, Welp LM, Urlaub H, Zerial M, Raunser S. Structural basis of mRNA binding by the human FERRY Rab5 effector complex. Mol Cell 2023; 83:1856-1871.e9. [PMID: 37267906 DOI: 10.1016/j.molcel.2023.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/05/2022] [Accepted: 05/05/2023] [Indexed: 06/04/2023]
Abstract
The pentameric FERRY Rab5 effector complex is a molecular link between mRNA and early endosomes in mRNA intracellular distribution. Here, we determine the cryo-EM structure of human FERRY. It reveals a unique clamp-like architecture that bears no resemblance to any known structure of Rab effectors. A combination of functional and mutational studies reveals that while the Fy-2 C-terminal coiled-coil acts as binding region for Fy-1/3 and Rab5, both coiled-coils and Fy-5 concur to bind mRNA. Mutations causing truncations of Fy-2 in patients with neurological disorders impair Rab5 binding or FERRY complex assembly. Thus, Fy-2 serves as a binding hub connecting all five complex subunits and mediating the binding to mRNA and early endosomes via Rab5. Our study provides mechanistic insights into long-distance mRNA transport and demonstrates that the particular architecture of FERRY is closely linked to a previously undescribed mode of RNA binding, involving coiled-coil domains.
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Affiliation(s)
- Dennis Quentin
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Jan S Schuhmacher
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Björn U Klink
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany; Center for Soft Nanoscience and Institute of Molecular Physics and Biophysics, 48149 Münster, Germany
| | - Jeni Lauer
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Tanvir R Shaikh
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Pim J Huis In 't Veld
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Luisa M Welp
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany; Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.
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9
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Yeh DW, Zhao X, Siddique HR, Zheng M, Choi HY, Machida T, Narayanan P, Kou Y, Punj V, Tahara SM, Feldman DE, Chen L, Machida K. MSI2 promotes translation of multiple IRES-containing oncogenes and virus to induce self-renewal of tumor initiating stem-like cells. Cell Death Discov 2023; 9:141. [PMID: 37117191 PMCID: PMC10147607 DOI: 10.1038/s41420-023-01427-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/22/2023] [Accepted: 04/03/2023] [Indexed: 04/30/2023] Open
Abstract
RNA-binding protein Musashi 2 (MSI2) is elevated in several cancers and is linked to poor prognosis. Here, we tested if MSI2 promotes MYC and viral mRNA translation to induce self-renewal via an internal ribosome entry sequence (IRES). We performed RIP-seq using anti-MSI2 antibody in tumor-initiating stem-like cells (TICs). MSI2 binds the internal ribosome entry site (IRES)-containing oncogene mRNAs including MYC, JUN and VEGFA as well as HCV IRES to increase their synthesis and promote self-renewal and tumor-initiation at the post-transcriptional level. MSI2 binds a lncRNA to interfere with processing of a miRNA that reduced MYC translation in basal conditions. Deregulation of this integrated MSI2-lncRNA-MYC regulatory loop drives self-renewal and tumorigenesis through increased IRES-dependent translation of MYC mRNA. Overexpression of MSI2 in TICs promoted their self-renewal and tumor-initiation properties. Inhibition of MSI2-RNA binding reduced HCV IRES activity, viral replication and liver hyperplasia in humanized mice predisposed by virus infection and alcohol high-cholesterol high-fat diet. Together MSI2, integrating the MYC oncogenic pathway, can be employed as a therapeutic target in the treatment of HCC patients. A hypothetical model shows that MSI2 binds and activates cap-independent translation of MYC, c-JUN mRNA and HCV through MSI2-binding to Internal Ribosome Entry Sites (IRES) resulting in upregulated MYC, c-JUN and viral protein synthesis and subsequent liver oncogenesis. Inhibitor of the interaction between MYC IRES and MSI2 reduces liver hyperplasia, viral mRNA translation and tumor formation.
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Affiliation(s)
- Da-Wei Yeh
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Xuyao Zhao
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Hifzur R Siddique
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
- Molecular Cancer Genetics & Translational Research Lab, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, 202002, India
| | - Mengmei Zheng
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Hye Yeon Choi
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Tatsuya Machida
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Padmini Narayanan
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Yi Kou
- Viterbi School of Engineering, University of Southern California, Los Angeles, 90089, USA
| | - Vasu Punj
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, 90033, USA
| | - Stanley M Tahara
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Douglas E Feldman
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA
| | - Lin Chen
- Viterbi School of Engineering, University of Southern California, Los Angeles, 90089, USA
| | - Keigo Machida
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, 90033, USA.
- Southern California Research Center for ALPD and Cirrhosis, Los Angeles, 90033, USA.
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10
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Bertoldo JB, Müller S, Hüttelmaier S. RNA-binding proteins in cancer drug discovery. Drug Discov Today 2023; 28:103580. [PMID: 37031812 DOI: 10.1016/j.drudis.2023.103580] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/11/2023]
Abstract
RNA-binding proteins (RBPs) are crucial players in tumorigenesis and, hence, promising targets in cancer drug discovery. However, they are largely regarded as 'undruggable', because of the often noncatalytic and complex interactions between protein and RNA, which limit the discovery of specific inhibitors. Nonetheless, over the past 10 years, drug discovery efforts have uncovered RBP inhibitors with clinical relevance, highlighting the disruption of RNA-protein networks as a promising avenue for cancer therapeutics. In this review, we discuss the role of structurally distinct RBPs in cancer, and the mechanisms of RBP-directed small-molecule inhibitors (SMOIs) focusing on drug-protein interactions, binding surfaces, potency, and translational potential. Additionally, we underline the limitations of RBP-targeting drug discovery assays and comment on future trends in the field.
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Affiliation(s)
- Jean B Bertoldo
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia; School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Simon Müller
- Institute for Molecular Medicine, Faculty of Medicine, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany; New York Genome Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Stefan Hüttelmaier
- Institute for Molecular Medicine, Faculty of Medicine, Martin-Luther University of Halle-Wittenberg, Halle (Saale), Germany.
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11
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Novel roles of RNA-binding proteins in drug resistance of breast cancer: from molecular biology to targeting therapeutics. Cell Death Discov 2023; 9:52. [PMID: 36759501 PMCID: PMC9911762 DOI: 10.1038/s41420-023-01352-x] [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: 11/24/2022] [Revised: 01/25/2023] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Therapy resistance remains a huge challenge for current breast cancer treatments. Exploring molecular mechanisms of therapy resistance might provide therapeutic targets for patients with advanced breast cancer and improve their prognosis. RNA-binding proteins (RBPs) play an important role in regulating therapy resistance. Here we summarize the functions of RBPs, highlight their tremendously important roles in regulating therapy sensitivity and resistance and we also reveal current therapeutic approaches reversing abnormal functions of RBPs in breast cancer.
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12
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Bai N, Adeshina Y, Bychkov I, Xia Y, Gowthaman R, Miller SA, Gupta AK, Johnson DK, Lan L, Golemis EA, Makhov PB, Xu L, Pillai MM, Boumber Y, Karanicolas J. Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523326. [PMID: 36711508 PMCID: PMC9882015 DOI: 10.1101/2023.01.09.523326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators of gene expression, and thus underlie many important biological processes. Here, we developed a strategy that entails extracting a "hotspot pharmacophore" from the structure of a protein-RNA complex, to create a template for designing small-molecule inhibitors and for exploring the selectivity of the resulting inhibitors. We demonstrate this approach by designing inhibitors of Musashi proteins MSI1 and MSI2, key regulators of mRNA stability and translation that are upregulated in many cancers. We report this novel series of MSI1/MSI2 inhibitors is specific and active in biochemical, biophysical, and cellular assays. This study extends the paradigm of "hotspots" from protein-protein complexes to protein-RNA complexes, supports the "druggability" of RNA-binding protein surfaces, and represents one of the first rationally-designed inhibitors of non-enzymatic RNA-binding proteins. Owing to its simplicity and generality, we anticipate that this approach may also be used to develop inhibitors of many other RNA-binding proteins; we also consider the prospects of identifying potential off-target interactions by searching for other RBPs that recognize their cognate RNAs using similar interaction geometries. Beyond inhibitors, we also expect that compounds designed using this approach can serve as warheads for new PROTACs that selectively degrade RNA-binding proteins.
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Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Yusuf Adeshina
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Igor Bychkov
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Yan Xia
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Ragul Gowthaman
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Sven A. Miller
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
| | | | - David K. Johnson
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Lan Lan
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Erica A. Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140
| | - Petr B. Makhov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
| | - Liang Xu
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City KS 66160
| | - Manoj M. Pillai
- Section of Hematology, Yale Cancer Center, New Haven CT 06520
- Department of Pathology, Yale University School of Medicine, New Haven CT 06520
| | - Yanis Boumber
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA 19140
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13
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(-)- Gossypol Inhibition of Musashi-Mediated Forgetting Improves Memory and Age-Dependent Memory Decline in Caenorhabditis elegans. Mol Neurobiol 2023; 60:820-835. [PMID: 36378468 PMCID: PMC9849318 DOI: 10.1007/s12035-022-03116-7] [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: 08/09/2022] [Accepted: 11/03/2022] [Indexed: 11/17/2022]
Abstract
Musashi RNA-binding proteins (MSIs) retain a pivotal role in stem cell maintenance, tumorigenesis, and nervous system development. Recently, we showed in C. elegans that Musashi (MSI-1) actively promotes forgetting upon associative learning via a 3'UTR-dependent translational expression of the Arp2/3 actin branching complex. Here, we investigated the evolutionary conserved role of MSI proteins and the effect of their pharmacological inhibition on memory. Expression of human Musashi 1 (MSI1) and Musashi 2 (MSI2) under the endogenous Musashi promoter fully rescued the phenotype of msi-1(lf) worms. Furthermore, pharmacological inhibition of human MSI1 and MSI2 activity using (-)- gossypol resulted in improved memory retention, without causing locomotor, chemotactic, or learning deficits. No drug effect was observed in msi-1(lf) treated worms. Using Western blotting and confocal microscopy, we found no changes in MSI-1 protein abundance following (-)- gossypol treatment, suggesting that Musashi gene expression remains unaltered and that the compound exerts its inhibitory effect post-translationally. Additionally, (-)- gossypol suppressed the previously seen rescue of the msi-1(lf) phenotype in worms expressing human MSI1 specifically in the AVA neuron, indicating that (-)- gossypol can regulate the Musashi pathway in a memory-related neuronal circuit in worms. Finally, treating aged worms with (-)- gossypol reversed physiological age-dependent memory decline. Taken together, our findings indicate that pharmacological inhibition of Musashi might represent a promising approach for memory modulation.
