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Shortridge MD, Chaubey B, Zhang HJ, Pavelitz T, Vidadala V, Tang C, Olsen GL, Calin GA, Varani G. Drug-Like Small Molecules That Inhibit Expression of the Oncogenic MicroRNA-21. ACS Chem Biol 2023; 18:237-250. [PMID: 36727622 PMCID: PMC10593481 DOI: 10.1021/acschembio.2c00502] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We report the discovery of drug-like small molecules that bind specifically to the precursor of the oncogenic and pro-inflammatory microRNA-21 with mid-nanomolar affinity. The small molecules target a local structure at the Dicer cleavage site and induce distinctive structural changes in the RNA, which correlate with specific inhibition of miRNA processing. Structurally conservative single nucleotide substitutions eliminate the conformational change induced by the small molecules, which is also not observed in other miRNA precursors. The most potent of these compounds reduces cellular proliferation and miR-21 levels in cancer cell lines without inhibiting kinases or classical receptors, while closely related compounds without this specific binding activity are inactive in cells. These molecules are highly ligand-efficient (MW < 330) and display specific biochemical and cellular activity by suppressing the maturation of miR-21, thereby providing an avenue toward therapeutic development in multiple diseases where miR-21 is abnormally expressed.
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Affiliation(s)
- Matthew D Shortridge
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Bhawna Chaubey
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Huanyu J Zhang
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Thomas Pavelitz
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Venkata Vidadala
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Changyan Tang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gregory L Olsen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - George A Calin
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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2
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Ye X, Yang W, Yi S, Zhao Y, Varani G, Jankowsky E, Yang F. Two distinct binding modes provide the RNA-binding protein RbFox with extraordinary sequence specificity. Nat Commun 2023; 14:701. [PMID: 36759600 PMCID: PMC9911399 DOI: 10.1038/s41467-023-36394-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Specificity of RNA-binding proteins for target sequences varies considerably. Yet, it is not understood how certain few proteins achieve markedly higher sequence specificity than most others. Here we show that the RNA Recognition Motif of RbFox accomplishes extraordinary sequence specificity by employing functionally and structurally distinct binding modes. Affinity measurements of RbFox for all binding site variants reveal the existence of two distinct binding modes. The first exclusively accommodates cognate and closely related RNAs with high affinity. The second mode accommodates all other RNAs with reduced affinity by imposing large thermodynamic penalties on non-cognate sequences. NMR studies indicate marked structural differences between the two binding modes, including large conformational rearrangements distant from the RNA-binding site. Distinct binding modes by a single RNA-binding module explain extraordinary sequence selectivity and reveal an unknown layer of functional diversity, cross talk and regulation in RNA-protein interactions.
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Affiliation(s)
- Xuan Ye
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, WA, USA
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Yanan Zhao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080, China
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA, USA.
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna Therapeutics, 200 Technology Square, Cambridge, MA, USA.
| | - Fan Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080, China.
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Sharma S, Pisignano G, Merulla J, Catapano CV, Varani G. A functional SNP regulates E-cadherin expression by dynamically remodeling the 3D structure of a promoter-associated non-coding RNA transcript. Nucleic Acids Res 2022; 50:11331-11343. [PMID: 36243981 DOI: 10.1093/nar/gkac875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 09/03/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Transcription of E-cadherin, a tumor suppressor that plays critical roles in cell adhesion and the epithelial-mesenchymal transition, is regulated by a promoter-associated non-coding RNA (paRNA). The sense-oriented paRNA (S-paRNA) includes a functional C/A single nucleotide polymorphism (SNP rs16260). The A-allele leads to decreased transcriptional activity and increased prostate cancer risk. The polymorphic site is known to affect binding of a microRNA-guided Argonaute 1 (AGO1) complex and recruitment of chromatin-modifying enzymes to silence the promoter. Yet the SNP is distant from the microRNA-AGO1 binding domain in both primary sequence and secondary structure, raising the question of how regulation occurs. Here we report the 3D NMR structure of the 104-nucleotide domain of the S-paRNA that encompasses the SNP and the microRNA-binding site. We show that the A to C change alters the locally dynamic and metastable structure of the S-paRNA, revealing how the single nucleotide mutation regulates the E-cadherin promoter through its effect on the non-coding RNA structure.
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Affiliation(s)
- Shrikant Sharma
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | | | - Jessica Merulla
- Institute of Oncology Research (IOR), Università della Svizzera italiana (USI), 6500 Bellinzona, Switzerland
| | - Carlo V Catapano
- Institute of Oncology Research (IOR), Università della Svizzera italiana (USI), 6500 Bellinzona, Switzerland
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
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4
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Abstract
Dengue virus, a single-stranded positive sense RNA virus, is the most prevalent mosquito-borne pathogen in the world. Like all RNA viruses, it uses conserved structural elements within its genome to control essential replicative steps. A 70 nt stem-loop RNA structure (called SLA), found at the 5'-end of the genome of all flaviviruses, functions as the promoter for viral replication. This highly conserved structure interacts with the viral polymerase NS5 to initiate RNA synthesis. Here, we report the NMR structure of a monomeric SLA from dengue virus serotype 1, assembled to high-resolution from independently folded structural elements. The DENV1 SLA has an L-shaped structure, where the top and side helices are coaxially stacked, and the bottom helix is roughly perpendicular to them. Because the sequence is highly conserved among different flavivirus genomes, it is very likely that the three-dimensional fold and local structure of SLA are also conserved among flaviviruses and required for efficient replication. This work provides structural insight into the dengue promoter and provides the foundation for the discovery of new antiviral drugs that target this essential replicative step.
