1
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Xu J, Zhao X, Liang X, Guo D, Wang J, Wang Q, Tang X. Development of miRNA-based PROTACs targeting Lin28 for breast cancer therapy. SCIENCE ADVANCES 2024; 10:eadp0334. [PMID: 39292784 PMCID: PMC11409961 DOI: 10.1126/sciadv.adp0334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 08/09/2024] [Indexed: 09/20/2024]
Abstract
Lin28, a highly conserved carcinogenic protein, plays an important role in the generation of cancer stem cells, contributing to the unfavorable prognosis of cancer patients. This RNA binding protein specifically binds to pri/pre-microRNA (miRNA) lethal-7 (let-7), impeding its miRNA maturation. The reduced expression of tumor suppressor miRNA let-7 fosters development and progression-related traits such as proliferation, invasion, metastasis, and drug resistance. We report a series of miRNA-based Lin28A-miRNA proteolysis-targeting chimeras (Lin28A-miRNA-PROTACs) designed to efficiently degrade Lin28A through a ubiquitin-proteasome-dependent mechanism, resulting in up-regulation of mature let-7 family. The augmented levels of matured let-7 miRNAs further exert inhibitory effects on cancer cell proliferation and migration, and increase its sensitivity to chemotherapy. In a mouse ectopic tumor model, Lin28A-miRNA-PROTAC demonstrates a substantial efficacy in inhibiting tumor growth. When combined with tamoxifen, the tumors exhibit gradual regression. This study displays an effective miRNA-based PROTACs to degrade Lin28A and inhibit tumor growth, providing a promising therapeutic avenue for cancer treatment with miRNA-based therapy.
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Affiliation(s)
- Jianfei Xu
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center and School of Pharmaceutical Sciences, Peking University, Xueyuan Rd, Beijing 100191, China
| | - Xiaoran Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center and School of Pharmaceutical Sciences, Peking University, Xueyuan Rd, Beijing 100191, China
| | - Xingxing Liang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center and School of Pharmaceutical Sciences, Peking University, Xueyuan Rd, Beijing 100191, China
| | - Dongyang Guo
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center and School of Pharmaceutical Sciences, Peking University, Xueyuan Rd, Beijing 100191, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center and School of Pharmaceutical Sciences, Peking University, Xueyuan Rd, Beijing 100191, China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center and School of Pharmaceutical Sciences, Peking University, Xueyuan Rd, Beijing 100191, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center and School of Pharmaceutical Sciences, Peking University, Xueyuan Rd, Beijing 100191, China
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2
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Yi G, Ye M, Carrique L, El-Sagheer A, Brown T, Norbury CJ, Zhang P, Gilbert RJC. Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs. Nat Struct Mol Biol 2024; 31:1426-1438. [PMID: 39054354 PMCID: PMC11402785 DOI: 10.1038/s41594-024-01357-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 06/17/2024] [Indexed: 07/27/2024]
Abstract
Tumor-suppressor let-7 pre-microRNAs (miRNAs) are regulated by terminal uridylyltransferases TUT7 and TUT4 that either promote let-7 maturation by adding a single uridine nucleotide to the pre-miRNA 3' end or mark them for degradation by the addition of multiple uridines. Oligo-uridylation is increased in cells by enhanced TUT7/4 expression and especially by the RNA-binding pluripotency factor LIN28A. Using cryogenic electron microscopy, we captured high-resolution structures of active forms of TUT7 alone, of TUT7 plus pre-miRNA and of both TUT7 and TUT4 bound with pre-miRNA and LIN28A. Our structures reveal that pre-miRNAs engage the enzymes in fundamentally different ways depending on the presence of LIN28A, which clamps them onto the TUTs to enable processive 3' oligo-uridylation. This study reveals the molecular basis for mono- versus oligo-uridylation by TUT7/4, as determined by the presence of LIN28A, and thus their mechanism of action in the regulation of cell fate and in cancer.
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Affiliation(s)
- Gangshun Yi
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Calleva Centre for Evolution and Human Science, Magdalen College, Oxford, UK
| | - Mingda Ye
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Loic Carrique
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Afaf El-Sagheer
- Chemistry Research Laboratory, University of Oxford, Oxford, UK
- Institute for Life Sciences, University of Southampton Highfield Campus, Southampton, UK
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Chris J Norbury
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Peijun Zhang
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Robert J C Gilbert
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Calleva Centre for Evolution and Human Science, Magdalen College, Oxford, UK.
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3
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Garg A, Shang R, Cvetanovic T, Lai EC, Joshua-Tor L. The structural landscape of Microprocessor mediated pri- let-7 miRNA processing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593372. [PMID: 38766155 PMCID: PMC11100773 DOI: 10.1101/2024.05.09.593372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
miRNA biogenesis is initiated upon cleavage of a primary miRNA (pri-miRNA) hairpin by the Microprocessor (MP), composed of the Drosha RNase III enzyme and its partner DGCR8. Multiple pri-miRNA sequence motifs affect MP recognition, fidelity, and efficiency. Here, we performed cryo-EM and biochemical studies of several let-7 family pri-miRNAs in complex with human MP. We show that MP has the structural plasticity to accommodate a range of pri-miRNAs. These structures revealed key features of the 5' UG sequence motif, more comprehensively represented as the "fUN" motif. Our analysis explains how cleavage of class-II pri-let-7 members harboring a bulged nucleotide generates a noncanonical precursor with a 1-nt 3' overhang. Finally, the MP-SRSF3-pri-let-7f1 structure reveals how SRSF3 contributes to MP fidelity by interacting with the CNNC-motif and Drosha's PAZ-like domain. Overall, this study sheds light on the mechanisms for flexible recognition, accurate cleavage, and regulated processing of different pri-miRNAs by MP.
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Affiliation(s)
- Ankur Garg
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road,Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
| | - Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Todor Cvetanovic
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road,Cold Spring Harbor, New York, 11724 USA
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, 430 East 67th St, ROC-10, New York, NY 10065, USA
| | - Leemor Joshua-Tor
- W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, One Bungtown Road,Cold Spring Harbor, New York, 11724 USA
- Howard Hughes Medical Institute, Cold Spring Harbor laboratory, One Bungtown Road, Cold Spring Harbor, New York, 11724 USA
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4
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Rosenblum SL, Soueid DM, Giambasu G, Vander Roest S, Pasternak A, DiMauro EF, Simov V, Garner AL. Live cell screening to identify RNA-binding small molecule inhibitors of the pre-let-7-Lin28 RNA-protein interaction. RSC Med Chem 2024; 15:1539-1546. [PMID: 38784453 PMCID: PMC11110735 DOI: 10.1039/d4md00123k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 03/16/2024] [Indexed: 05/25/2024] Open
Abstract
Dysregulation of the networking of RNA-binding proteins (RBPs) and RNAs drives many human diseases, including cancers, and the targeting of RNA-protein interactions (RPIs) has emerged as an exciting area of RNA-targeted drug discovery. Accordingly, methods that enable the discovery of cell-active small molecule modulators of RPIs are needed to propel this emerging field forward. Herein, we describe the application of live-cell assay technology, RNA interaction with protein-mediated complementation assay (RiPCA), for high-throughput screening to identify small molecule inhibitors of the pre-let-7d-Lin28A RPI. Utilizing a combination of RNA-biased small molecules and virtual screening hits, we discovered an RNA-binding small molecule that can disrupt the pre-let-7-Lin28 interaction demonstrating the potential of RiPCA for advancing RPI-targeted drug discovery.
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Affiliation(s)
- Sydney L Rosenblum
- Program in Chemical Biology, University of Michigan 210 Washtenaw Avenue Ann Arbor MI 48109 USA
| | - Dalia M Soueid
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan 1600 Huron Parkway, NCRC B520 Ann Arbor MI 48109 USA
| | - George Giambasu
- Computational Chemistry, Merck & Co., Inc. Boston MA 02115 USA
| | - Steve Vander Roest
- Center for Chemical Genomics, Life Sciences Institute, University of Michigan 210 Washtenaw Avenue Ann Arbor MI 48109 USA
| | | | - Erin F DiMauro
- Discovery Chemistry, Merck & Co., Inc. Boston MA 02115 USA
| | - Vladimir Simov
- Discovery Chemistry, Merck & Co., Inc. Boston MA 02115 USA
| | - Amanda L Garner
- Program in Chemical Biology, University of Michigan 210 Washtenaw Avenue Ann Arbor MI 48109 USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan 1600 Huron Parkway, NCRC B520 Ann Arbor MI 48109 USA
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5
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Raja R, Sundararaj R, Kandasamy R. Identification of small molecule inhibitors against Lin28/let-7 to suppress tumor progression and its alleviation role in LIN28-dependent glucose metabolism. Med Oncol 2024; 41:118. [PMID: 38630184 DOI: 10.1007/s12032-024-02350-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/04/2024] [Indexed: 04/19/2024]
Abstract
The reciprocal suppression of an RNA-binding protein LIN28 (human abnormal cell lineage 28) and miRNA Let-7 (Lethal 7) is considered to have a prime role in hepatocellular carcinoma (HCC). Though targeting this inhibition interaction is effective for therapeutics, it causes other unfavorable effects on glucose metabolism and increased insulin resistance. Hence, this study aims to identify small molecules targeting Lin28/let-7 interaction along with additional potency to improve insulin sensitivity. Of 22,14,996 small molecules screened by high throughput virtual screening, 6 molecules, namely 41354, 1558, 12437, 23837, 15710, and 8319 were able to block the LIN28 interaction with let-7 and increase the insulin sensitivity via interacting with PPARγ (peroxisome proliferator-activated receptors γ). MM-GBSA (Molecular Mechanics-Generalized Born Surface Area) analysis is used to re-score the binding affinity of docked complexes. Upon further analysis, it is also seen that these molecules have superior ADME (Absorption, Distribution, Metabolism, and Excretion) properties and form stable complexes with the targets for a significant period in a biologically simulated environment (Molecular Dynamics simulation) for 100 ns. From our results, we hypothesize that these identified 6 small molecules can be potential candidates for HCC treatment and the glucose metabolic disorder caused by the HCC treatment.