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14
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Identification and characterization of RBM12 as a novel regulator of fetal hemoglobin expression. Blood Adv 2022; 6:5956-5968. [PMID: 35622975 PMCID: PMC9678958 DOI: 10.1182/bloodadvances.2022007904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/21/2022] [Indexed: 02/01/2023] Open
Abstract
The fetal-to-adult hemoglobin transition is clinically relevant because reactivation of fetal hemoglobin (HbF) significantly reduces morbidity and mortality associated with sickle cell disease (SCD) and β-thalassemia. Most studies on the developmental regulation of the globin genes, including genome-wide genetics screens, have focused on DNA binding proteins, including BCL11A and ZBTB7A/LRF and their cofactors. Our understanding of RNA binding proteins (RBPs) in this process is much more limited. Two RBPs, LIN28B and IGF2BP1, are known posttranscriptional regulators of HbF production, but a global view of RBPs is still lacking. Here, we carried out a CRISPR/Cas9-based screen targeting RBPs harboring RNA methyltransferase and/or RNA recognition motif (RRM) domains and identified RNA binding motif 12 (RBM12) as a novel HbF suppressor. Depletion of RBM12 induced HbF expression and attenuated cell sickling in erythroid cells derived from patients with SCD with minimal detrimental effects on cell maturation. Transcriptome and proteome profiling revealed that RBM12 functions independently of major known HbF regulators. Enhanced cross-linking and immunoprecipitation followed by high-throughput sequencing revealed strong preferential binding of RBM12 to 5' untranslated regions of transcripts, narrowing down the mechanism of RBM12 action. Notably, we pinpointed the first of 5 RRM domains as essential, and, in conjunction with a linker domain, sufficient for RBM12-mediated HbF regulation. Our characterization of RBM12 as a negative regulator of HbF points to an additional regulatory layer of the fetal-to-adult hemoglobin switch and broadens the pool of potential therapeutic targets for SCD and β-thalassemia.
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15
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Mehta M, Raguraman R, Ramesh R, Munshi A. RNA binding proteins (RBPs) and their role in DNA damage and radiation response in cancer. Adv Drug Deliv Rev 2022; 191:114569. [PMID: 36252617 PMCID: PMC10411638 DOI: 10.1016/j.addr.2022.114569] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 01/24/2023]
Abstract
Traditionally majority of eukaryotic gene expression is influenced by transcriptional and post-transcriptional events. Alterations in the expression of proteins that act post-transcriptionally can affect cellular signaling and homeostasis. RNA binding proteins (RBPs) are a family of proteins that specifically bind to RNAs and are involved in post-transcriptional regulation of gene expression and important cellular processes such as cell differentiation and metabolism. Deregulation of RNA-RBP interactions and any changes in RBP expression or function can lead to various diseases including cancer. In cancer cells, RBPs play an important role in regulating the expression of tumor suppressors and oncoproteins involved in various cell-signaling pathways. Several RBPs such as HuR, AUF1, RBM38, LIN28, RBM24, tristetrapolin family and Musashi play critical roles in various types of cancers and their aberrant expression in cancer cells makes them an attractive therapeutic target for cancer treatment. In this review we provide an overview of i). RBPs involved in cancer progression and their mechanism of action ii). the role of RBPs, including HuR, in breast cancer progression and DNA damage response and iii). explore RBPs with emphasis on HuR as therapeutic target for breast cancer therapy.
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Affiliation(s)
- Meghna Mehta
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajeswari Raguraman
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajagopal Ramesh
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Anupama Munshi
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA.
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16
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Targeting the "undruggable": RNA-binding proteins in the spotlight in cancer therapy. Semin Cancer Biol 2022; 86:69-83. [PMID: 35772609 DOI: 10.1016/j.semcancer.2022.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/19/2022] [Accepted: 06/24/2022] [Indexed: 01/27/2023]
Abstract
Tumors refractory to conventional therapy belong to specific subpopulations of cancer cells, which have acquired a higher number of mutations/epigenetic changes than the majority of cancer cells. This property provides them the ability to become resistant to therapy. Aberrant expression of certain RNA-binding proteins (RBPs) can regulate the sensitivity of tumor cells to chemotherapeutic drugs by binding to specific regions present in the 3´-UTR of certain mRNAs to promote or repress mRNA translation or by interacting with other proteins (including RBPs) and non-coding RNAs that are part of ribonucleoprotein complexes. In particular, an increasing interest in the RBPs involved in chemoresistance has recently emerged. In this review, we discuss how RBPs are not only affected by chemotherapeutic treatments, but also play an active role in therapeutic responses via the direct modulation of crucial cancer-related proteins. A special focus is being placed on the development of therapeutic strategies targeting these RBPs.
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17
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Zhang X, Su K, Liu Y, Zhu D, Pan Y, Ke X, Qu Y. Small Molecule Palmatine Targeting Musashi-2 in Colorectal Cancer. Front Pharmacol 2022; 12:793449. [PMID: 35153752 PMCID: PMC8830500 DOI: 10.3389/fphar.2021.793449] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/09/2021] [Indexed: 11/13/2022] Open
Abstract
Musashi-2 (MSI2) is an evolutionally conserved RNA-binding protein and recently considered as an attractive therapeutic target in a wide spectrum of malignancies. However, MSI2-engaged mRNAs are not well profiled, and no MSI2-dependent antagonist is available so far. In the study, we created MSI2 knockout cancer cells and demonstrated that MSI2 is required for the survival of colorectal cancer HCT116 cells but not non-small cell lung cancer A549 cells. In addition, the global profiling of the transcriptome and proteomics of MSI2 knockout colorectal cells revealed 38 candidate MSI2-targeted genes. In a loss–rescue screening, palmatine was identified as a functional MSI2 antagonist inhibiting the MSI2-dependent growth of colorectal cancer cells. Finally, we confirmed that palmatine is directly bound to MSI2 at its C-terminal. Our findings not only indicated MSI2 as a promising therapeutic target of colorectal cancer but also provided a small molecule palmatine as a direct and functional MSI2 antagonist for cancer therapy.
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Affiliation(s)
- Xue Zhang
- Shanghai Frontiers Science Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Kaiyan Su
- Shanghai Frontiers Science Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Yifan Liu
- Shanghai Frontiers Science Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Darong Zhu
- Shanghai Frontiers Science Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuting Pan
- Shanghai Frontiers Science Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xisong Ke
- Shanghai Frontiers Science Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Xisong Ke, ; Yi Qu,
| | - Yi Qu
- Shanghai Frontiers Science Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Xisong Ke, ; Yi Qu,
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18
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Wang J, Lan L, Wu X, Xu L, Miao Y. Mechanism of RNA recognition by a Musashi RNA-binding protein. Curr Res Struct Biol 2021; 4:10-20. [PMID: 34988468 PMCID: PMC8695263 DOI: 10.1016/j.crstbi.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 10/31/2021] [Accepted: 12/07/2021] [Indexed: 12/21/2022] Open
Abstract
The Musashi RNA-binding proteins (RBPs) regulate translation of target mRNAs and maintenance of cell stemness and tumorigenesis. Musashi-1 (MSI1), long considered as an intestinal and neural stem cell marker, has been more recently found to be over expressed in many cancers. It has served as an important drug target for treating acute myeloid leukemia and solid tumors such as ovarian, colorectal and bladder cancer. One of the reported binding targets of MSI1 is Numb, a negative regulator of the Notch signaling. However, the dynamic mechanism of Numb RNA binding to MSI1 remains unknown, largely hindering effective drug design targeting this critical interaction. Here, we have performed extensive all-atom microsecond-timescale simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method, which successfully captured multiple times of spontaneous and highly accurate binding of the Numb RNA from bulk solvent to the MSI1 protein target site. GaMD simulations revealed that Numb RNA binding to MSI1 involved largely induced fit in both the RNA and protein. The simulations also identified important low-energy intermediate conformational states during RNA binding, in which Numb interacted mainly with the β2-β3 loop and C terminus of MSI1. The mechanistic understanding of RNA binding obtained from our GaMD simulations is expected to facilitate rational structure-based drug design targeting MSI1 and other RBPs.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology, University of Kansas, Lawrence, KS, 66047, USA
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Lan Lan
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Xiaoqing Wu
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
| | - Liang Xu
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
- Department of Radiation Oncology, The University of Kansas Cancer Center, Kansas City, KS, 66160, USA
| | - Yinglong Miao
- Center for Computational Biology, University of Kansas, Lawrence, KS, 66047, USA
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, 66047, USA
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19
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Zhu S, Choudhury NR, Rooney S, Pham NT, Koszela J, Kelly D, Spanos C, Rappsilber J, Auer M, Michlewski G. RNA pull-down confocal nanoscanning (RP-CONA) detects quercetin as pri-miR-7/HuR interaction inhibitor that decreases α-synuclein levels. Nucleic Acids Res 2021; 49:6456-6473. [PMID: 34107032 PMCID: PMC8216281 DOI: 10.1093/nar/gkab484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 05/11/2021] [Accepted: 05/21/2021] [Indexed: 12/18/2022] Open
Abstract
RNA-protein interactions are central to all gene expression processes and contribute to a variety of human diseases. Therapeutic approaches targeting RNA-protein interactions have shown promising effects on some diseases that are previously regarded as 'incurable'. Here, we developed a fluorescent on-bead screening platform, RNA Pull-Down COnfocal NAnoscanning (RP-CONA), to identify RNA-protein interaction modulators in eukaryotic cell extracts. Using RP-CONA, we identified small molecules that disrupt the interaction between HuR, an inhibitor of brain-enriched miR-7 biogenesis, and the conserved terminal loop of pri-miR-7-1. Importantly, miR-7's primary target is an mRNA of α-synuclein, which contributes to the aetiology of Parkinson's disease. Our method identified a natural product quercetin as a molecule able to upregulate cellular miR-7 levels and downregulate the expression of α-synuclein. This opens up new therapeutic avenues towards treatment of Parkinson's disease as well as provides a novel methodology to search for modulators of RNA-protein interaction.