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Affiliation(s)
- Yi-Ting Sun
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
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5
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Shortridge MD, Olsen GL, Yang W, Walker MJ, Varani G. A Slow Dynamic RNA Switch Regulates Processing of microRNA-21. J Mol Biol 2022; 434:167694. [PMID: 35752213 PMCID: PMC10593484 DOI: 10.1016/j.jmb.2022.167694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/17/2022] [Accepted: 06/17/2022] [Indexed: 11/25/2022]
Abstract
The microRNAs are non-coding RNAs which post-transcriptionally regulate the expression of many eukaryotic genes, and whose dysregulation is a driver of human disease. Here we report the discovery of a very slow (0.1 s-1) conformational rearrangement at the Dicer cleavage site of pre-miR-21, which regulates the relative concentration of readily- and inefficiently-processed RNA structural states. We show that this dynamic switch is affected by single nucleotide mutations and can be biased by small molecule and peptide ligands, which can direct the microRNA to occupy the inefficiently processed state and reduce processing efficiency. This result reveals a new mechanism of RNA regulation and suggests a chemical approach to suppressing or activating pathogenic microRNAs by selective stabilization of their unprocessed or processed states.
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Affiliation(s)
| | - Greg L Olsen
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA; Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen, Guangdong Province 518036, China
| | - Matthew J Walker
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA; Neoleukin Therapeutics, 188 East Blaine St, Suite 450, Seattle, WA 98102, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA.
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Earle SG, Lobanovska M, Lavender H, Tang C, Exley RM, Ramos-Sevillano E, Browning DF, Kostiou V, Harrison OB, Bratcher HB, Varani G, Tang CM, Wilson DJ, Maiden MCJ. Genome-wide association studies reveal the role of polymorphisms affecting factor H binding protein expression in host invasion by Neisseria meningitidis. PLoS Pathog 2021; 17:e1009992. [PMID: 34662348 PMCID: PMC8553145 DOI: 10.1371/journal.ppat.1009992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/28/2021] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
Many invasive bacterial diseases are caused by organisms that are ordinarily harmless components of the human microbiome. Effective interventions against these microbes require an understanding of the processes whereby symbiotic or commensal relationships transition into pathology. Here, we describe bacterial genome-wide association studies (GWAS) of Neisseria meningitidis, a common commensal of the human respiratory tract that is nevertheless a leading cause of meningitis and sepsis. An initial GWAS discovered bacterial genetic variants, including single nucleotide polymorphisms (SNPs), associated with invasive meningococcal disease (IMD) versus carriage in several loci across the meningococcal genome, encoding antigens and other extracellular components, confirming the polygenic nature of the invasive phenotype. In particular, there was a significant peak of association around the fHbp locus, encoding factor H binding protein (fHbp), which promotes bacterial immune evasion of human complement by recruiting complement factor H (CFH) to the meningococcal surface. The association around fHbp with IMD was confirmed by a validation GWAS, and we found that the SNPs identified in the validation affected the 5' region of fHbp mRNA, altering secondary RNA structures, thereby increasing fHbp expression and enhancing bacterial escape from complement-mediated killing. This finding is consistent with the known link between complement deficiencies and CFH variation with human susceptibility to IMD. These observations demonstrate the importance of human and bacterial genetic variation across the fHbp:CFH interface in determining IMD susceptibility, the transition from carriage to disease.
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Affiliation(s)
- Sarah G. Earle
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Mariya Lobanovska
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Hayley Lavender
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Changyan Tang
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
| | - Rachel M. Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Douglas F. Browning
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Vasiliki Kostiou
- Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, Oxford, United Kingdom
| | | | | | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
- * E-mail: (GV); (CMT); (DJW); (MCJM)
| | - Christoph M. Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail: (GV); (CMT); (DJW); (MCJM)
| | - Daniel J. Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
- Department for Continuing Education, University of Oxford, Oxford, United Kingdom
- * E-mail: (GV); (CMT); (DJW); (MCJM)
| | - Martin C. J. Maiden
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (GV); (CMT); (DJW); (MCJM)
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7
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Shortridge MD, Varani G. Efficient NMR Screening Approach to Discover Small Molecule Fragments Binding Structured RNA. ACS Med Chem Lett 2021; 12:1253-1260. [PMID: 34413954 DOI: 10.1021/acsmedchemlett.1c00109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/07/2021] [Indexed: 01/27/2023] Open
Abstract
We describe a scalable nuclear magnetic resonance (NMR) screening approach to identify and prioritize small molecule fragments that bind to structured RNAs. This approach is target agnostic and, therefore, amenable to many RNA structures and libraries, and it provides initial hits for further synthetic elaboration and structure-based drug discovery efforts. We demonstrate the approach on the pre-miR-21 stem-loop, which is of significant interest in oncology and metabolic diseases. We screened the pre-miR-21 hairpin using a small (420 compounds) commercially available fragment library and identified 18 hits in the first round of triage screening. This was further refined to four fragments which passed all screening cascade filters. Among these four hits, a thiadiazole fragment was demonstrated to bind the Dicer cleavage site of pre-miR-21 by target-detected NMR experiments and through the observation of clear intermolecular NOEs.