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Affiliation(s)
- Rachanaa Raja
- Centre for Excellence in Nanobio Translational Research, Department of Pharmaceutical Technology, University College of Engineering, Anna University (BIT Campus), Tiruchirappalli, Tamil Nadu, India
| | - Rajamanikandan Sundararaj
- Centre for Drug Discovery, Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India
| | - Ruckmani Kandasamy
- Centre for Excellence in Nanobio Translational Research, Department of Pharmaceutical Technology, University College of Engineering, Anna University (BIT Campus), Tiruchirappalli, Tamil Nadu, India.
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6
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Oyejobi GK, Yan X, Sliz P, Wang L. Regulating Protein-RNA Interactions: Advances in Targeting the LIN28/Let-7 Pathway. Int J Mol Sci 2024; 25:3585. [PMID: 38612395 PMCID: PMC11011352 DOI: 10.3390/ijms25073585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Originally discovered in C. elegans, LIN28 is an evolutionarily conserved zinc finger RNA-binding protein (RBP) that post-transcriptionally regulates genes involved in developmental timing, stem cell programming, and oncogenesis. LIN28 acts via two distinct mechanisms. It blocks the biogenesis of the lethal-7 (let-7) microRNA (miRNA) family, and also directly binds messenger RNA (mRNA) targets, such as IGF-2 mRNA, and alters downstream splicing and translation events. This review focuses on the molecular mechanism of LIN28 repression of let-7 and current strategies to overcome this blockade for the purpose of cancer therapy. We highlight the value of the LIN28/let-7 pathway as a drug target, as multiple oncogenic proteins that the pathway regulates are considered undruggable due to their inaccessible cellular location and lack of cavities for small molecule binding.
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Affiliation(s)
- Greater Kayode Oyejobi
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430072, China; (G.K.O.); (X.Y.)
| | - Xiaodan Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430072, China; (G.K.O.); (X.Y.)
| | - Piotr Sliz
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Longfei Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430072, China; (G.K.O.); (X.Y.)
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7
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Borgelt L, Hohnen L, Pallesen JS, Hommen P, Goebel GL, Bosica F, Liu Y, O’Mahony G, Wu P. N-Biphenyl Pyrrolinones and Dibenzofurans as RNA-Binding Protein LIN28 Inhibitors Disrupting the LIN28- Let-7 Interaction. ACS Med Chem Lett 2023; 14:1707-1715. [PMID: 38116413 PMCID: PMC10726440 DOI: 10.1021/acsmedchemlett.3c00341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/27/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
The RNA-binding protein LIN28 is a regulator of miRNA let-7 biogenesis. Inhibitors of LIN28 are highly sought after given the central role that LIN28 plays in tumorigenesis and development of cancer stem cells as well as LIN28's association with poor clinical prognosis. Although LIN28 inhibitors of different scaffolds have been reported, the potential of most LIN28 inhibiting small molecules was not fully explored since very limited structure-activity relationship (SAR) studies have been performed. We previously identified trisubstituted pyrrolinones as a new class of LIN28 inhibitors disrupting the LIN28-let-7 interaction. Here, we performed extensive SAR by evaluating 95 small molecules and identified new trisubstituted pyrrolinones featuring either an N-biphenyl or N-dibenzofuran substituent, overthrowing the existing conclusion that a salicylic acid moiety is indispensable for activity. Exchange of the negatively charged salicylic acid moiety in LIN28 inhibitors with a heterocyclic substituent is beneficial for membrane permeability, leading to increased activity in a cellular assay, and will potentially reduce toxicity.
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Affiliation(s)
- Lydia Borgelt
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn
Str. 6, Dortmund 44227, Germany
| | - Lisa Hohnen
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Biochemistry, Ruhr-University
Bochum, Universitätsstr.
150, Bochum 44801, Germany
| | - Jakob S. Pallesen
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Pascal Hommen
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn
Str. 6, Dortmund 44227, Germany
| | - Georg L. Goebel
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn
Str. 6, Dortmund 44227, Germany
| | - Francesco Bosica
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Yang Liu
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn
Str. 6, Dortmund 44227, Germany
| | - Gavin O’Mahony
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Peng Wu
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
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8
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Davidge B, McDermott SM, Carnes J, Lewis I, Tracy M, Stuart KD. Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA editing catalytic complexes in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2023; 29:1591-1609. [PMID: 37474258 PMCID: PMC10578492 DOI: 10.1261/rna.079691.123] [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: 04/19/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life-cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multiprotein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing, and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations, most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the zinc fingers (ZFs), an intrinsically disordered region (IDR), and several within or near the carboxy-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing, whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.
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Affiliation(s)
- Brittney Davidge
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
| | - Jason Carnes
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Isaac Lewis
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Maxwell Tracy
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
| | - Kenneth D Stuart
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, Washington 98109, USA
- Department of Pediatrics, University of Washington, Seattle, Washington 98195, USA
- Department of Global Health, University of Washington, Seattle, Washington 98195, USA
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9
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Borgelt L, Huang F, Hohnen L, Qiu X, Goebel GL, Hommen P, Wu P. Spirocyclic Chromenopyrazole Inhibitors Disrupting the Interaction between the RNA-Binding Protein LIN28 and Let-7. Chembiochem 2023; 24:e202300168. [PMID: 37129525 DOI: 10.1002/cbic.202300168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/21/2023] [Accepted: 05/02/2023] [Indexed: 05/03/2023]
Abstract
Small-molecule inhibitors of the RNA-binding and regulating protein LIN28 have the potential to be developed as chemical probes for biological perturbation and as therapeutic candidates. Reported small molecules disrupting the interaction between LIN28 and let-7 miRNA suffer from moderate to weak inhibitory activity and flat structure-activity relationship, which hindered the development of next-generation LIN28 inhibitors that warrant further evaluations. We report herein the identification of new LIN28 inhibitors utilizing a spirocyclization strategy based on a chromenopyrazole scaffold. Representative compounds 2-5 showed potent in vitro inhibitory activity against LIN28-let-7 interaction and single-digit micromolar potency in inhibiting the proliferation of LIN28-expressing JAR cancer cells. The spirocyclic compound 5 incorporated a position that is amenable for functional group appendage and further structural modifications. The binding mode of compound 5 with the LIN28 cold shock domain was rationalized via a molecular docking analysis.
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Affiliation(s)
- Lydia Borgelt
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 15, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Fubao Huang
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 15, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
| | - Lisa Hohnen
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 15, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstr. 150, Bochum, 44780, Germany
| | - Xiaqiu Qiu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 15, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Georg L Goebel
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 15, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Pascal Hommen
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 15, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Peng Wu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 15, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
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10
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Hommen P, Hwang J, Huang F, Borgelt L, Hohnen L, Wu P. Chromenopyrazole-Peptide Conjugates as Small-Molecule Based Inhibitors Disrupting the Protein-RNA Interaction of LIN28-let-7. Chembiochem 2023; 24:e202300376. [PMID: 37224100 DOI: 10.1002/cbic.202300376] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 05/24/2023] [Indexed: 05/26/2023]
Abstract
Targeting the protein-RNA interaction of LIN28 and let-7 is a promising strategy for the development of novel anticancer therapeutics. However, a limited number of small-molecule inhibitors disrupting the LIN28-let-7 interaction with potent efficacy are available. Herein, we developed a novel LIN28-inhibiting strategy by targeting selective hotspot amino acids at the LIN28-let-7 binding interface with small-molecule-based bifunctional conjugates. Starting from reported small-molecule LIN28 inhibitors, we identified a feasible linker-attachment position after performing a structure-activity relationship exploration based on the LIN28-targeting chromenopyrazoles. In parallel, a virtual alanine scan identified hotspot residues at the protein-RNA binding interface, based on which we designed a set of peptides to enhance the interaction with the identified hotspot residues. Conjugation of the tailor-designed peptides with linker-attached chromenopyrazoles yielded a series of bifunctional small-molecule-peptide conjugates, represented by compound 83 (PH-223), as a new LIN28-targeting chemical modality. Our result demonstrated an unexplored rational design approach using bifunctional conjugates to target protein-RNA interactions.
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Affiliation(s)
- Pascal Hommen
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Jimin Hwang
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Fubao Huang
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
| | - Lydia Borgelt
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Str. 6, Dortmund, 44227, Germany
| | - Lisa Hohnen
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstr. 150, Bochum, 44780, Germany
| | - Peng Wu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Str. 11, Dortmund, 44227, Germany
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11
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Li Q, Kang C. Targeting RNA-binding proteins with small molecules: Perspectives, pitfalls and bifunctional molecules. FEBS Lett 2023; 597:2031-2047. [PMID: 37519019 DOI: 10.1002/1873-3468.14710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
RNA-binding proteins (RBPs) play vital roles in organisms through binding with RNAs to regulate their functions. Small molecules affecting the function of RBPs have been developed, providing new avenues for drug discovery. Herein, we describe the perspectives on developing small molecule regulators of RBPs. The following types of small molecule modulators are of great interest in drug discovery: small molecules binding to RBPs to affect interactions with RNA molecules, bifunctional molecules binding to RNA or RBP to influence their interactions, and other types of molecules that affect the stability of RNA or RBPs. Moreover, we emphasize that the bifunctional molecules may play important roles in small molecule development to overcome the challenges encountered in the process of drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore, Singapore
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12
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Davidge B, McDermott SM, Carnes J, Lewis I, Tracy M, Stuart KD. Multiple domains of the integral KREPA3 protein are critical for the structure and precise functions of RNA Editing Catalytic Complexes in Trypanosoma brucei. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537538. [PMID: 37131796 PMCID: PMC10153193 DOI: 10.1101/2023.04.19.537538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The gRNA directed U-insertion and deletion editing of mitochondrial mRNAs that is essential in different life cycle stages for the protozoan parasite Trypanosoma brucei is performed by three similar multi-protein catalytic complexes (CCs) that contain the requisite enzymes. These CCs also contain a common set of eight proteins that have no apparent direct catalytic function, including six that have an OB-fold domain. We show here that one of these OB-fold proteins, KREPA3 (A3), has structural homology to other editing proteins, is essential for editing and is multifunctional. We investigated A3 function by analyzing the effects of single amino acid loss of function mutations most of which were identified by screening bloodstream form (BF) parasites for loss of growth following random mutagenesis. Mutations in the ZFs, an intrinsically disordered region (IDR) and several within or near the C-terminal OB-fold domain variably impacted CC structural integrity and editing. Some mutations resulted in almost complete loss of CCs and its proteins and editing whereas others retained CCs but had aberrant editing. All but a mutation which is near the OB-fold affected growth and editing in BF but not procyclic form (PF) parasites. These data indicate that multiple positions within A3 have essential functions that contribute to the structural integrity of CCs, the precision of editing and the developmental differences in editing between BF and PF stages.