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Affiliation(s)
- Siran Zhu
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
| | - Nila Roy Choudhury
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
| | - Saul Rooney
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
| | - Nhan T Pham
- School of Biological Sciences, IQB3, University of Edinburgh, Edinburgh EH9 9FF, UK
| | - Joanna Koszela
- School of Biological Sciences, IQB3, University of Edinburgh, Edinburgh EH9 9FF, UK
| | - David Kelly
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Christos Spanos
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Juri Rappsilber
- The Wellcome Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
- Department of Biotechnology, Technische Universität Berlin, Berlin 13355, Germany
| | - Manfred Auer
- School of Biological Sciences, IQB3, University of Edinburgh, Edinburgh EH9 9FF, UK
| | - Gracjan Michlewski
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology in Warsaw, Warsaw 02-109, Poland
- Infection Medicine, University of Edinburgh, The Chancellor’s Building, Edinburgh EH16 4SB, UK
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, Zhejiang 314400, P.R. China
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20
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Rico-Jiménez M, Ceballos-Pérez G, Gómez-Liñán C, Estévez AM. An RNA-binding protein complex regulates the purine-dependent expression of a nucleobase transporter in trypanosomes. Nucleic Acids Res 2021; 49:3814-3825. [PMID: 33744953 PMCID: PMC8053114 DOI: 10.1093/nar/gkab181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional regulation of gene expression is particularly important in trypanosomatid protozoa. RNA-binding proteins (RBPs) regulate mRNA stability and translation, yet information about how RBPs are able to link environmental cues to post-transcriptional control is scarce. In Trypanosoma brucei, we have previously characterized a short RNA stem-loop cis-element (PuRE, Purine Responsive Element) within the 3'-UTR of the NT8 nucleobase transporter mRNA that is necessary and sufficient to confer a strong repression of gene expression in response to purines. In this study, we have identified a protein complex composed of two RNA-binding proteins (PuREBP1 and PuREBP2) that binds to the PuRE in vitro and to NT8 mRNA in vivo. Depletion of PuREBP1 by RNA interference results in the upregulation of just NT8 and the mRNAs encoding the amino acid transporter AATP6 paralogues. Moreover, we found that the PuREBP1/2 complex is associated with only a handful of mRNAs, and that it is responsible for the observed purine-dependent regulation of NT8 expression.
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Affiliation(s)
- Miriam Rico-Jiménez
- Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Gloria Ceballos-Pérez
- Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Claudia Gómez-Liñán
- Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Antonio M Estévez
- Instituto de Parasitología y Biomedicina 'López-Neyra', IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
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21
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Bley N, Hmedat A, Müller S, Rolnik R, Rausch A, Lederer M, Hüttelmaier S. Musashi-1-A Stemness RBP for Cancer Therapy? BIOLOGY 2021; 10:407. [PMID: 34062997 PMCID: PMC8148009 DOI: 10.3390/biology10050407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 12/12/2022]
Abstract
The RNA-binding protein Musashi-1 (MSI1) promotes stemness during development and cancer. By controlling target mRNA turnover and translation, MSI1 is implicated in the regulation of cancer hallmarks such as cell cycle or Notch signaling. Thereby, the protein enhanced cancer growth and therapy resistance to standard regimes. Due to its specific expression pattern and diverse functions, MSI1 represents an interesting target for cancer therapy in the future. In this review we summarize previous findings on MSI1's implications in developmental processes of other organisms. We revisit MSI1's expression in a set of solid cancers, describe mechanistic details and implications in MSI1 associated cancer hallmark pathways and highlight current research in drug development identifying the first MSI1-directed inhibitors with anti-tumor activity.
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Affiliation(s)
- Nadine Bley
- Department for Molecular Cell Biology, Institute for Molecular Medicine, Martin Luther University Halle/Wittenberg, Charles Tanford Protein Center, Kurt–Mothes–Str. 3A, 06120 Halle, Germany; (A.H.); (S.M.); (R.R.); (A.R.); (M.L.); (S.H.)
- Core Facility Imaging, Institute for Molecular Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt–Mothes–Str. 3A, 06120 Halle, Germany
| | - Ali Hmedat
- Department for Molecular Cell Biology, Institute for Molecular Medicine, Martin Luther University Halle/Wittenberg, Charles Tanford Protein Center, Kurt–Mothes–Str. 3A, 06120 Halle, Germany; (A.H.); (S.M.); (R.R.); (A.R.); (M.L.); (S.H.)
| | - Simon Müller
- Department for Molecular Cell Biology, Institute for Molecular Medicine, Martin Luther University Halle/Wittenberg, Charles Tanford Protein Center, Kurt–Mothes–Str. 3A, 06120 Halle, Germany; (A.H.); (S.M.); (R.R.); (A.R.); (M.L.); (S.H.)
| | - Robin Rolnik
- Department for Molecular Cell Biology, Institute for Molecular Medicine, Martin Luther University Halle/Wittenberg, Charles Tanford Protein Center, Kurt–Mothes–Str. 3A, 06120 Halle, Germany; (A.H.); (S.M.); (R.R.); (A.R.); (M.L.); (S.H.)
| | - Alexander Rausch
- Department for Molecular Cell Biology, Institute for Molecular Medicine, Martin Luther University Halle/Wittenberg, Charles Tanford Protein Center, Kurt–Mothes–Str. 3A, 06120 Halle, Germany; (A.H.); (S.M.); (R.R.); (A.R.); (M.L.); (S.H.)
- Core Facility Imaging, Institute for Molecular Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt–Mothes–Str. 3A, 06120 Halle, Germany
| | - Marcell Lederer
- Department for Molecular Cell Biology, Institute for Molecular Medicine, Martin Luther University Halle/Wittenberg, Charles Tanford Protein Center, Kurt–Mothes–Str. 3A, 06120 Halle, Germany; (A.H.); (S.M.); (R.R.); (A.R.); (M.L.); (S.H.)
| | - Stefan Hüttelmaier
- Department for Molecular Cell Biology, Institute for Molecular Medicine, Martin Luther University Halle/Wittenberg, Charles Tanford Protein Center, Kurt–Mothes–Str. 3A, 06120 Halle, Germany; (A.H.); (S.M.); (R.R.); (A.R.); (M.L.); (S.H.)
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22
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Baroni M, Yi C, Choudhary S, Lei X, Kosti A, Grieshober D, Velasco M, Qiao M, Burns SS, Araujo PR, DeLambre T, Son MY, Plateroti M, Ferreira MAR, Hasty EP, Penalva LOF. Musashi1 Contribution to Glioblastoma Development via Regulation of a Network of DNA Replication, Cell Cycle and Division Genes. Cancers (Basel) 2021; 13:1494. [PMID: 33804958 PMCID: PMC8036803 DOI: 10.3390/cancers13071494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/17/2021] [Accepted: 03/21/2021] [Indexed: 11/21/2022] Open
Abstract
RNA-binding proteins (RBPs) function as master regulators of gene expression. Alterations in their levels are often observed in tumors with numerous oncogenic RBPs identified in recent years. Musashi1 (Msi1) is an RBP and stem cell gene that controls the balance between self-renewal and differentiation. High Msi1 levels have been observed in multiple tumors including glioblastoma and are often associated with poor patient outcomes and tumor growth. A comprehensive genomic analysis identified a network of cell cycle/division and DNA replication genes and established these processes as Msi1's core regulatory functions in glioblastoma. Msi1 controls this gene network via two mechanisms: direct interaction and indirect regulation mediated by the transcription factors E2F2 and E2F8. Moreover, glioblastoma lines with Msi1 knockout (KO) displayed increased sensitivity to cell cycle and DNA replication inhibitors. Our results suggest that a drug combination strategy (Msi1 + cell cycle/DNA replication inhibitors) could be a viable route to treat glioblastoma.