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Affiliation(s)
- Brittney Davidge
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Jason Carnes
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Isaac Lewis
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Maxwell Tracy
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
| | - Kenneth D Stuart
- Center for Global Infectious Disease Research (CGIDR), Seattle Children's Research Institute, Seattle, WA 98109
- Department of Pediatrics, University of Washington, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
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13
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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: 11] [Impact Index Per Article: 11.0] [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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14
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Yamamoto H, Uchida Y, Kurimoto R, Chiba T, Matsushima T, Ito Y, Inotsume M, Miyata K, Watanabe K, Inada M, Goshima N, Uchida T, Asahara H. RNA-binding protein LIN28A upregulates transcription factor HIF1α by posttranscriptional regulation via direct binding to UGAU motifs. J Biol Chem 2023; 299:102791. [PMID: 36509142 PMCID: PMC9823215 DOI: 10.1016/j.jbc.2022.102791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Hypoxia-inducible factor 1α (HIF1α) is a transcription factor that regulates angiogenesis under hypoxic conditions. To investigate the posttranscriptional regulatory mechanism of HIF1α, we performed a cell-based screening to reveal potential cis-elements and the regulatory RNA-binding proteins that act as trans-factors. We found that LIN28A promoted HIF1α protein expression independently of the downregulation of microRNA let-7, which is also directly mediated by LIN28A. Transcriptome analysis and evaluation of RNA stability using RNA-seq and SLAM-seq analyses, respectively, revealed that LIN28A upregulates HIF1A expression via mRNA stabilization. To investigate the physical association of LIN28A with HIF1A mRNA, we performed enhanced crosslinking immunoprecipitation in 293FT cells and integrally analyzed the transcriptome. We observed that LIN28A associates with HIF1A mRNA via its cis-element motif "UGAU". The "UGAU" motifs are recognized by the cold shock domain of LIN28A, and the introduction of a loss-of-function mutation to the cold shock domain diminished the upregulatory activities performed by LIN28A. Finally, the microvessel density assay showed that the expression of LIN28A promoted angiogenesis in vivo. In conclusion, our study elucidated the role of LIN28A in enhancing the HIF1α axis at the posttranscription layer.
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Affiliation(s)
- Hiroto Yamamoto
- Department of Systems BioMedicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; Department of Anesthesiology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yutaro Uchida
- Department of Systems BioMedicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Ryota Kurimoto
- Department of Systems BioMedicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tomoki Chiba
- Department of Systems BioMedicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takahide Matsushima
- Department of Systems BioMedicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yoshiaki Ito
- Department of Systems BioMedicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Maiko Inotsume
- Department of Systems BioMedicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kohei Miyata
- Department Obstetrics and Gynecology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Kenta Watanabe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Masaki Inada
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Naoki Goshima
- Biomedicinal Information Research Center, The National Institute of Advanced Industrial Science and Technology, Tokyo, Japan; Department of Human Science, Faculty of Human Science, Musashino University, Tokyo, Japan
| | - Tokujiro Uchida
- Department of Anesthesiology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine, Tokyo Medical and Dental University (TMDU), Tokyo, Japan; Department of Molecular and Experimental Medicine, The Scripps Research Institute, San Diego, California, USA.
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15
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Rosenblum SL, Garner AL. Optimization of RiPCA for the Live-Cell Detection of Pre-MicroRNA-Protein Interactions. Chembiochem 2022; 23:e202200508. [PMID: 36322053 PMCID: PMC9831681 DOI: 10.1002/cbic.202200508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/31/2022] [Indexed: 11/06/2022]
Abstract
Advancements in methods for identifying RNA-protein interactions (RPIs) on a large scale has necessitated the development of assays for validation of these interactions, particularly in living cells. We previously reported the development of RiPCA (RNA interaction with protein-mediated complementation assay) to enable the cellular detection of the well-characterized interaction between the pre-microRNA, pre-let-7, and its RNA-binding protein (RBP) partner Lin28. In this study, the applicability of RiPCA for the detection of putative pre-miRNA-protein interactions was explored using an improved RiPCA protocol, termed RiPCA 2.0. RiPCA 2.0 was adapted to detect the sequence specificity of the RBPs hnRNP A1, Msi1, and Msi2 for reported pre-microRNA binding partners. Additionally, the ability of RiPCA 2.0 to detect site-specific binding was explored. Collectively, this work highlights the versatility of RiPCA 2.0 in detecting cellular RPIs.
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Affiliation(s)
| | - Amanda L. Garner
- Department of Medicinal ChemistryUniversity of MichiganAnn ArborMichigan48109USA
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16
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Discovery of Novel Lin28 Inhibitors to Suppress Cancer Cell Stemness. Cancers (Basel) 2022; 14:cancers14225687. [PMID: 36428779 PMCID: PMC9688808 DOI: 10.3390/cancers14225687] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
Lin28 is a pluripotency factor that regulates cancer cell stem-like phenotypes to promote cancer development and therapy-resistant tumor progression. It acts through its cold shock domain and zinc knuckle domain (ZKD) to interact with the Let-7 pre-microRNA and block Let-7 biosynthesis. Chemical inhibition of Lin28 from interacting with Let-7 presents a therapeutic strategy for cancer therapy. Herein, we present the computer-aided development of small molecules by in silico screening 18 million compounds from the ZINC20 library, followed by the biological validation of 163 predicted compounds to confirm 15 new Lin28 inhibitors. We report three lead compounds, Ln7, Ln15, and Ln115, that target the ZKD of both Lin28A and Lin28B isoforms and block Lin28 from binding Let-7. They restore Let-7 expression and suppress tumor oncogenes such as SOX2 in cancer cells and show strong inhibitory effects on cancer cell stem-like phenotypes. However, minimal impacts of these compounds were observed on Lin28-negative cells, confirming the on-target effects of these compounds. We conclude from this study the discovery of several new Lin28 inhibitors as promising candidate compounds that warrant further drug development into potential anticancer therapies.
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17
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Lin Z, Radaeva M, Cherkasov A, Dong X. Lin28 Regulates Cancer Cell Stemness for Tumour Progression. Cancers (Basel) 2022; 14:4640. [PMID: 36230562 PMCID: PMC9564245 DOI: 10.3390/cancers14194640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/15/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Tumours develop therapy resistance through complex mechanisms, one of which is that cancer stem cell (CSC) populations within the tumours present self-renewable capability and phenotypical plasticity to endure therapy-induced stress conditions and allow tumour progression to the therapy-resistant state. Developing therapeutic strategies to cope with CSCs requires a thorough understanding of the critical drivers and molecular mechanisms underlying the aforementioned processes. One such hub regulator of stemness is Lin28, an RNA-binding protein. Lin28 blocks the synthesis of let-7, a tumour-suppressor microRNA, and acts as a global regulator of cell differentiation and proliferation. Lin28also targets messenger RNAs and regulates protein translation. In this review, we explain the role of the Lin28/let-7 axis in establishing stemness, epithelial-to-mesenchymal transition, and glucose metabolism reprogramming. We also highlight the role of Lin28 in therapy-resistant prostate cancer progression and discuss the emergence of Lin28-targeted therapeutics and screening methods.
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Affiliation(s)
- Zhuohui Lin
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Faculty of Food and Land Systems, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Mariia Radaeva
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Artem Cherkasov
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Xuesen Dong
- The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
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18
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Stein RL, Wilson DM. Kinetic and Mechanistic Studies of the Terminal Uridylyltransferase, Zcchc11 (TUT4). Biochemistry 2022; 61:1614-1624. [PMID: 35797480 DOI: 10.1021/acs.biochem.2c00146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Zcchc11 (TUT4, TENT3A, Z11) is a nucleotidyltransferase that catalyzes the 3'-polyuridylation of RNA. Our interest in this enzyme stems from its role in blocking the biogenesis of let-7, a family of microRNAs whose members act as tumor suppressors. Z11 polyuridylates pre-let-7, the precursor of let-7, when pre-let-7 is complexed with LIN28, an RNA-binding protein. Polyuridylation of pre-let-7 marks it for degradation. In addition to this LIN28-dependent activity, Z11 also has LIN28-independent activities. In this paper, we report the results of experiments that characterize LIN28-independent activities of Z11. Significant observations include the following. (1) Z11 uridylates not only mature let-7 species but also substrates as small as dinucleotides. (2) For both let-7i and the diribonucleotide AG, Z11 follows a steady-state ordered mechanism, with UTP adding before RNA. (3) Uridylation kinetics of let-7i (UGAGGUAGUAGUUUGUGCUGUU) and two truncated derivatives, GCUGUU and UU, indicate that Z11 manifests selectivity in Km,RNA; kcat,RNA values for the three substrates are nearly identical. (4) Z11 preferentially uridylates RNA lacking base-pairing near the 3' terminus. (5) Selectivity of Z11 toward ribonucleoside triphosphates is similar for let-7i and AG, with XTP preference: UTP > CTP > ATP ≫ GTP. Selectivity is manifested in Km,XTP, with kcat,XTP values being similar for UTP, CTP, and ATP. (6) Kinetic parameters for RNA turnover are dependent on the structure of the nucleoside triphosphate, consistent with recent structural data indicating stacking of the nucleoside triphosphate base with the base of the 3'-nucleotide of the substrate RNA (Faehnle et al., Nat. Struct. Mol. Biol. 2017, 24, 658).
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Affiliation(s)
- Ross L Stein
- Twentyeight-Seven Therapeutics, 490 Arsenal Way, Watertown, Massachusetts 02472, United States
| | - David M Wilson
- Twentyeight-Seven Therapeutics, 490 Arsenal Way, Watertown, Massachusetts 02472, United States
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19
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LIN28 Family in Testis: Control of Cell Renewal, Maturation, Fertility and Aging. Int J Mol Sci 2022; 23:ijms23137245. [PMID: 35806250 PMCID: PMC9266904 DOI: 10.3390/ijms23137245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/20/2022] [Accepted: 06/25/2022] [Indexed: 12/12/2022] Open
Abstract
Male reproductive development starts early in the embryogenesis with somatic and germ cell differentiation in the testis. The LIN28 family of RNA-binding proteins promoting pluripotency has two members—LIN28A and LIN28B. Their function in the testis has been investigated but many questions about their exact role based on the expression patterns remain unclear. LIN28 expression is detected in the gonocytes and the migrating, mitotically active germ cells of the fetal testis. Postnatal expression of LIN28 A and B showed differential expression, with LIN28A expressed in the undifferentiated spermatogonia and LIN28B in the elongating spermatids and Leydig cells. LIN28 interferes with many signaling pathways, leading to cell proliferation, and it is involved in important testicular physiological processes, such as cell renewal, maturation, fertility, and aging. In addition, aberrant LIN28 expression is associated with testicular cancer and testicular disorders, such as hypogonadotropic hypogonadism and Klinefelter’s syndrome. This comprehensive review encompasses current knowledge of the function of LIN28 paralogs in testis and other tissues and cells because many studies suggest LIN28AB as a promising target for developing novel therapeutic agents.
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20
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Medhi R, Price J, Furlan G, Gorges B, Sapetschnig A, Miska EA. RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type. RNA (NEW YORK, N.Y.) 2022; 28:353-370. [PMID: 34949722 PMCID: PMC8848932 DOI: 10.1261/rna.078976.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
The human terminal uridyl transferases TUT4 and TUT7 (TUT4/7) catalyze the additions of uridines at the 3' end of RNAs, including the precursors of the tumor suppressor miRNA let-7 upon recruitment by the oncoprotein LIN28A. As a consequence, let-7 family miRNAs are down-regulated. Disruption of this TUT4/7 activity inhibits tumorigenesis. Hence, targeting TUT4/7 could be a potential anticancer therapy. In this study, we investigate TUT4/7-mediated RNA regulation in two cancer cell lines by establishing catalytic knockout models. Upon TUT4/7 mutation, we observe a significant reduction in miRNA uridylation, which results in defects in cancer cell properties such as cell proliferation and migration. With the loss of TUT4/7-mediated miRNA uridylation, the uridylated miRNA variants are replaced by adenylated isomiRs. Changes in miRNA modification profiles are accompanied by deregulation of expression levels in specific cases. Unlike let-7s, most miRNAs do not depend on LIN28A for TUT4/7-mediated regulation. Additionally, we identify TUT4/7-regulated cell-type-specific miRNA clusters and deregulation in their corresponding mRNA targets. Expression levels of miR-200c-3p and miR-141-3p are regulated by TUT4/7 in a cancer cell-type-specific manner. Subsequently, BCL2, which is a well-established target of miR-200c is up-regulated. Therefore, TUT4/7 loss causes deregulation of miRNA-mRNA networks in a cell-type-specific manner. Understanding of the underlying biology of such cell-type-specific deregulation will be an important aspect of targeting TUT4/7 for potential cancer therapies.
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Affiliation(s)
- Ragini Medhi
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Jonathan Price
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Giulia Furlan
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Beronia Gorges
- STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Alexandra Sapetschnig
- STORM Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Eric A Miska
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
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21
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Zou H, Luo J, Guo Y, Liu Y, Wang Y, Deng L, Li P. RNA-binding protein complex LIN28/MSI2 enhances cancer stem cell-like properties by modulating Hippo-YAP1 signaling and independently of Let-7. Oncogene 2022; 41:1657-1672. [PMID: 35102250 PMCID: PMC8913359 DOI: 10.1038/s41388-022-02198-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/30/2021] [Accepted: 01/18/2022] [Indexed: 02/07/2023]
Abstract
The RNA binding protein LIN28 directly modulates the stability and translation of target mRNAs independently of Let-7; however, the key downstream targets of LIN28 in this process are largely unknown. Here, we revealed that Hippo signaling effector YAP1 functioned as a key downstream regulator of LIN28 to modulate the cancer stem cell (CSC)-like properties and tumor progressions in triple negative breast cancer (TNBC). LIN28 was overexpressed in BC tissues and cell lines, and significantly correlated with poorer overall survivals in patients. Ectopic LIN28 expression enhanced, while knockdown of LIN28A inhibited the CSC-like properties, cell growth and invasive phenotypes of TNBC cells in vitro and in vivo. Transcriptome analysis demonstrated LIN28 overexpression significantly induced the expressions of YAP1 downstream genes, while reduced the transcripts of YAP1 upstream kinases, such as MST1/2 and LATS1/2, and knockdown of LIN28A exhibited the opposite effects. Furthermore, constitutive activation of YAP1 in LIN28 knockdown TNBC cells could rescue the cell growth and invasive phenotypes in vitro and in vivo. Mechanistically, instead of the dependence of Let-7, LIN28 recruited RNA binding protein MSI2 in a manner dependent on the LIN28 CSD domain and MSI2 RRM domain, to directly induce the mRNA decay of YAP1 upstream kinases, leading to the inhibition of Hippo pathway and activation of YAP1, which eventually gave rise to increased CSC populations, enhanced tumor cell growth and invasive phenotypes. Accordingly, co-upregulations of LIN28 and MSI2 in TNBC tissues were strongly associated with YAP1 protein level and tumor malignance. Taken together, our findings unravel a novel LIN28/MSI2-YAP1 regulatory axis to induce the CSC-like properties, tumor growth and metastasis, independently of Let-7, which may serve as a potential therapeutic strategy for the treatment of a subset of TNBC with LIN28 overexpression.
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Affiliation(s)
- Hailin Zou
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Juan Luo
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Yibo Guo
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Yuhong Liu
- Department of General Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Yun Wang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Liang Deng
- Department of General Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, Guangdong, People's Republic of China
| | - Peng Li
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, Guangdong, People's Republic of China.
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, No. 628 Zhenyuan Road, Shenzhen, 518107, Guangdong, People's Republic of China.
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22
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Goebel GL, Hohnen L, Borgelt L, Hommen P, Qiu X, Lightfoot H, Wu P. Small molecules with tetrahydroquinoline-containing Povarov scaffolds as inhibitors disrupting the Protein-RNA interaction of LIN28-let-7. Eur J Med Chem 2022; 228:114014. [PMID: 34883291 DOI: 10.1016/j.ejmech.2021.114014] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/15/2021] [Accepted: 11/24/2021] [Indexed: 12/29/2022]
Abstract
Inhibition of the RNA-binding protein LIN28 and disruption of the protein-RNA interaction of LIN28-let-7 with small molecules holds great potential to develop new anticancer therapeutics. Herein, we report the LIN28 inhibitory activities of a series of 30 small molecules with a tricyclic tetrahydroquinoline (THQ)-containing scaffold obtained from a Povarov reaction. The THQ molecules were structurally optimized by varying the 2-benzoic acid substituent, the fused ring at 3- and 4-positions, and the substituents at the phenyl moiety of the tetrahydroquinoline core. Among the tested compounds, GG-43 showed dose-dependent inhibition in an EMSA validation assay and low micromolar inhibitory activity in a fluorescence polarization-based assay measuring disruption of LIN28-let-7 interaction. Binding mode between GG-43 and the cold shock domain of LIN28 was proposed via a molecular docking analysis. The study provides one of the first systematic analyses on structural features that are required for LIN28 inhibition, and indicates the necessity to develop small molecules with new scaffolds as LIN28-targeting probes and therapeutic candidates. In parallel, this study demonstrates the polypharmacological nature of tricyclic THQ-containing scaffolds accessible through Povarov reactions.
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Affiliation(s)
- Georg L Goebel
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn Strasse 6, Dortmund, 44227, Germany
| | - Lisa Hohnen
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätstr. 150, Bochum, 44780, Germany
| | - Lydia Borgelt
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn Strasse 6, Dortmund, 44227, Germany
| | - Pascal Hommen
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn Strasse 6, Dortmund, 44227, Germany
| | - Xiaqiu Qiu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn Strasse 6, Dortmund, 44227, Germany
| | - Helen Lightfoot
- Safety & Mechanistic Pharmacology, Clinical Pharmacology and Safety Sciences, AstraZeneca, Cambridge, UK
| | - Peng Wu
- Chemical Genomics Centre, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany; Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, 44227, Germany.
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23
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Budkina K, El Hage K, Clément MJ, Desforges B, Bouhss A, Joshi V, Maucuer A, Hamon L, Ovchinnikov LP, Lyabin DN, Pastré D. YB-1 unwinds mRNA secondary structures in vitro and negatively regulates stress granule assembly in HeLa cells. Nucleic Acids Res 2021; 49:10061-10081. [PMID: 34469566 PMCID: PMC8464072 DOI: 10.1093/nar/gkab748] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 01/16/2023] Open
Abstract
In the absence of the scanning ribosomes that unwind mRNA coding sequences and 5'UTRs, mRNAs are likely to form secondary structures and intermolecular bridges. Intermolecular base pairing of non polysomal mRNAs is involved in stress granule (SG) assembly when the pool of mRNAs freed from ribosomes increases during cellular stress. Here, we unravel the structural mechanisms by which a major partner of dormant mRNAs, YB-1 (YBX1), unwinds mRNA secondary structures without ATP consumption by using its conserved cold-shock domain to destabilize RNA stem/loops and its unstructured C-terminal domain to secure RNA unwinding. At endogenous levels, YB-1 facilitates SG disassembly during arsenite stress recovery. In addition, overexpression of wild-type YB-1 and to a lesser extent unwinding-defective mutants inhibit SG assembly in HeLa cells. Through its mRNA-unwinding activity, YB-1 may thus inhibit SG assembly in cancer cells and package dormant mRNA in an unfolded state, thus preparing mRNAs for translation initiation.