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Affiliation(s)
- Mirella Baroni
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA; (M.B.); (C.Y.); (X.L.); (A.K.); (D.G.); (M.V.); (M.Q.); (P.R.A.); (T.D.)
| | - Caihong Yi
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA; (M.B.); (C.Y.); (X.L.); (A.K.); (D.G.); (M.V.); (M.Q.); (P.R.A.); (T.D.)
- Third Xiangya Hospital, Central South University, Changsha 410000, China
| | - Saket Choudhary
- Computational Biology and Bioinformatics, University of Southern California, Los Angeles, CA 90089, USA;
| | - Xiufen Lei
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA; (M.B.); (C.Y.); (X.L.); (A.K.); (D.G.); (M.V.); (M.Q.); (P.R.A.); (T.D.)
| | - Adam Kosti
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA; (M.B.); (C.Y.); (X.L.); (A.K.); (D.G.); (M.V.); (M.Q.); (P.R.A.); (T.D.)
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Denise Grieshober
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA; (M.B.); (C.Y.); (X.L.); (A.K.); (D.G.); (M.V.); (M.Q.); (P.R.A.); (T.D.)
| | - Mitzli Velasco
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA; (M.B.); (C.Y.); (X.L.); (A.K.); (D.G.); (M.V.); (M.Q.); (P.R.A.); (T.D.)
| | - Mei Qiao
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA; (M.B.); (C.Y.); (X.L.); (A.K.); (D.G.); (M.V.); (M.Q.); (P.R.A.); (T.D.)
| | - Suzanne S. Burns
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA; (M.B.); (C.Y.); (X.L.); (A.K.); (D.G.); (M.V.); (M.Q.); (P.R.A.); (T.D.)
| | - Patricia R. Araujo
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA; (M.B.); (C.Y.); (X.L.); (A.K.); (D.G.); (M.V.); (M.Q.); (P.R.A.); (T.D.)
| | - Talia DeLambre
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA; (M.B.); (C.Y.); (X.L.); (A.K.); (D.G.); (M.V.); (M.Q.); (P.R.A.); (T.D.)
| | - Mi Young Son
- Department of Molecular Medicine, Sam and Ann Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX 78229, USA; (M.Y.S.); (E.P.H.)
| | - Michelina Plateroti
- Team: Development, Cancer and Stem Cells, Université de Strasbourg, Inserm, IRFAC/UMR-S1113, FMTS, 67200 Strasbourg, France;
| | | | - E. Paul Hasty
- Department of Molecular Medicine, Sam and Ann Barshop Institute for Longevity and Aging Studies, UT Health San Antonio, San Antonio, TX 78229, USA; (M.Y.S.); (E.P.H.)
| | - Luiz O. F. Penalva
- Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA; (M.B.); (C.Y.); (X.L.); (A.K.); (D.G.); (M.V.); (M.Q.); (P.R.A.); (T.D.)
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA
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23
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The methyltransferase SETD2 couples transcription and splicing by engaging mRNA processing factors through its SHI domain. Nat Commun 2021; 12:1443. [PMID: 33664260 PMCID: PMC7933334 DOI: 10.1038/s41467-021-21663-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Heterogeneous ribonucleoproteins (hnRNPs) are RNA binding molecules that are involved in key processes such as RNA splicing and transcription. One such hnRNP protein, hnRNP L, regulates alternative splicing (AS) by binding to pre-mRNA transcripts. However, it is unclear what factors contribute to hnRNP L-regulated AS events. Using proteomic approaches, we identified several key factors that co-purify with hnRNP L. We demonstrate that one such factor, the histone methyltransferase SETD2, specifically interacts with hnRNP L in vitro and in vivo. This interaction occurs through a previously uncharacterized domain in SETD2, the SETD2-hnRNP Interaction (SHI) domain, the deletion of which, leads to a reduced H3K36me3 deposition. Functionally, SETD2 regulates a subset of hnRNP L-targeted AS events. Our findings demonstrate that SETD2, by interacting with Pol II as well as hnRNP L, can mediate the crosstalk between the transcription and the splicing machinery. The methylation of Histone 3 at Lysine 36 (H3K36) has been implicated in the regulation of transcription and coupled processes such as mRNA splicing. Here the authors show that the histone methyltransferase SETD2 interacts with hnRNP L to mediate the crosstalk between the transcription and splicing machineries.
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24
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Sun H, Ren Q, Zhao X, Tian Y, Pan J, Wei Q, Li Y, Chen Y, Zhang H, Zhang W, Jiang S. Regional similarities and differences in mature human milk fatty acids in Chinese population: A systematic review. Prostaglandins Leukot Essent Fatty Acids 2020; 162:102184. [PMID: 33045533 DOI: 10.1016/j.plefa.2020.102184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 11/21/2022]
Abstract
Maternal factors such as the diet can impact human milk fatty acid profiles. We hypothesized that mature human milk fatty acid profiles differ among regions of China. To test our hypothesis, we conducted a systematic review to calculate regional average contents of fatty acids and the statistical significance of regional differences in fatty acids. We searched both Chinese and English literature databases and selected 21 articles, including 11 in Chinese and 10 in English. We categorized regions of China by 3 ways: 1) north vs. south; 2) inland vs. coastal; 3) socioeconomic development levels. The ratios of ΣSFAs:ΣMUFAs:ΣPUFAs were similar between regions and the average was 1:1:0.7. Contents of palmitic, oleic, and linoleic acids were also similar between regions and together they accounted for more than 70% of all fatty acids in mature human milk. Conversely, concentrations of ALA and DHA differed more than palmitic, oleic, and linoleic acids. We also found that it might be necessary to reduce maternal dietary contents of potentially harmful fatty acids such as erucic acid to minimize detrimental effects on infant health. To our knowledge, this study represents the first systematic review that quantitatively investigated the regional similarities and differences in mature human milk fatty acid contents and is therefore significant for academia and policy makers.
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Affiliation(s)
- Han Sun
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Qiqi Ren
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Xuejun Zhao
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Yueyue Tian
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Jiancun Pan
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Qiaosi Wei
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Yuanyuan Li
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Yong Chen
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Huaqin Zhang
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China
| | - Wei Zhang
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China.
| | - Shilong Jiang
- Nutrition and Metabolism Research Division, Innovation Center, Heilongjiang Feihe Dairy Co., Ltd., C-12, 10A Jiuxianqiao Road, Chaoyang District, Beijing, 100015, China.
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25
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Kang D, Lee Y, Lee JS. RNA-Binding Proteins in Cancer: Functional and Therapeutic Perspectives. Cancers (Basel) 2020; 12:cancers12092699. [PMID: 32967226 PMCID: PMC7563379 DOI: 10.3390/cancers12092699] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary RNA-binding proteins (RBPs) play central roles in regulating posttranscriptional expression of genes. Many of them are known to be deregulated in a wide variety of cancers. Dysregulated RBPs influence the expression levels of target RNAs related to cancer phenotypes, such as proliferation, apoptosis, angiogenesis, senescence, and EMT/invasion/metastasis. Thus, understanding the molecular functions of RBPs and their roles in cancer-related phenotypes can lead to improved therapeutic strategies. Abstract RNA-binding proteins (RBPs) crucially regulate gene expression through post-transcriptional regulation, such as by modulating microRNA (miRNA) processing and the alternative splicing, alternative polyadenylation, subcellular localization, stability, and translation of RNAs. More than 1500 RBPs have been identified to date, and many of them are known to be deregulated in cancer. Alterations in the expression and localization of RBPs can influence the expression levels of oncogenes, tumor-suppressor genes, and genome stability-related genes. RBP-mediated gene regulation can lead to diverse cancer-related cellular phenotypes, such as proliferation, apoptosis, angiogenesis, senescence, and epithelial-mesenchymal transition (EMT)/invasion/metastasis. This regulation can also be associated with cancer prognosis. Thus, RBPs can be potential targets for the development of therapeutics for the cancer treatment. In this review, we describe the molecular functions of RBPs, their roles in cancer-related cellular phenotypes, and various approaches that may be used to target RBPs for cancer treatment.
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Affiliation(s)
- Donghee Kang
- Medical Research Center, College of Medicine, Inha University, Incheon 22212, Korea; (D.K.); (Y.L.)
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Korea
- Program in Biomedical Science & Engineering, Inha University Graduate School, Incheon 22212, Korea
| | - Yerim Lee
- Medical Research Center, College of Medicine, Inha University, Incheon 22212, Korea; (D.K.); (Y.L.)
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Korea
| | - Jae-Seon Lee
- Medical Research Center, College of Medicine, Inha University, Incheon 22212, Korea; (D.K.); (Y.L.)
- Department of Molecular Medicine, College of Medicine, Inha University, Incheon 22212, Korea
- Program in Biomedical Science & Engineering, Inha University Graduate School, Incheon 22212, Korea
- Correspondence: ; Tel.: +82-32-860-9832
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26
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Weiße J, Rosemann J, Krauspe V, Kappler M, Eckert AW, Haemmerle M, Gutschner T. RNA-Binding Proteins as Regulators of Migration, Invasion and Metastasis in Oral Squamous Cell Carcinoma. Int J Mol Sci 2020; 21:E6835. [PMID: 32957697 PMCID: PMC7555251 DOI: 10.3390/ijms21186835] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/06/2023] Open
Abstract
Nearly 7.5% of all human protein-coding genes have been assigned to the class of RNA-binding proteins (RBPs), and over the past decade, RBPs have been increasingly recognized as important regulators of molecular and cellular homeostasis. RBPs regulate the post-transcriptional processing of their target RNAs, i.e., alternative splicing, polyadenylation, stability and turnover, localization, or translation as well as editing and chemical modification, thereby tuning gene expression programs of diverse cellular processes such as cell survival and malignant spread. Importantly, metastases are the major cause of cancer-associated deaths in general, and particularly in oral cancers, which account for 2% of the global cancer mortality. However, the roles and architecture of RBPs and RBP-controlled expression networks during the diverse steps of the metastatic cascade are only incompletely understood. In this review, we will offer a brief overview about RBPs and their general contribution to post-transcriptional regulation of gene expression. Subsequently, we will highlight selected examples of RBPs that have been shown to play a role in oral cancer cell migration, invasion, and metastasis. Last but not least, we will present targeting strategies that have been developed to interfere with the function of some of these RBPs.