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Affiliation(s)
- Karina Budkina
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France.,Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290, Russian Federation
| | - Krystel El Hage
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | | | | | - Ahmed Bouhss
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Vandana Joshi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Alexandre Maucuer
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Loic Hamon
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
| | - Lev P Ovchinnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290, Russian Federation
| | - Dmitry N Lyabin
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290, Russian Federation
| | - David Pastré
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91025 Evry, France
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24
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Tan FE, Sathe S, Wheeler EC, Yeo GW. Non-microRNA binding competitively inhibits LIN28 regulation. Cell Rep 2021; 36:109517. [PMID: 34380031 PMCID: PMC8670721 DOI: 10.1016/j.celrep.2021.109517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/28/2021] [Accepted: 07/20/2021] [Indexed: 12/18/2022] Open
Abstract
RNA binding protein (RBP) expression is finite. For RBPs that are vastly outnumbered by their potential target sites, a simple competition for binding can set the magnitude of post-transcriptional control. Here, we show that LIN28, best known for its direct regulation of let-7 miRNA biogenesis, is also indirectly regulated by its widespread binding of non-miRNA transcripts. Approximately 99% of LIN28 binding sites are found on non-miRNA transcripts, like protein coding and ribosomal RNAs. These sites are bound specifically and strongly, but they do not appear to mediate direct post-transcriptional regulation. Instead, non-miRNA sites act to sequester LIN28 protein and effectively change its functional availability, thus impeding the regulation of let-7 in cells. Together, these data show that the binding properties of the transcriptome broadly influence the ability of an RBP to mediate changes in RNA metabolism and gene expression.
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Affiliation(s)
- Frederick E Tan
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Emily C Wheeler
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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25
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Borgelt L, Li F, Hommen P, Lampe P, Hwang J, Goebel GL, Sievers S, Wu P. Trisubstituted Pyrrolinones as Small-Molecule Inhibitors Disrupting the Protein-RNA Interaction of LIN28 and Let-7. ACS Med Chem Lett 2021; 12:893-898. [PMID: 34136077 PMCID: PMC8201479 DOI: 10.1021/acsmedchemlett.0c00546] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
Modulation of protein-RNA interaction (PRI) using small molecules is a promising strategy to develop therapeutics. LIN28 is an RNA-binding protein that blocks the maturation of the tumor suppressor let-7 microRNAs. Herein, we performed a fluorescence polarization-based screening and identified trisubstituted pyrrolinones as small-molecule inhibitors disrupting the LIN28-let-7 interaction. The most potent compound C902 showed dose-dependent inhibition in an EMSA validation assay, enhanced thermal stability of the cold shock domain of LIN28, and increased mature let-7 levels in JAR cells. The structure-activity relationship study revealed key structural features contributing to either PRI inhibition or stabilization of protein-protein interaction (PPI). The pyrrolinones identified in this study not only represent a new class of LIN28-binding molecules that diversify the limited available LIN28 inhibitors but also represent the first examples of small molecules that showed substituent-dependent PRI inhibitory and PPI activating activities.
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Affiliation(s)
- Lydia Borgelt
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
| | - Fu Li
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
| | - Pascal Hommen
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
| | - Philipp Lampe
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
- Compound
Management and Screening Center, Dortmund 44227, Germany
| | - Jimin Hwang
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
| | - Georg L. Goebel
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
| | - Sonja Sievers
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
- Compound
Management and Screening Center, Dortmund 44227, Germany
| | - Peng Wu
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Dortmund 44227, Germany
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26
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Gaza A, Fritz V, Malek L, Wormser L, Treiber N, Danner J, Kremer AE, Thasler WE, Siebler J, Meister G, Neurath MF, Hellerbrand C, Bosserhoff AK, Dietrich P. Identification of novel targets of miR-622 in hepatocellular carcinoma reveals common regulation of cooperating genes and outlines the oncogenic role of zinc finger CCHC-type containing 11. Neoplasia 2021; 23:502-514. [PMID: 33901943 PMCID: PMC8099721 DOI: 10.1016/j.neo.2021.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/26/2022] Open
Abstract
The poor prognosis of advanced hepatocellular carcinoma (HCC) is driven by diverse features including dysregulated microRNAs inducing drug resistance and stemness. Lin-28 homolog A (LIN28A) and its partner zinc finger CCHC-type containing 11 (ZCCHC11) cooperate in binding, oligouridylation and subsequent degradation of tumorsuppressive let-7 precursor microRNAs. Functionally, activation of LIN28A was recently shown to promote stemness and chemoresistance in HCC. However, the expression and regulation of LIN28A in HCC had been unclear. Moreover, the expression, regulation and function of ZCCHC11 in liver cancer remained elusive. In contrast to "one-microRNA-one-target" interactions, we identified common binding sites for miR-622 in both LIN28A and ZCCHC11, suggesting miR-622 to function as a superior pathway regulator. Applying comprehensive microRNA database screening, human hepatocytes and HCC cell lines, patient-derived tissue samples as well as "The Cancer Genome Atlas" (TCGA) patient cohorts, we demonstrated that loss of tumorsuppressive miR-622 mediates derepression and overexpression of LIN28A in HCC. Moreover, the cooperator of LIN28A, ZCCHC11, was newly identified as a prognostic and therapeutic target of miR-622 in liver cancer. Together, identification of novel miR-622 target genes revealed common regulation of cooperating genes and outlines the previously unknown oncogenic role of ZCCHC11 in liver cancer.
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Affiliation(s)
- Anne Gaza
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany
| | - Valerie Fritz
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Lara Malek
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Laura Wormser
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
| | - Johannes Danner
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
| | - Andreas E Kremer
- Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany
| | - Wolfgang E Thasler
- Department of General and Visceral Surgery, Red Cross Hospital of Munich, Germany
| | - Jürgen Siebler
- Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
| | - Markus F Neurath
- Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany; Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Claus Hellerbrand
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Anja K Bosserhoff
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Peter Dietrich
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany.
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27
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Lin28, a major translation reprogramming factor, gains access to YB-1-packaged mRNA through its cold-shock domain. Commun Biol 2021; 4:359. [PMID: 33742080 PMCID: PMC7979924 DOI: 10.1038/s42003-021-01862-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
The RNA-binding protein Lin28 (Lin28a) is an important pluripotency factor that reprograms translation and promotes cancer progression. Although Lin28 blocks let-7 microRNA maturation, Lin28 also binds to a large set of cytoplasmic mRNAs directly. However, how Lin28 regulates the processing of many mRNAs to reprogram global translation remains unknown. We show here, using a structural and cellular approach, a mixing of Lin28 with YB-1 (YBX1) in the presence of mRNA owing to their cold-shock domain, a conserved β-barrel structure that binds to ssRNA cooperatively. In contrast, the other RNA binding-proteins without cold-shock domains tested, HuR, G3BP-1, FUS and LARP-6, did not mix with YB-1. Given that YB-1 is the core component of dormant mRNPs, a model in which Lin28 gains access to mRNPs through its co-association with YB-1 to mRNA may provide a means for Lin28 to reprogram translation. We anticipate that the translational plasticity provided by mRNPs may contribute to Lin28 functions in development and adaptation of cancer cells to an adverse environment. Samsonova et al. show a cooperative association of Lin28 and YB-1 for their target mRNA through their cold-shock domain, which is a conserved β-barrel structure that binds to single-stranded RNA. This study suggests that the association of Lin28 with YB-1 in mRNPs may contribute to the translational plasticity during development and the adaptation of cancer cells to adverse environments.
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28
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Ghidini A, Cléry A, Halloy F, Allain FHT, Hall J. RNA‐PROTACs: Degraders of RNA‐Binding Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Alice Ghidini
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Antoine Cléry
- Department of Biology ETH Zurich Hönggerbergring 64 8093 Zurich Switzerland
| | - François Halloy
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | | | - Jonathan Hall
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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29
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Ghidini A, Cléry A, Halloy F, Allain FHT, Hall J. RNA-PROTACs: Degraders of RNA-Binding Proteins. Angew Chem Int Ed Engl 2021; 60:3163-3169. [PMID: 33108679 PMCID: PMC7898822 DOI: 10.1002/anie.202012330] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/08/2020] [Indexed: 12/19/2022]
Abstract
Defects in the functions of RNA binding proteins (RBPs) are at the origin of many diseases; however, targeting RBPs with conventional drugs has proven difficult. PROTACs are a new class of drugs that mediate selective degradation of a target protein through a cell's ubiquitination machinery. PROTACs comprise a moiety that binds the selected protein, conjugated to a ligand of an E3 ligase. Herein, we introduce RNA-PROTACs as a new concept in the targeting of RBPs. These chimeric structures employ small RNA mimics as targeting groups that dock the RNA-binding site of the RBP, whereupon a conjugated E3-recruiting peptide derived from the HIF-1α protein directs the RBP for proteasomal degradation. We performed a proof-of-concept demonstration with the degradation of two RBPs-a stem cell factor LIN28 and a splicing factor RBFOX1-and showed their use in cancer cell lines. The RNA-PROTAC approach opens the way to rapid, selective targeting of RBPs in a rational and general fashion.
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Affiliation(s)
- Alice Ghidini
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Antoine Cléry
- Department of BiologyETH ZurichHönggerbergring 648093ZurichSwitzerland
| | - François Halloy
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | | | - Jonathan Hall
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
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30
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Rosenblum SL, Lorenz DA, Garner AL. A live-cell assay for the detection of pre-microRNA-protein interactions. RSC Chem Biol 2021; 2:241-247. [PMID: 33817642 PMCID: PMC8006716 DOI: 10.1039/d0cb00055h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
Recent efforts in genome-wide sequencing and proteomics have revealed the fundamental roles that RNA-binding proteins (RBPs) play in the life cycle and function of coding and non-coding RNAs. While these methodologies provide a systems-level view of the networking of RNA and proteins, approaches to enable the cellular validation of discovered interactions are lacking. Leveraging the power of bioorthogonal chemistry- and split-luciferase-based assay technologies, we have devised a conceptually new assay for the live-cell detection of RNA-protein interactions (RPIs), RNA interaction with Protein-mediated Complementation Assay, or RiPCA. As proof-of-concept, we utilized the interaction of the pre-microRNA, pre-let-7, with its binding partner, Lin28. Using this system, we have demonstrated the selective detection of the pre-let-7-Lin28 RPI in both the cytoplasm and nucleus. Furthermore, we determined that this technology can be used to discern relative affinities for specific sequences as well as of individual RNA binding domains. Thus, RiPCA has the potential to serve as a useful tool in supporting the investigation of cellular RPIs.
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Affiliation(s)
- Sydney L Rosenblum
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , USA .
| | - Daniel A Lorenz
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , USA .
| | - Amanda L Garner
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , USA .
- Department of Medicinal Chemistry , College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109 , USA
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31
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Heinemann U, Roske Y. Cold-Shock Domains-Abundance, Structure, Properties, and Nucleic-Acid Binding. Cancers (Basel) 2021; 13:cancers13020190. [PMID: 33430354 PMCID: PMC7825780 DOI: 10.3390/cancers13020190] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Proteins are composed of compact domains, often of known three-dimensional structure, and natively unstructured polypeptide regions. The abundant cold-shock domain is among the set of canonical nucleic acid-binding domains and conserved from bacteria to man. Proteins containing cold-shock domains serve a large variety of biological functions, which are mostly linked to DNA or RNA binding. These functions include the regulation of transcription, RNA splicing, translation, stability and sequestration. Cold-shock domains have a simple architecture with a conserved surface ideally suited to bind single-stranded nucleic acids. Because the binding is mostly by non-specific molecular interactions which do not involve the sugar-phosphate backbone, cold-shock domains are not strictly sequence-specific and do not discriminate reliably between DNA and RNA. Many, but not all functions of cold shock-domain proteins in health and disease can be understood based of the physical and structural properties of their cold-shock domains. Abstract The cold-shock domain has a deceptively simple architecture but supports a complex biology. It is conserved from bacteria to man and has representatives in all kingdoms of life. Bacterial cold-shock proteins consist of a single cold-shock domain and some, but not all are induced by cold shock. Cold-shock domains in human proteins are often associated with natively unfolded protein segments and more rarely with other folded domains. Cold-shock proteins and domains share a five-stranded all-antiparallel β-barrel structure and a conserved surface that binds single-stranded nucleic acids, predominantly by stacking interactions between nucleobases and aromatic protein sidechains. This conserved binding mode explains the cold-shock domains’ ability to associate with both DNA and RNA strands and their limited sequence selectivity. The promiscuous DNA and RNA binding provides a rationale for the ability of cold-shock domain-containing proteins to function in transcription regulation and DNA-damage repair as well as in regulating splicing, translation, mRNA stability and RNA sequestration.
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32
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Varela-Rodríguez H, Abella-Quintana DG, Espinal-Centeno A, Varela-Rodríguez L, Gomez-Zepeda D, Caballero-Pérez J, García-Medel PL, Brieba LG, Ordaz-Ortiz JJ, Cruz-Ramirez A. Functional Characterization of the Lin28/let-7 Circuit During Forelimb Regeneration in Ambystoma mexicanum and Its Influence on Metabolic Reprogramming. Front Cell Dev Biol 2020; 8:562940. [PMID: 33330447 PMCID: PMC7710800 DOI: 10.3389/fcell.2020.562940] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022] Open
Abstract
The axolotl (Ambystoma mexicanum) is a caudate amphibian, which has an extraordinary ability to restore a wide variety of damaged structures by a process denominated epimorphosis. While the origin and potentiality of progenitor cells that take part during epimorphic regeneration are known to some extent, the metabolic changes experienced and their associated implications, remain unexplored. However, a circuit with a potential role as a modulator of cellular metabolism along regeneration is that formed by Lin28/let-7. In this study, we report two Lin28 paralogs and eight mature let-7 microRNAs encoded in the axolotl genome. Particularly, in the proliferative blastema stage amxLin28B is more abundant in the nuclei of blastemal cells, while the microRNAs amx-let-7c and amx-let-7a are most downregulated. Functional inhibition of Lin28 factors increase the levels of most mature let-7 microRNAs, consistent with an increment of intermediary metabolites of the Krebs cycle, and phenotypic alterations in the outgrowth of the blastema. In summary, we describe the primary components of the Lin28/let-7 circuit and their function during axolotl regeneration, acting upstream of metabolic reprogramming events.
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Affiliation(s)
- Hugo Varela-Rodríguez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Diana G Abella-Quintana
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Annie Espinal-Centeno
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | | | - David Gomez-Zepeda
- Mass Spectrometry and Metabolomics Laboratory, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Juan Caballero-Pérez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Paola L García-Medel
- Structural Biochemistry Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Luis G Brieba
- Structural Biochemistry Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - José J Ordaz-Ortiz
- Mass Spectrometry and Metabolomics Laboratory, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
| | - Alfredo Cruz-Ramirez
- Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico
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Rangel-Guerrero SI, Franco-Urquijo PA, Martínez-Salas E, Alvarez-Salas LM. Structural insights of the pre-let-7 interaction with LIN28B. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 40:194-211. [PMID: 33319653 DOI: 10.1080/15257770.2020.1859116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The Let-7:LIN28 regulatory loop is a paradigm in miRNA regulation. LIN28 harbors two RNA binding domains, which interact with well-conserved sequences in pre-let-7 RNAs, the GNGAY and the GGAG motifs. Here, the differential binding between LIN28B and pre-let-7 members was associated with the structural characteristics of the pre-let-7 family mapped by SHAPE, uncovering diverse structural patterns within pre-let-7 members. Pre-let-7 mutants supported a relevant role of the GGAG motif location and the preE-stem stability for the interaction with LIN28B. Based on these results, we propose a core RNA structure for LIN28B interaction.
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Affiliation(s)
- Sergio Israel Rangel-Guerrero
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | - Pablo Alberto Franco-Urquijo
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
| | | | - Luis Marat Alvarez-Salas
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, México City, Mexico
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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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Dou J, Zhang H, Chen R, Shu Z, Yuan H, Zhao X, Wang Y, Huang J, Zhou A, Yu J. SUMOylation modulates the LIN28A-let-7 signaling pathway in response to cellular stresses in cancer cells. Mol Oncol 2020; 14:2288-2312. [PMID: 32333719 PMCID: PMC7463354 DOI: 10.1002/1878-0261.12694] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/03/2020] [Accepted: 04/22/2020] [Indexed: 12/19/2022] Open
Abstract
LIN28A is a conserved RNA-binding protein that inhibits the biogenesis of let-7 microRNAs, thus promoting cancer progression. However, mechanisms underlying the activation of the LIN28A-let-7 signaling pathway remain poorly understood. Here, we show that LIN28A is SUMOylated in vivo and in vitro at K15, which is increased by hypoxia but reduced by chemotherapy drugs such as Cisplatin and Paclitaxel. SUMOylation of LIN28A aggravates its inhibition of let-7 maturation, resulting in a stark reduction in let-7, which promotes cancer cell proliferation, migration, invasion, and tumor growth in vivo. Mechanistically, SUMOylation of LIN28A increases its binding affinity with the precursor let-7 (pre-let-7), which subsequently enhances LIN28A-mediated recruitment of terminal uridylyltransferase TUT4 and simultaneously blocks DICER processing of pre-let-7, thereby reducing mature let-7 production. These effects are abolished in SUMOylation-deficient mutant LIN28A-K15R. In summary, these findings shed light on a novel mechanism by which SUMOylation could regulate the LIN28A-let-7 pathway in response to cellular stress in cancer cells.
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Affiliation(s)
- Jinzhuo Dou
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hailong Zhang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ran Chen
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zimei Shu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haihua Yuan
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xian Zhao
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanli Wang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Huang
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aiwu Zhou
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Basic Clinical Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Budkina KS, Zlobin NE, Kononova SV, Ovchinnikov LP, Babakov AV. Cold Shock Domain Proteins: Structure and Interaction with Nucleic Acids. BIOCHEMISTRY (MOSCOW) 2020; 85:S1-S19. [DOI: 10.1134/s0006297920140011] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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A nanobody targeting the LIN28:let-7 interaction fragment of TUT4 blocks uridylation of let-7. Proc Natl Acad Sci U S A 2020; 117:4653-4663. [PMID: 32060122 PMCID: PMC7060709 DOI: 10.1073/pnas.1919409117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Terminal uridylyltransferases are writers of poly(U) tails in diverse RNA uridylation pathways. In the let-7 pathway, the LIN28:pre-let-7:TUTase ribonucleoprotein complex regulates the processing and maturation of the let-7 microRNA, and plays an important role in both physiology and disease. The presence of redundant TUTase orthologs and the diverse pathways poses challenges to revealing the molecular mechanisms of TUTases. We developed a precise tool to identify nanobodies that inhibited the LIN28:pre-let-7:TUTase interaction. The nanobody Nb-S2A4 specifically interacted with the LIN28:let-7 interaction fragment in TUT4, which is critical for oligouridylation and monouridylation of let-7. Our data illustrate that the nanobody tool is effective in distinguishing functions among protein orthologs and diverse pathways. The LIN28:pre-let-7:TUTase ternary complex regulates pluripotency and oncogenesis by controlling processing of the let-7 family of microRNAs. The complex oligouridylates the 3′ ends of pre-let-7 molecules, leading to their degradation via the DIS3L2 exonuclease. Previous studies suggest that components of this complex are potential therapeutic targets in malignancies that aberrantly express LIN28. In this study we developed a functional epitope selection approach to identify nanobody inhibitors of the LIN28:pre-let-7:TUT4 complex. We demonstrate that one of the identified nanobodies, Nb-S2A4, targets the 106-residue LIN28:let-7 interaction (LLI) fragment of TUT4. Nb-S2A4 can effectively inhibit oligouridylation and monouridylation of pre-let-7g in vitro. Expressing Nb-S2A4 allows maturation of the let-7 species in cells expressing LIN28, highlighting the therapeutic potential of targeting the LLI fragment.
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Wang L, Rowe RG, Jaimes A, Yu C, Nam Y, Pearson DS, Zhang J, Xie X, Marion W, Heffron GJ, Daley GQ, Sliz P. Small-Molecule Inhibitors Disrupt let-7 Oligouridylation and Release the Selective Blockade of let-7 Processing by LIN28. Cell Rep 2019; 23:3091-3101. [PMID: 29874593 PMCID: PMC6511231 DOI: 10.1016/j.celrep.2018.04.116] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 02/27/2018] [Accepted: 04/26/2018] [Indexed: 12/29/2022] Open
Abstract
LIN28 is an RNA-binding protein that regulates the maturation of the let-7 family of microRNAs by bipartite interactions with let-7 precursors through its two distinct cold shock and zinc-knuckle domains. Through inhibition of let-7 biogenesis, LIN28 functions as a pluripotency factor, as well as a driver of tumorigenesis. Here, we report a fluorescence polarization assay to identify small-molecule inhibitors for both domains of LIN28 involved in let-7 interactions. Of 101,017 compounds screened, six inhibit LIN28:let-7 binding and impair LIN28-mediated let-7 oligouridylation. Upon further characterization, we demonstrate that the LIN28 inhibitor TPEN destabilizes the zinc-knuckle domain of LIN28, while LI71 binds the cold shock domain to suppress LIN28's activity against let-7 in leukemia cells and embryonic stem cells. Our results demonstrate selective pharmacologic inhibition of individual domains of LIN28 and provide a foundation for therapeutic inhibition of the let-7 biogenesis pathway in LIN28-driven diseases.