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Affiliation(s)
- Jonas Weiße
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (J.W.); (J.R.); (V.K.)
| | - Julia Rosemann
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (J.W.); (J.R.); (V.K.)
| | - Vanessa Krauspe
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (J.W.); (J.R.); (V.K.)
| | - Matthias Kappler
- Department of Oral and Maxillofacial Plastic Surgery, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Alexander W. Eckert
- Department of Cranio Maxillofacial Surgery, Paracelsus Medical University, 90471 Nuremberg, Germany;
| | - Monika Haemmerle
- Institute of Pathology, Section for Experimental Pathology, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany;
| | - Tony Gutschner
- Junior Research Group ‘RNA Biology and Pathogenesis’, Medical Faculty, Martin-Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany; (J.W.); (J.R.); (V.K.)
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27
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Lara J, Diacovich L, Trajtenberg F, Larrieux N, Malchiodi EL, Fernández MM, Gago G, Gramajo H, Buschiazzo A. Mycobacterium tuberculosis FasR senses long fatty acyl-CoA through a tunnel and a hydrophobic transmission spine. Nat Commun 2020; 11:3703. [PMID: 32710080 PMCID: PMC7382501 DOI: 10.1038/s41467-020-17504-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 06/30/2020] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis is a pathogen with a unique cell envelope including very long fatty acids, implicated in bacterial resistance and host immune modulation. FasR is a TetR-like transcriptional activator that plays a central role in sensing mycobacterial long-chain fatty acids and regulating lipid biosynthesis. Here we disclose crystal structures of M. tuberculosis FasR in complex with acyl effector ligands and with DNA, uncovering its molecular sensory and switching mechanisms. A long tunnel traverses the entire effector-binding domain, enabling long fatty acyl effectors to bind. Only when the tunnel is entirely occupied, the protein dimer adopts a rigid configuration with its DNA-binding domains in an open state, leading to DNA dissociation. The protein-folding hydrophobic core connects the two domains, and is completed into a continuous spine when the effector binds. Such a transmission spine is conserved in a large number of TetR-like regulators, offering insight into effector-triggered allosteric functional control. FasR is a TetR-like transcriptional activator that plays a central role in sensing mycobacterial long-chain fatty acids and regulating lipid biosynthesis in Mycobacterium tuberculosis. Here authors present crystal structures of M. tuberculosis FasR in complex with acyl effector ligands and with DNA, uncovering its molecular sensory and switching mechanisms.
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Affiliation(s)
- Julia Lara
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Lautaro Diacovich
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, 2000, Argentina.,Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Rosario, 2000, Argentina
| | - Felipe Trajtenberg
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, 11400, Uruguay
| | - Nicole Larrieux
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, 11400, Uruguay
| | - Emilio L Malchiodi
- Instituto de Estudios de la Inmunidad Humoral (IDEHU/CONICET-UBA), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, 1113, Argentina
| | - Marisa M Fernández
- Instituto de Estudios de la Inmunidad Humoral (IDEHU/CONICET-UBA), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, 1113, Argentina
| | - Gabriela Gago
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, 2000, Argentina
| | - Hugo Gramajo
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, 2000, Argentina.
| | - Alejandro Buschiazzo
- Laboratory of Molecular and Structural Microbiology, Institut Pasteur de Montevideo, Montevideo, 11400, Uruguay. .,Integrative Microbiology of Zoonotic Agents, International Joint Research Unit, Department of Microbiology, Institut Pasteur, Paris, 75724, Cedex 15, France.
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Abstract
Protein-RNA interactions have crucial roles in various cellular activities, which, when dysregulated, can lead to a range of human diseases. The identification of small molecules that target the interaction between RNA-binding proteins (RBPs) and RNA is progressing rapidly and represents a novel strategy for the discovery of chemical probes that facilitate understanding of the cellular functions of RBPs and of therapeutic agents with new mechanisms of action. In this Review, I present a current overview of targeting emerging RBPs using small-molecule inhibitors and recent progress in this burgeoning field. Small-molecule inhibitors that were reported for three representative emerging classes of RBPs, the microRNA-binding protein LIN28, the single-stranded or double-stranded RNA-binding Toll-like receptors and the CRISPR-associated (Cas) proteins, are highlighted from a medicinal-chemistry and chemical-biology perspective. However, although this field is burgeoning, challenges remain in the discovery and characterization of small-molecule inhibitors of RBPs.
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29
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RNA-Targeted Therapies and High-Throughput Screening Methods. Int J Mol Sci 2020; 21:ijms21082996. [PMID: 32340368 PMCID: PMC7216119 DOI: 10.3390/ijms21082996] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
RNA-binding proteins (RBPs) are involved in regulating all aspects of RNA metabolism, including processing, transport, translation, and degradation. Dysregulation of RNA metabolism is linked to a plethora of diseases, such as cancer, neurodegenerative diseases, and neuromuscular disorders. Recent years have seen a dramatic shift in the knowledge base, with RNA increasingly being recognised as an attractive target for precision medicine therapies. In this article, we are going to review current RNA-targeted therapies. Furthermore, we will scrutinise a range of drug discoveries targeting protein-RNA interactions. In particular, we will focus on the interplay between Lin28 and let-7, splicing regulatory proteins and survival motor neuron (SMN) pre-mRNA, as well as HuR, Musashi, proteins and their RNA targets. We will highlight the mechanisms RBPs utilise to modulate RNA metabolism and discuss current high-throughput screening strategies. This review provides evidence that we are entering a new era of RNA-targeted medicine.
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30
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Kilchert C, Sträßer K, Kunetsky V, Änkö ML. From parts lists to functional significance-RNA-protein interactions in gene regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1582. [PMID: 31883228 DOI: 10.1002/wrna.1582] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/03/2019] [Accepted: 12/07/2019] [Indexed: 12/17/2022]
Abstract
Hundreds of canonical RNA binding proteins facilitate diverse and essential RNA processing steps in cells forming a central regulatory point in gene expression. However, recent discoveries including the identification of a large number of noncanonical proteins bound to RNA have changed our view on RNA-protein interactions merely as necessary steps in RNA biogenesis. As the list of proteins interacting with RNA has expanded, so has the scope of regulation through RNA-protein interactions. In addition to facilitating RNA metabolism, RNA binding proteins help to form subcellular structures and membraneless organelles, and provide means to recruit components of macromolecular complexes to their sites of action. Moreover, RNA-protein interactions are not static in cells but the ribonucleoprotein (RNP) complexes are highly dynamic in response to cellular cues. The identification of novel proteins in complex with RNA and ways cells use these interactions to control cellular functions continues to broaden the scope of RNA regulation in cells and the current challenge is to move from cataloguing the components of RNPs into assigning them functions. This will not only facilitate our understanding of cellular homeostasis but may bring in key insights into human disease conditions where RNP components play a central role. This review brings together the classical view of regulation accomplished through RNA-protein interactions with the novel insights gained from the identification of RNA binding interactomes. We discuss the challenges in combining molecular mechanism with cellular functions on the journey towards a comprehensive understanding of the regulatory functions of RNA-protein interactions in cells. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications aRNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Cornelia Kilchert
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Katja Sträßer
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Vladislav Kunetsky
- Institute of Biochemistry, Justus-Liebig University Giessen, Giessen, Germany
| | - Minna-Liisa Änkö
- Centre for Reproductive Health and Centre for Cancer Research, Hudson Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Molecular and Translational Science, School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
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31
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Sagar A, Xue B. Recent Advances in Machine Learning Based Prediction of RNA-protein Interactions. Protein Pept Lett 2019; 26:601-619. [PMID: 31215361 DOI: 10.2174/0929866526666190619103853] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 04/04/2019] [Accepted: 06/01/2019] [Indexed: 12/18/2022]
Abstract
The interactions between RNAs and proteins play critical roles in many biological processes. Therefore, characterizing these interactions becomes critical for mechanistic, biomedical, and clinical studies. Many experimental methods can be used to determine RNA-protein interactions in multiple aspects. However, due to the facts that RNA-protein interactions are tissuespecific and condition-specific, as well as these interactions are weak and frequently compete with each other, those experimental techniques can not be made full use of to discover the complete spectrum of RNA-protein interactions. To moderate these issues, continuous efforts have been devoted to developing high quality computational techniques to study the interactions between RNAs and proteins. Many important progresses have been achieved with the application of novel techniques and strategies, such as machine learning techniques. Especially, with the development and application of CLIP techniques, more and more experimental data on RNA-protein interaction under specific biological conditions are available. These CLIP data altogether provide a rich source for developing advanced machine learning predictors. In this review, recent progresses on computational predictors for RNA-protein interaction were summarized in the following aspects: dataset, prediction strategies, and input features. Possible future developments were also discussed at the end of the review.