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Affiliation(s)
- Longfei Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - R Grant Rowe
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adriana Jaimes
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Chunxiao Yu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Yunsun Nam
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | | | - Jin Zhang
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Xiangyu Xie
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - William Marion
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Gregory J Heffron
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - George Q Daley
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA; Division of Hematology, Brigham and Women's Hospital, Boston, MA, USA; Manton Center for Orphan Disease Research, Boston, MA, USA
| | - Piotr Sliz
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
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Chen X, Li A, Sun BF, Yang Y, Han YN, Yuan X, Chen RX, Wei WS, Liu Y, Gao CC, Chen YS, Zhang M, Ma XD, Liu ZW, Luo JH, Lyu C, Wang HL, Ma J, Zhao YL, Zhou FJ, Huang Y, Xie D, Yang YG. 5-methylcytosine promotes pathogenesis of bladder cancer through stabilizing mRNAs. Nat Cell Biol 2019; 21:978-990. [PMID: 31358969 DOI: 10.1038/s41556-019-0361-y] [Citation(s) in RCA: 403] [Impact Index Per Article: 80.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 06/12/2019] [Indexed: 01/16/2023]
Abstract
Although 5-methylcytosine (m5C) is a widespread modification in RNAs, its regulation and biological role in pathological conditions (such as cancer) remain unknown. Here, we provide the single-nucleotide resolution landscape of messenger RNA m5C modifications in human urothelial carcinoma of the bladder (UCB). We identify numerous oncogene RNAs with hypermethylated m5C sites causally linked to their upregulation in UCBs and further demonstrate YBX1 as an m5C 'reader' recognizing m5C-modified mRNAs through the indole ring of W65 in its cold-shock domain. YBX1 maintains the stability of its target mRNA by recruiting ELAVL1. Moreover, NSUN2 and YBX1 are demonstrated to drive UCB pathogenesis by targeting the m5C methylation site in the HDGF 3' untranslated region. Clinically, a high coexpression of NUSN2, YBX1 and HDGF predicts the poorest survival. Our findings reveal an unprecedented mechanism of RNA m5C-regulated oncogene activation, providing a potential therapeutic strategy for UCB.
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Affiliation(s)
- Xin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ang Li
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bao-Fa Sun
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Ya-Nan Han
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xun Yuan
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Ri-Xin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wen-Su Wei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanchao Liu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Chun-Chun Gao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Sheng Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mengmeng Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Multiscale Research Institute for Complex Systems, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiao-Dan Ma
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhuo-Wei Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jun-Hang Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Cong Lyu
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hai-Lin Wang
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Centre of Genetics and Development, Multiscale Research Institute for Complex Systems, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Yong-Liang Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Fang-Jian Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Huang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.
| | - Dan Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China. .,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
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40
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Crystal structure of the Lin28-interacting module of human terminal uridylyltransferase that regulates let-7 expression. Nat Commun 2019; 10:1960. [PMID: 31036859 PMCID: PMC6488673 DOI: 10.1038/s41467-019-09966-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/10/2019] [Indexed: 01/02/2023] Open
Abstract
Lin28-dependent oligo-uridylylation of precursor let-7 (pre-let-7) by terminal uridylyltransferase 4/7 (TUT4/7) represses let-7 expression by blocking Dicer processing, and regulates cell differentiation and proliferation. The interaction between the Lin28:pre-let-7 complex and the N-terminal Lin28-interacting module (LIM) of TUT4/7 is required for pre-let-7 oligo-uridylylation by the C-terminal catalytic module (CM) of TUT4/7. Here, we report crystallographic and biochemical analyses of the LIM of human TUT4. The LIM consists of the N-terminal Cys2His2-type zinc finger (ZF) and the non-catalytic nucleotidyltransferase domain (nc-NTD). The ZF of LIM adopts a distinct structural domain, and its structure is homologous to those of double-stranded RNA binding zinc fingers. The interaction between the ZF and pre-let-7 stabilizes the Lin28:pre-let-7:TUT4 ternary complex, and enhances the oligo-uridylylation reaction by the CM. Thus, the ZF in LIM and the zinc-knuckle in the CM, which interacts with the oligo-uridylylated tail, together facilitate Lin28-dependent pre-let-7 oligo-uridylylation.
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41
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Liu Y, Dong N, Miao J, Li C, Wang X, Ruan J. Lin28 promotes dental pulp cell proliferation via upregulation of cyclin-dependent proteins and interaction with let-7a/IGF2BP2 pathways. Biomed Pharmacother 2019; 113:108742. [PMID: 30851545 DOI: 10.1016/j.biopha.2019.108742] [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: 11/03/2018] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 01/23/2023] Open
Abstract
Caries, pulpitis, and trauma are the main causes of dental pulp damage. The regeneration capacity of dental pulp declines with age. Lin28 is a conserved RNA-binding protein in higher eukaryotes that regulates several important cellular functions associated with development, glucose metabolism, differentiation, and pluripotency. Conditional reactivation of Lin28 gene in adult mice markedly accelerates the wound-healing process in injured digits. However, little is known about its functions and molecular mechanism in human dental pulp. The aim of this study was to investigate the effects and mechanism of overexpression of Lin28 gene on the proliferation of human dental pulp cells (HDPCs). For this purpose, a number of molecular and biochemical analytical techniques, including the ethynyl-2'-deoxyuridine (EdU) incorporation assay, RNA-protein immunoprecipitation (RIP) analysis, and luciferase assays, were used for detailed characterization. In addition, factors regulating HDPCs activation were explored through gain-of-function and loss-of-function analyses. The results demonstrate that Lin28 promotes cell proliferation and the S-G2/M transition of HDPCs and directly binds to a group of cell cycle regulatory mRNAs in HDPCs. Through bioinformatics analysis and luciferase assays, we confirmed that let-7a targets IGF2BP2. Silencing of IGF2BP2 showed similar cellular and molecular effects as let-7a. Similarly, restoration of IGF2BP2 counteracted the effects of let-7a expression. In conclusion, Lin28 promotes cell proliferation by regulation of both mRNA translation (let-7-independent) and miRNA biogenesis (let-7-dependent). Lin28 can promote the expression of pro-proliferative genes by directly enhancing their translation to maintain a tight control over HDPC proliferation.
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Affiliation(s)
- Yan Liu
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, Department of Preventive Dentistry, College of Stomatology, Xi'an Jiaotong University, 98 Xiwu Road, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Ning Dong
- Department of Pediatric Dentistry, College of Stomatology, Xi'an Jiaotong University, 98 Xiwu Road, Xi'an, Shaanxi, 710004, People's Republic of China
| | - Jiyu Miao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Chenxing Li
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Xiaofei Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, People's Republic of China
| | - Jianping Ruan
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, Department of Preventive Dentistry, College of Stomatology, Xi'an Jiaotong University, 98 Xiwu Road, Xi'an, Shaanxi, 710004, People's Republic of China.
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D'Agostino VG, Sighel D, Zucal C, Bonomo I, Micaelli M, Lolli G, Provenzani A, Quattrone A, Adami V. Screening Approaches for Targeting Ribonucleoprotein Complexes: A New Dimension for Drug Discovery. SLAS DISCOVERY 2019; 24:314-331. [PMID: 30616427 DOI: 10.1177/2472555218818065] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA-binding proteins (RBPs) are pleiotropic factors that control the processing and functional compartmentalization of transcripts by binding primarily to mRNA untranslated regions (UTRs). The competitive and/or cooperative interplay between RBPs and an array of coding and noncoding RNAs (ncRNAs) determines the posttranscriptional control of gene expression, influencing protein production. Recently, a variety of well-recognized and noncanonical RBP domains have been revealed by modern system-wide analyses, underlying an evolving classification of ribonucleoproteins (RNPs) and their importance in governing physiological RNA metabolism. The possibility of targeting selected RNA-protein interactions with small molecules is now expanding the concept of protein "druggability," with new implications for medicinal chemistry and for a deeper characterization of the mechanism of action of bioactive compounds. Here, taking SF3B1, HuR, LIN28, and Musashi proteins as paradigmatic case studies, we review the strategies applied for targeting RBPs, with emphasis on the technological advancements to study protein-RNA interactions and on the requirements of appropriate validation strategies to parallel high-throughput screening (HTS) efforts.
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Affiliation(s)
- Vito Giuseppe D'Agostino
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Denise Sighel
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Chiara Zucal
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Isabelle Bonomo
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Mariachiara Micaelli
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Graziano Lolli
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Alessandro Provenzani
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Alessandro Quattrone
- 1 University of Trento, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
| | - Valentina Adami
- 2 University of Trento, HTS Core Facility, Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, Italy
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Lim D, Byun WG, Park SB. Restoring Let-7 microRNA Biogenesis Using a Small-Molecule Inhibitor of the Protein-RNA Interaction. ACS Med Chem Lett 2018; 9:1181-1185. [PMID: 30613323 DOI: 10.1021/acsmedchemlett.8b00323] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/08/2018] [Indexed: 12/19/2022] Open
Abstract
Abnormal function of RNA-binding proteins can lead to dysregulation of RNA function, causing a variety of disease states. Thus, developing small-molecule modulators of protein-RNA interactions is one of the key challenges in chemical biology. Herein, we performed a high-throughput screening of chemical libraries using a Förster resonance energy transfer-based Lin28-let-7 interaction assay to identify a potent small-molecule inhibitor of the protein-microRNA interaction, as it is an important target implicated in stem cell-like phenotypes in cancer cells. The new inhibitor KCB3602 selectively restored cellular let-7 microRNA levels, decreased the expression of a panel of oncogenes responsible for cancer stem cell maintenance, and showed potential anticancer activities. We expect that our Lin28-let-7 interaction inhibitor will provide a good starting point for pharmacological eradication of cancer stem cells.