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Affiliation(s)
- Amit Sagar
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, Tampa, Florida 33620, United States
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32
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Voutsadakis IA. The pluripotency network in colorectal cancer pathogenesis and prognosis: an update. Biomark Med 2019; 12:653-665. [PMID: 29944017 DOI: 10.2217/bmm-2017-0369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Stemness characteristics are defining properties of cancer initiating cells and are associated with the ability to metastasize and survive in hostile environments. Establishment of the stem cell network depends on the action of a set of core transcription factors that work in concert with other ancillary proteins that are also important during embryonic development. New data consolidate the role of core pluripotency transcription factors OCT4, SOX2 and NANOG as adverse prognostic factors in colorectal cancer. mRNA-binding proteins LIN28 and Musashi, that are associated with stemness, and epigenetic modifiers such as de-acetylase SIRT1 may also have prognostic value in colorectal cancer. This paper provides an update of the stem cell factors in the pathogenesis and prognosis of colorectal cancer.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, Sault Ste Marie, Ontario, Canada.,Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, Ontario, Canada
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33
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Mohibi S, Chen X, Zhang J. Cancer the'RBP'eutics-RNA-binding proteins as therapeutic targets for cancer. Pharmacol Ther 2019; 203:107390. [PMID: 31302171 DOI: 10.1016/j.pharmthera.2019.07.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
RNA-binding proteins (RBPs) play a critical role in the regulation of various RNA processes, including splicing, cleavage and polyadenylation, transport, translation and degradation of coding RNAs, non-coding RNAs and microRNAs. Recent studies indicate that RBPs not only play an instrumental role in normal cellular processes but have also emerged as major players in the development and spread of cancer. Herein, we review the current knowledge about RNA binding proteins and their role in tumorigenesis as well as the potential to target RBPs for cancer therapeutics.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States.
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Minuesa G, Albanese SK, Xie W, Kazansky Y, Worroll D, Chow A, Schurer A, Park SM, Rotsides CZ, Taggart J, Rizzi A, Naden LN, Chou T, Gourkanti S, Cappel D, Passarelli MC, Fairchild L, Adura C, Glickman JF, Schulman J, Famulare C, Patel M, Eibl JK, Ross GM, Bhattacharya S, Tan DS, Leslie CS, Beuming T, Patel DJ, Goldgur Y, Chodera JD, Kharas MG. Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia. Nat Commun 2019; 10:2691. [PMID: 31217428 PMCID: PMC6584500 DOI: 10.1038/s41467-019-10523-3] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/16/2019] [Indexed: 12/30/2022] Open
Abstract
The MUSASHI (MSI) family of RNA binding proteins (MSI1 and MSI2) contribute to a wide spectrum of cancers including acute myeloid leukemia. We find that the small molecule Ro 08-2750 (Ro) binds directly and selectively to MSI2 and competes for its RNA binding in biochemical assays. Ro treatment in mouse and human myeloid leukemia cells results in an increase in differentiation and apoptosis, inhibition of known MSI-targets, and a shared global gene expression signature similar to shRNA depletion of MSI2. Ro demonstrates in vivo inhibition of c-MYC and reduces disease burden in a murine AML leukemia model. Thus, we identify a small molecule that targets MSI's oncogenic activity. Our study provides a framework for targeting RNA binding proteins in cancer.
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Affiliation(s)
- Gerard Minuesa
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Steven K Albanese
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Wei Xie
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yaniv Kazansky
- Weill Cornell Medical College, Tri-Institutional MD-PhD Program, Rockefeller University and Sloan Kettering Institute, New York, NY, 10065, USA
| | - Daniel Worroll
- Department of Pharmacology, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
| | - Arthur Chow
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Alexandra Schurer
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Sun-Mi Park
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Christina Z Rotsides
- Chemical Biology Program, Sloan Kettering Institute and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - James Taggart
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Andrea Rizzi
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Levi N Naden
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Timothy Chou
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Saroj Gourkanti
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | | | - Maria C Passarelli
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Weill Cornell Medical College, Tri-Institutional MD-PhD Program, Rockefeller University and Sloan Kettering Institute, New York, NY, 10065, USA
| | - Lauren Fairchild
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Carolina Adura
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - J Fraser Glickman
- High-Throughput and Spectroscopy Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Jessica Schulman
- Hematologic Oncology Tissue Bank, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Christopher Famulare
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Minal Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Joseph K Eibl
- Northern Ontario School of Medicine, Sudbury, ON, P3E 2C6, Canada
| | - Gregory M Ross
- Northern Ontario School of Medicine, Sudbury, ON, P3E 2C6, Canada
| | | | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Thijs Beuming
- Schrödinger, Inc., 120 West 45th Street, New York, NY, 10036, USA
| | - Dinshaw J Patel
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yehuda Goldgur
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Michael G Kharas
- Molecular Pharmacology Program, Experimental Therapeutics Center and Center for Stem Cell Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.
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GAPDH as a model non-canonical AU-rich RNA binding protein. Semin Cell Dev Biol 2019; 86:162-173. [DOI: 10.1016/j.semcdb.2018.03.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/13/2018] [Accepted: 03/20/2018] [Indexed: 02/06/2023]
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Abstract
MicroRNAs (miRNAs) are important regulators of gene expression that bind complementary target mRNAs and repress their expression. Precursor miRNA molecules undergo nuclear and cytoplasmic processing events, carried out by the endoribonucleases DROSHA and DICER, respectively, to produce mature miRNAs that are loaded onto the RISC (RNA-induced silencing complex) to exert their biological function. Regulation of mature miRNA levels is critical in development, differentiation, and disease, as demonstrated by multiple levels of control during their biogenesis cascade. Here, we will focus on post-transcriptional mechanisms and will discuss the impact of cis-acting sequences in precursor miRNAs, as well as trans-acting factors that bind to these precursors and influence their processing. In particular, we will highlight the role of general RNA-binding proteins (RBPs) as factors that control the processing of specific miRNAs, revealing a complex layer of regulation in miRNA production and function.
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Affiliation(s)
- Gracjan Michlewski
- Division of Infection and Pathway Medicine, University of Edinburgh, Edinburgh EH16 4SB, United Kingdom
- Zhejiang University-University of Edinburgh Institute, Zhejiang University, Zhejiang 314400, P.R. China
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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37
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Claridge B, Kastaniegaard K, Stensballe A, Greening DW. Post-translational and transcriptional dynamics - regulating extracellular vesicle biology. Expert Rev Proteomics 2018; 16:17-31. [PMID: 30457403 DOI: 10.1080/14789450.2019.1551135] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Introduction: Extracellular vesicles (EVs) are secreted into their extracellular environment, contain a specific repertoire of cellular cargo, and represent a novel vehicle for cell-cell communication. Protein post-translational modifications (PTMs) are emerging as major effectors of EV biology and function, and in turn, regulate cellular signaling. Areas covered: Discovery and investigation of PTMs such as methylation, glycosylation, acetylation, phosphorylation, sumoylation, and many others has established fundamental roles for PTMs within EVs and associated EV function. The application of enrichment strategies for modifications, high-resolution quantitative mass spectrometry-based proteomics, and improved technological approaches have provided key insights into identification and characterization of EV-based PTMs. Recently, an overwhelming appreciation for the diversity of modifications, including post-transcriptional modifications, dynamic roles of these modifications, and their emerging interplay, including protein-protein, protein-lipid, protein-RNA, and variable RNA modifications, is emerging. At a cellular level, such interplay is essential for gene expression/genome organization, protein function and localization, RNA metabolism, cell division, and cell signaling. Expert commentary: The understanding of these modifications and interactions will provide strategies toward how distinct cargo is localized, sorted, and delivered through EVs to mediate intercellular function, with further understanding of such modifications and intermolecular interactions will provide advances in EV-based therapeutic strategies.
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Affiliation(s)
- Bethany Claridge
- a Department of Biochemistry and Genetics , La Trobe Institute for Molecular Science, La Trobe University , Melbourne , Australia
| | - Kenneth Kastaniegaard
- b Department of Health Science and Technology , Laboratory for Medical Mass Spectrometry, Aalborg University , Aalborg Ø , Denmark
| | - Allan Stensballe
- b Department of Health Science and Technology , Laboratory for Medical Mass Spectrometry, Aalborg University , Aalborg Ø , Denmark
| | - David W Greening
- a Department of Biochemistry and Genetics , La Trobe Institute for Molecular Science, La Trobe University , Melbourne , Australia
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Hu F, Liu C, Xie F, Lin X, Yang J, Wang C, Huang Q. MSI2 knockdown represses extrahepatic cholangiocarcinoma growth and invasion by inhibiting epithelial-mesenchymal transition. Onco Targets Ther 2018; 11:4035-4046. [PMID: 30034243 PMCID: PMC6049051 DOI: 10.2147/ott.s170739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Purpose To investigate the expression and functional role of Musashi2 (MSI2), an RNA-binding protein, in extrahepatic cholangiocarcinoma (eCCA). Patients and methods We measured MSI2 expression in human specimens and cell lines using Western blot and quantitative real-time polymerase chain reaction, and we analyzed its association with clinicopathologic features in eCCA patients. Univariate and multivariate analyses were performed to identify risk factors correlated with overall survival and disease-free survival. Functional experiments were used to study the mechanisms of MSI2 in regulating eCCA cell growth, migration, and invasion. Results MSI2 expression was upregulated significantly in both human specimens and cell lines, and high MSI2 expression was associated with lymph node metastasis, advanced TNM stage, and poor prognosis in eCCA patients. Additionally, MSI2 overexpression promoted eCCA cell growth, migration, and invasion, while MSI2 knockdown repressed eCCA cell migration and invasion by inhibiting epithelial–mesenchymal transition. Conclusion MSI2 is an independent prognostic factor for eCCA patients, and MSI2 downregulation inhibits eCCA cell growth and metastasis. MSI2 may be a potential therapeutic target for eCCA patients.