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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
| | - 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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44
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Wang L, Fu TM, Zhou Y, Xia S, Greka A, Wu H. Structures and gating mechanism of human TRPM2. Science 2018; 362:science.aav4809. [PMID: 30467180 DOI: 10.1126/science.aav4809] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/10/2018] [Indexed: 12/11/2022]
Abstract
Transient receptor potential (TRP) melastatin 2 (TRPM2) is a cation channel associated with numerous diseases. It has a C-terminal NUDT9 homology (NUDT9H) domain responsible for binding adenosine diphosphate (ADP)-ribose (ADPR), and both ADPR and calcium (Ca2+) are required for TRPM2 activation. Here we report cryo-electron microscopy structures of human TRPM2 alone, with ADPR, and with ADPR and Ca2+ NUDT9H forms both intra- and intersubunit interactions with the N-terminal TRPM homology region (MHR1/2/3) in the apo state but undergoes conformational changes upon ADPR binding, resulting in rotation of MHR1/2 and disruption of the intersubunit interaction. The binding of Ca2+ further engages transmembrane helices and the conserved TRP helix to cause conformational changes at the MHR arm and the lower gating pore to potentiate channel opening. These findings explain the molecular mechanism of concerted TRPM2 gating by ADPR and Ca2+ and provide insights into the gating mechanism of other TRP channels.
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Affiliation(s)
- Longfei Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Tian-Min Fu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Yiming Zhou
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shiyu Xia
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Anna Greka
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
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Yashiro Y, Tomita K. Function and Regulation of Human Terminal Uridylyltransferases. Front Genet 2018; 9:538. [PMID: 30483311 PMCID: PMC6240794 DOI: 10.3389/fgene.2018.00538] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/24/2018] [Indexed: 11/21/2022] Open
Abstract
RNA uridylylation plays a pivotal role in the biogenesis and metabolism of functional RNAs, and regulates cellular gene expression. RNA uridylylation is catalyzed by a subset of proteins from the non-canonical terminal nucleotidyltransferase family. In human, three proteins (TUT1, TUT4, and TUT7) have been shown to exhibit template-independent uridylylation activity at 3′-end of specific RNAs. TUT1 catalyzes oligo-uridylylation of U6 small nuclear (sn) RNA, which catalyzes mRNA splicing. Oligo-uridylylation of U6 snRNA is required for U6 snRNA maturation, U4/U6-di-snRNP formation, and U6 snRNA recycling during mRNA splicing. TUT4 and TUT7 catalyze mono- or oligo-uridylylation of precursor let-7 (pre–let-7). Let-7 RNA is broadly expressed in somatic cells and regulates cellular proliferation and differentiation. Mono-uridylylation of pre–let-7 by TUT4/7 promotes subsequent Dicer processing to up-regulate let-7 biogenesis. Oligo-uridylylation of pre–let-7 by TUT4/7 is dependent on an RNA-binding protein, Lin28. Oligo-uridylylated pre–let-7 is less responsive to processing by Dicer and degraded by an exonuclease DIS3L2. As a result, let-7 expression is repressed. Uridylylation of pre–let-7 depends on the context of the 3′-region of pre–let-7 and cell type. In this review, we focus on the 3′ uridylylation of U6 snRNA and pre-let-7, and describe the current understanding of mechanism of activity and regulation of human TUT1 and TUT4/7, based on their crystal structures that have been recently solved.
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Affiliation(s)
- Yuka Yashiro
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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Zigáčková D, Vaňáčová Š. The role of 3' end uridylation in RNA metabolism and cellular physiology. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0171. [PMID: 30397107 DOI: 10.1098/rstb.2018.0171] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2018] [Indexed: 12/14/2022] Open
Abstract
Most eukaryotic RNAs are posttranscriptionally modified. The majority of modifications promote RNA maturation, others may regulate function and stability. The 3' terminal non-templated oligouridylation is a widespread modification affecting many cellular RNAs at some stage of their life cycle. It has diverse roles in RNA metabolism. The most prevalent is the regulation of stability and quality control. On the cellular and organismal level, it plays a critical role in a number of pathways, such as cell cycle regulation, cell death, development or viral infection. Defects in uridylation have been linked to several diseases. This review summarizes the current knowledge about the role of the 3' terminal oligo(U)-tailing in biology of various RNAs in eukaryotes and describes key factors involved in these pathways.This article is part of the theme issue '5' and 3' modifications controlling RNA degradation'.
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Affiliation(s)
- Dagmar Zigáčková
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5/A35, Brno 625 00, Czech Republic
| | - Štěpánka Vaňáčová
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5/A35, Brno 625 00, Czech Republic
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Warkocki Z, Liudkovska V, Gewartowska O, Mroczek S, Dziembowski A. Terminal nucleotidyl transferases (TENTs) in mammalian RNA metabolism. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2018.0162. [PMID: 30397099 PMCID: PMC6232586 DOI: 10.1098/rstb.2018.0162] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2018] [Indexed: 12/15/2022] Open
Abstract
In eukaryotes, almost all RNA species are processed at their 3′ ends and most mRNAs are polyadenylated in the nucleus by canonical poly(A) polymerases. In recent years, several terminal nucleotidyl transferases (TENTs) including non-canonical poly(A) polymerases (ncPAPs) and terminal uridyl transferases (TUTases) have been discovered. In contrast to canonical polymerases, TENTs' functions are more diverse; some, especially TUTases, induce RNA decay while others, such as cytoplasmic ncPAPs, activate translationally dormant deadenylated mRNAs. The mammalian genome encodes 11 different TENTs. This review summarizes the current knowledge about the functions and mechanisms of action of these enzymes. This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
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Affiliation(s)
- Zbigniew Warkocki
- Department of RNA Metabolism, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznan, Poland
| | - Vladyslava Liudkovska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Olga Gewartowska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland .,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
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48
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Treiber T, Treiber N, Meister G. Regulation of microRNA biogenesis and its crosstalk with other cellular pathways. Nat Rev Mol Cell Biol 2018; 20:5-20. [DOI: 10.1038/s41580-018-0059-1] [Citation(s) in RCA: 628] [Impact Index Per Article: 104.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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49
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Ustianenko D, Chiu HS, Treiber T, Weyn-Vanhentenryck SM, Treiber N, Meister G, Sumazin P, Zhang C. LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs. Mol Cell 2018; 71:271-283.e5. [PMID: 30029005 PMCID: PMC6238216 DOI: 10.1016/j.molcel.2018.06.029] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 04/27/2018] [Accepted: 06/19/2018] [Indexed: 02/06/2023]
Abstract
LIN28 is a bipartite RNA-binding protein that post-transcriptionally inhibits the biogenesis of let-7 microRNAs to regulate development and influence disease states. However, the mechanisms of let-7 suppression remain poorly understood because LIN28 recognition depends on coordinated targeting by both the zinc knuckle domain (ZKD), which binds a GGAG-like element in the precursor, and the cold shock domain (CSD), whose binding sites have not been systematically characterized. By leveraging single-nucleotide-resolution mapping of LIN28 binding sites in vivo, we determined that the CSD recognizes a (U)GAU motif. This motif partitions the let-7 microRNAs into two subclasses, precursors with both CSD and ZKD binding sites (CSD+) and precursors with ZKD but no CSD binding sites (CSD-). LIN28 in vivo recognition-and subsequent 3' uridylation and degradation-of CSD+ precursors is more efficient, leading to their stronger suppression in LIN28-activated cells and cancers. Thus, CSD binding sites amplify the regulatory effects of LIN28.
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Affiliation(s)
- Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Hua-Sheng Chiu
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Sebastien M Weyn-Vanhentenryck
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Nora Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Pavel Sumazin
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA.
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50
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Menezes MR, Balzeau J, Hagan JP. 3' RNA Uridylation in Epitranscriptomics, Gene Regulation, and Disease. Front Mol Biosci 2018; 5:61. [PMID: 30057901 PMCID: PMC6053540 DOI: 10.3389/fmolb.2018.00061] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 06/14/2018] [Indexed: 12/31/2022] Open
Abstract
Emerging evidence implicates a wide range of post-transcriptional RNA modifications that play crucial roles in fundamental biological processes including regulating gene expression. Collectively, they are known as epitranscriptomics. Recent studies implicate 3' RNA uridylation, the non-templated addition of uridine(s) to the terminal end of RNA, as a key player in epitranscriptomics. In this review, we describe the functional roles and significance of 3' terminal RNA uridylation that has diverse functions in regulating both mRNAs and non-coding RNAs. In mammals, three Terminal Uridylyl Transferases (TUTases) are primarily responsible for 3' RNA uridylation. These enzymes are also referred to as polyU polymerases. TUTase 1 (TUT1) is implicated in U6 snRNA maturation via uridylation. The TUTases TUT4 and/or TUT7 are the predominant mediators of all other cellular uridylation. Terminal uridylation promotes turnover for many polyadenylated mRNAs, replication-dependent histone mRNAs that lack polyA-tails, and aberrant structured noncoding RNAs. In addition, uridylation regulates biogenesis of a subset of microRNAs and generates isomiRs, sequent variant microRNAs that have altered function in specific cases. For example, the RNA binding protein and proto-oncogene LIN28A and TUT4 work together to polyuridylate pre-let-7, thereby blocking biogenesis and function of the tumor suppressor let-7 microRNA family. In contrast, monouridylation of Group II pre-miRNAs creates an optimal 3' overhang that promotes recognition and subsequent cleavage by the Dicer-TRBP complex that then yields the mature microRNA. Also, uridylation may play a role in non-canonical microRNA biogenesis. The overall significance of 3' RNA uridylation is discussed with an emphasis on mammalian development, gene regulation, and disease, including cancer and Perlman syndrome. We also introduce recent changes to the HUGO-approved gene names for multiple terminal nucleotidyl transferases that affects in part TUTase nomenclature (TUT1/TENT1, TENT2/PAPD4/GLD2, TUT4/ZCCHC11/TENT3A, TUT7/ZCCHC6/TENT3B, TENT4A/PAPD7, TENT4B/PAPD5, TENT5A/FAM46A, TENT5B/FAM46B, TENT5C/FAM46C, TENT5D/FAM46D, MTPAP/TENT6/PAPD1).
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Affiliation(s)
- Miriam R Menezes
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Julien Balzeau
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - John P Hagan
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX, United States
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