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Affiliation(s)
- Feihu Hu
- Department of General Surgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China, .,Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Anhui Provincial Hospital, Heifei, China,
| | - Chenhai Liu
- Department of General Surgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China, .,Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Anhui Provincial Hospital, Heifei, China,
| | - Fang Xie
- Department of General Surgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China, .,Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Anhui Provincial Hospital, Heifei, China,
| | - Xiansheng Lin
- Department of General Surgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China, .,Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Anhui Provincial Hospital, Heifei, China,
| | - Ji Yang
- Department of General Surgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China, .,Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Anhui Provincial Hospital, Heifei, China,
| | - Chao Wang
- Department of General Surgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China, .,Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Anhui Provincial Hospital, Heifei, China,
| | - Qiang Huang
- Department of General Surgery, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, China, .,Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, Anhui Provincial Hospital, Heifei, China,
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Chatterji P, Rustgi AK. RNA Binding Proteins in Intestinal Epithelial Biology and Colorectal Cancer. Trends Mol Med 2018; 24:490-506. [PMID: 29627433 DOI: 10.1016/j.molmed.2018.03.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 12/14/2022]
Abstract
The intestinal epithelium is highly proliferative and consists of crypt invaginations that house stem cells and villus projections with differentiated cells. There exists a dynamic equilibrium between proliferation, migration, differentiation, and senescence that is regulated by several factors. Among these are RNA binding proteins (RBPs) that bind their targets in a both context dependent and independent manner. RBP-RNA complexes act as rheostats by regulating expression of RNAs both co- and post-transcriptionally. This is important, especially in response to intestinal injury, to fuel regeneration. The manner in which these RBPs function in the intestine and their interactions with other pivotal pathways in colorectal cancer may provide a framework for new insights and potential therapeutic applications.
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Affiliation(s)
- Priya Chatterji
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA
| | - Anil K Rustgi
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, 421 Curie Blvd., Philadelphia, PA 19104, USA.
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40
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RNA-binding proteins control gene expression and cell fate in the immune system. Nat Immunol 2018; 19:120-129. [PMID: 29348497 DOI: 10.1038/s41590-017-0028-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/29/2017] [Indexed: 12/19/2022]
Abstract
RNA-binding proteins (RBPs) are essential for the development and function of the immune system. They interact dynamically with RNA to control its biogenesis and turnover by transcription-dependent and transcription-independent mechanisms. In this Review, we discuss the molecular mechanisms by which RBPs allow gene expression changes to occur at different speeds and to varying degrees, and which RBPs regulate the diversity of the transcriptome and proteome. These proteins are nodes for integration of transcriptional and signaling networks and are intimately linked to intermediary metabolism. They are essential components of regulatory feedback mechanisms that maintain immune tolerance and limit inflammation. The role of RBPs in malignancy and autoimmunity has led to their emergence as targets for the development of new therapeutic modalities.
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Abstract
RNA-binding proteins (RBPs) are typically thought of as proteins that bind RNA through one or multiple globular RNA-binding domains (RBDs) and change the fate or function of the bound RNAs. Several hundred such RBPs have been discovered and investigated over the years. Recent proteome-wide studies have more than doubled the number of proteins implicated in RNA binding and uncovered hundreds of additional RBPs lacking conventional RBDs. In this Review, we discuss these new RBPs and the emerging understanding of their unexpected modes of RNA binding, which can be mediated by intrinsically disordered regions, protein-protein interaction interfaces and enzymatic cores, among others. We also discuss the RNA targets and molecular and cellular functions of the new RBPs, as well as the possibility that some RBPs may be regulated by RNA rather than regulate RNA.
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42
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Human oncoprotein Musashi-2 N-terminal RNA recognition motif backbone assignment and identification of RNA-binding pocket. Oncotarget 2017; 8:106587-106597. [PMID: 29290973 PMCID: PMC5739758 DOI: 10.18632/oncotarget.22540] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/30/2017] [Indexed: 12/13/2022] Open
Abstract
RNA-binding protein Musashi-2 (MSI2) is a key regulator in stem cells, it is over-expressed in a variety of cancers and its higher expression is associated with poor prognosis. Like Musashi-1, it contains two N-terminal RRMs (RNA-recognition Motifs, also called RBDs (RNA-binding Domains)), RRM1 and RRM2, which mediate the binding to their target mRNAs. Previous studies have obtained the three-dimensional structures of the RBDs of Musashi-1 and the RBD1:RNA complex. Here we show the binding of MSI2-RRM1 to a 15nt Numb RNA in Fluorescence Polarization assay and time resolved Fluorescence Resonance Energy Transfer assay. Using nuclear magnetic resonance (NMR) spectroscopy we assigned the backbone resonances of MSI2-RRM1, and characterized the direct interaction of RRM1 to Numb RNA r(GUAGU). Our NMR titration and structure modeling studies showed that MSI2-RRM1 and MSI1-RBD1 have similar RNA binding events and binding pockets. This work adds significant information to MSI2-RRM1 structure and RNA binding pocket, and contributes to the development of MSI2 specific and MSI1/MSI2 dual inhibitors.
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Chu M, Novak SM, Cover C, Wang AA, Chinyere IR, Juneman EB, Zarnescu DC, Wong PK, Gregorio CC. Increased Cardiac Arrhythmogenesis Associated With Gap Junction Remodeling With Upregulation of RNA-Binding Protein FXR1. Circulation 2017; 137:605-618. [PMID: 29101288 DOI: 10.1161/circulationaha.117.028976] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 10/23/2017] [Indexed: 11/16/2022]
Abstract
BACKGROUND Gap junction remodeling is well established as a consistent feature of human heart disease involving spontaneous ventricular arrhythmia. The mechanisms responsible for gap junction remodeling that include alterations in the distribution of, and protein expression within, gap junctions are still debated. Studies reveal that multiple transcriptional and posttranscriptional regulatory pathways are triggered in response to cardiac disease, such as those involving RNA-binding proteins. The expression levels of FXR1 (fragile X mental retardation autosomal homolog 1), an RNA-binding protein, are critical to maintain proper cardiac muscle function; however, the connection between FXR1 and disease is not clear. METHODS To identify the mechanisms regulating gap junction remodeling in cardiac disease, we sought to identify the functional properties of FXR1 expression, direct targets of FXR1 in human left ventricle dilated cardiomyopathy (DCM) biopsy samples and mouse models of DCM through BioID proximity assay and RNA immunoprecipitation, how FXR1 regulates its targets through RNA stability and luciferase assays, and functional consequences of altering the levels of this important RNA-binding protein through the analysis of cardiac-specific FXR1 knockout mice and mice injected with 3xMyc-FXR1 adeno-associated virus. RESULTS FXR1 expression is significantly increased in tissue samples from human and mouse models of DCM via Western blot analysis. FXR1 associates with intercalated discs, and integral gap junction proteins Cx43 (connexin 43), Cx45 (connexin 45), and ZO-1 (zonula occludens-1) were identified as novel mRNA targets of FXR1 by using a BioID proximity assay and RNA immunoprecipitation. Our findings show that FXR1 is a multifunctional protein involved in translational regulation and stabilization of its mRNA targets in heart muscle. In addition, introduction of 3xMyc-FXR1 via adeno-associated virus into mice leads to the redistribution of gap junctions and promotes ventricular tachycardia, showing the functional significance of FXR1 upregulation observed in DCM. CONCLUSIONS In DCM, increased FXR1 expression appears to play an important role in disease progression by regulating gap junction remodeling. Together this study provides a novel function of FXR1, namely, that it directly regulates major gap junction components, contributing to proper cell-cell communication in the heart.
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Affiliation(s)
- Miensheng Chu
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
| | - Stefanie Mares Novak
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
| | - Cathleen Cover
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
| | - Anne A Wang
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
| | | | | | | | - Pak Kin Wong
- University of Arizona, Tucson. Department of Biomedical Engineering at Pennsylvania State University, University Park (P.K.W.)
| | - Carol C Gregorio
- Department of Cellular and Molecular Medicine and Sarver Molecular Cardiovascular Research Program (M.C., S.M.N., C.C., A.A.W., C.C.G.)
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Iwaoka R, Nagata T, Tsuda K, Imai T, Okano H, Kobayashi N, Katahira M. Backbone and side chain assignments of the second RNA-binding domain of Musashi-1 in its free form and in complex with 5-mer RNA. BIOMOLECULAR NMR ASSIGNMENTS 2017; 11:265-268. [PMID: 28808919 DOI: 10.1007/s12104-017-9760-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 08/07/2017] [Indexed: 06/07/2023]
Abstract
Musashi1 (Msi1) is an RNA-binding protein that is involved in cell fate determination. Here, we report the 1H, 15N, and 13C resonance assignments of Msi1 second RNA-binding domain in free form and in complex with RNA. The assignments can be utilized for NMR structure and dynamics analyses of the Msi1:RNA complex, and moreover, for chemical shift perturbation analyses to evaluate the binding of potential small molecule inhibitors against Msi1:RNA interaction.
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Affiliation(s)
- Ryo Iwaoka
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Takashi Nagata
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
| | - Kengo Tsuda
- RIKEN Center for Life Science Technologies, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takao Imai
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Naohiro Kobayashi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
- Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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Structural Insight into the Recognition of r(UAG) by Musashi-1 RBD2, and Construction of a Model of Musashi-1 RBD1-2 Bound to the Minimum Target RNA. Molecules 2017; 22:molecules22071207. [PMID: 28753936 PMCID: PMC6152312 DOI: 10.3390/molecules22071207] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 07/14/2017] [Accepted: 07/14/2017] [Indexed: 12/23/2022] Open
Abstract
Musashi-1 (Msi1) controls the maintenance of stem cells and tumorigenesis through binding to its target mRNAs and subsequent translational regulation. Msi1 has two RNA-binding domains (RBDs), RBD1 and RBD2, which recognize r(GUAG) and r(UAG), respectively. These minimal recognition sequences are connected by variable linkers in the Msi1 target mRNAs, however, the molecular mechanism by which Msi1 recognizes its targets is not yet understood. We previously determined the solution structure of the Msi1 RBD1:r(GUAGU) complex. Here, we determined the first structure of the RBD2:r(GUAGU) complex. The structure revealed that the central trinucleotide, r(UAG), is specifically recognized by the intermolecular hydrogen-bonding and aromatic stacking interactions. Importantly, the C-terminal region, which is disordered in the free form, took a certain conformation, resembling a helix. The observation of chemical shift perturbation and intermolecular NOEs, together with increases in the heteronuclear steady-state {1H}-15N NOE values on complex formation, indicated the involvement of the C-terminal region in RNA binding. On the basis of the two complex structures, we built a structural model of consecutive RBDs with r(UAGGUAG) containing both minimal recognition sequences, which resulted in no steric hindrance. The model suggests recognition of variable lengths (n) of the linker up to n = 50 may be possible.
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Kumar S, Downie Ruiz Velasco A, Michlewski G. Oleic Acid Induces MiR-7 Processing through Remodeling of Pri-MiR-7/Protein Complex. J Mol Biol 2017; 429:1638-1649. [PMID: 28483648 PMCID: PMC5462424 DOI: 10.1016/j.jmb.2017.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 05/01/2017] [Accepted: 05/02/2017] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRs) play a vital role in governing cell function, with their levels tightly controlled at transcriptional and post-transcriptional levels. Different sets of RNA-binding proteins interact with primary miRs (pri-miRs) and precursor-miR transcripts (pre-miRs), controlling their biogenesis post-transcriptionally. The Hu antigen R (HuR)-mediated binding of Musashi homolog2 (MSI2) to the conserved terminal loop of pri-miR-7 regulates the levels of brain-enriched miR-7 formation in a tissue-specific manner. Here, we show that oleic acid (OA) inhibits the binding of proteins containing RNA recognition motifs (RRM) to the conserved terminal loop of pri-miR-7. Using electrophoretic mobility shift assays in HeLa cell extracts, we show that OA treatment disrupts pre-miR/protein complexes. Furthermore, OA rescues in vitro processing of pri-miR-7, which is otherwise blocked by HuR and MSI2 proteins. On the contrary, pri-miR-16 shows reduced processing in the presence of OA. This indicates that OA may inhibit the binding of other RRM-containing protein/s necessary for miR-16 processing. Finally, we demonstrate that OA induces mature miR-7 production in HeLa cells. Together, our results demonstrate that OA can regulate the processing of pri-miRs by remodeling their protein complexes. This provides a new tool to study RNA processing and a potential lead for small molecules that target the miR-7 biogenesis pathway. OA inhibits the binding of proteins containing RRM. OA rescues processing of pri-miR-7 in vitro. OA induces mature miR-7 production in HeLa cells.
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Affiliation(s)
- Santosh Kumar
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Angela Downie Ruiz Velasco
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK
| | - Gracjan Michlewski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3BF, UK.
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Kharas MG, Lengner CJ. Stem Cells, Cancer, and MUSASHI in Blood and Guts. Trends Cancer 2017; 3:347-356. [PMID: 28718412 DOI: 10.1016/j.trecan.2017.03.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 01/08/2023]
Abstract
The mammalian MSI family of RNA-binding proteins (RBPs) have important roles as oncoproteins in an array of tumor types, including leukemias, glioblastomas, and pancreatic, breast, lung, and colorectal cancers. The mammalian Msi genes, Msi1 and Msi2, have been most thoroughly investigated in two highly proliferative tissues prone to oncogenic transformation: the hematopoietic lineage and the intestinal epithelium. Despite their vast phenotypic differences, MSI proteins appear to have an analogous role in governing the stem cell compartment in both of these tissues, potentially providing a paradigm for a broader understanding of MSI function and oncogenic activities. In this review, we focus on the function of MSI in the blood and the intestine, and discuss therapeutic strategies for targeting this pathway.
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Affiliation(s)
- Michael G Kharas
- Molecular Pharmacology Program and Center for Cell Engineering, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
| | - Christopher J Lengner
- Department of Biomedical Sciences, School of Veterinary Medicine, and Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA.
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Kudinov AE, Karanicolas J, Golemis EA, Boumber Y. Musashi RNA-Binding Proteins as Cancer Drivers and Novel Therapeutic Targets. Clin Cancer Res 2017; 23:2143-2153. [PMID: 28143872 DOI: 10.1158/1078-0432.ccr-16-2728] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 12/12/2022]
Abstract
Aberrant gene expression that drives human cancer can arise from epigenetic dysregulation. Although much attention has focused on altered activity of transcription factors and chromatin-modulating proteins, proteins that act posttranscriptionally can potently affect expression of oncogenic signaling proteins. The RNA-binding proteins (RBP) Musashi-1 (MSI1) and Musashi-2 (MSI2) are emerging as regulators of multiple critical biological processes relevant to cancer initiation, progression, and drug resistance. Following identification of Musashi as a regulator of progenitor cell identity in Drosophila, the human Musashi proteins were initially linked to control of maintenance of hematopoietic stem cells, then stem cell compartments for additional cell types. More recently, the Musashi proteins were found to be overexpressed and prognostic of outcome in numerous cancer types, including colorectal, lung, and pancreatic cancers; glioblastoma; and several leukemias. MSI1 and MSI2 bind and regulate the mRNA stability and translation of proteins operating in essential oncogenic signaling pathways, including NUMB/Notch, PTEN/mTOR, TGFβ/SMAD3, MYC, cMET, and others. On the basis of these activities, MSI proteins maintain cancer stem cell populations and regulate cancer invasion, metastasis, and development of more aggressive cancer phenotypes, including drug resistance. Although RBPs are viewed as difficult therapeutic targets, initial efforts to develop MSI-specific inhibitors are promising, and RNA interference-based approaches to inhibiting these proteins have had promising outcomes in preclinical studies. In the interim, understanding the function of these translational regulators may yield insight into the relationship between mRNA expression and protein expression in tumors, guiding tumor-profiling analysis. This review provides a current overview of Musashi as a cancer driver and novel therapeutic target. Clin Cancer Res; 23(9); 2143-53. ©2017 AACR.
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Affiliation(s)
- Alexander E Kudinov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yanis Boumber
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, Pennsylvania. .,Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
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Lim D, Byun WG, Koo JY, Park H, Park SB. Discovery of a Small-Molecule Inhibitor of Protein–MicroRNA Interaction Using Binding Assay with a Site-Specifically Labeled Lin28. J Am Chem Soc 2016; 138:13630-13638. [DOI: 10.1021/jacs.6b06965] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Donghyun Lim
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
| | - Wan Gi Byun
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Ja Young Koo
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Hankum Park
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
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de Araujo PR, Gorthi A, da Silva AE, Tonapi SS, Vo DT, Burns SC, Qiao M, Uren PJ, Yuan ZM, Bishop AJR, Penalva LOF. Musashi1 Impacts Radio-Resistance in Glioblastoma by Controlling DNA-Protein Kinase Catalytic Subunit. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:2271-8. [PMID: 27470713 PMCID: PMC5012509 DOI: 10.1016/j.ajpath.2016.05.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/13/2016] [Indexed: 12/30/2022]
Abstract
The conserved RNA-binding protein Musashi1 (MSI1) has been characterized as a stem cell marker, controlling the balance between self-renewal and differentiation and as a key oncogenic factor in numerous solid tumors, including glioblastoma. To explore the potential use of MSI1 targeting in therapy, we studied MSI1 in the context of radiation sensitivity. Knockdown of MSI1 led to a decrease in cell survival and an increase in DNA damage compared to control in cells treated with ionizing radiation. We subsequently examined mechanisms of double-strand break repair and found that loss of MSI1 reduces the frequency of nonhomologous end-joining. This phenomenon could be attributed to the decreased expression of DNA-protein kinase catalytic subunit, which we have previously identified as a target of MSI1. Collectively, our results suggest a role for MSI1 in double-strand break repair and that its inhibition may enhance the effect of radiotherapy.
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Affiliation(s)
- Patricia Rosa de Araujo
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas; Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas
| | - Aparna Gorthi
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas; Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas
| | - Acarizia E da Silva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas; Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas
| | - Sonal S Tonapi
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas; Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas
| | - Dat T Vo
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas; Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas
| | - Suzanne C Burns
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas
| | - Mei Qiao
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas
| | - Philip J Uren
- Molecular and Computational Biology Section, Division of Biological Sciences, University of Southern California, Los Angeles, California
| | - Zhi-Min Yuan
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, Massachusetts
| | - Alexander J R Bishop
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas; Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas.
| | - Luiz O F Penalva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center, San Antonio, Texas; Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas.
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