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Affiliation(s)
- Matthew D. Shortridge
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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8
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Marrella A, Fedi A, Varani G, Vaccari I, Fato M, Firpo G, Guida P, Aceto N, Scaglione S. High blood flow shear stress values are associated with circulating tumor cells cluster disaggregation in a multi-channel microfluidic device. PLoS One 2021; 16:e0245536. [PMID: 33444361 PMCID: PMC7808575 DOI: 10.1371/journal.pone.0245536] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/01/2021] [Indexed: 12/14/2022] Open
Abstract
Metastasis represents a dynamic succession of events involving tumor cells which disseminate through the organism via the bloodstream. Circulating tumor cells (CTCs) can flow the bloodstream as single cells or as multicellular aggregates (clusters), which present a different potential to metastasize. The effects of the bloodstream-related physical constraints, such as hemodynamic wall shear stress (WSS), on CTC clusters are still unclear. Therefore, we developed, upon theoretical and CFD modeling, a new multichannel microfluidic device able to simultaneously reproduce different WSS characterizing the human circulatory system, where to analyze the correlation between SS and CTC clusters behavior. Three physiological WSS levels (i.e. 2, 5, 20 dyn/cm2) were generated, reproducing values typical of capillaries, veins and arteries. As first validation, triple-negative breast cancer cells (MDA-MB-231) were injected as single CTCs showing that higher values of WSS are correlated with a decreased viability. Next, the SS-mediated disaggregation of CTC clusters was computationally investigated in a vessels-mimicking domain. Finally, CTC clusters were injected within the three different circuits and subjected to the three different WSS, revealing that increasing WSS levels are associated with a raising clusters disaggregation after 6 hours of circulation. These results suggest that our device may represent a valid in vitro tool to carry out systematic studies on the biological significance of blood flow mechanical forces and eventually to promote new strategies for anticancer therapy.
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Affiliation(s)
- Alessandra Marrella
- National Research Council (CNR), Institute of Electronic, Computer and Telecommunications (IEIIT), Genoa, Italy
| | - Arianna Fedi
- National Research Council (CNR), Institute of Electronic, Computer and Telecommunications (IEIIT), Genoa, Italy
- Department of Computer Science, Bioengineering, Robotics and Systems Engineering, University of Genoa, Genoa, Italy
| | - Gabriele Varani
- National Research Council (CNR), Institute of Electronic, Computer and Telecommunications (IEIIT), Genoa, Italy
| | - Ivan Vaccari
- National Research Council (CNR), Institute of Electronic, Computer and Telecommunications (IEIIT), Genoa, Italy
| | - Marco Fato
- Department of Computer Science, Bioengineering, Robotics and Systems Engineering, University of Genoa, Genoa, Italy
| | - Giuseppe Firpo
- Department of Physics, University of Genoa, Genoa, Italy
| | - Patrizia Guida
- Department of Physics, University of Genoa, Genoa, Italy
| | - Nicola Aceto
- Department of Biomedicine, Cancer Metastasis Laboratory, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Silvia Scaglione
- National Research Council (CNR), Institute of Electronic, Computer and Telecommunications (IEIIT), Genoa, Italy
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9
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Zappi D, Coronado E, Soljan V, Basile G, Varani G, Turemis M, Giardi MT. A microbial sensor platform based on bacterial bioluminescence (luxAB) and green fluorescent protein (gfp) reporters for in situ monitoring of toxicity of wastewater nitrification process dynamics. Talanta 2021; 221:121438. [DOI: 10.1016/j.talanta.2020.121438] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/13/2020] [Accepted: 07/19/2020] [Indexed: 10/23/2022]
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10
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Chen B, Dragomir MP, Fabris L, Bayraktar R, Knutsen E, Liu X, Tang C, Li Y, Shimura T, Ivkovic TC, De los Santos MC, Anfossi S, Shimizu M, Shah MY, Ling H, Shen P, Multani AS, Pardini B, Burks JK, Katayama H, Reineke LC, Huo L, Syed M, Song S, Ferracin M, Oki E, Fromm B, Ivan C, Bhuvaneshwar K, Gusev Y, Mimori K, Menter D, Sen S, Matsuyama T, Uetake H, Vasilescu C, Kopetz S, Parker-Thornburg J, Taguchi A, Hanash SM, Girnita L, Slaby O, Goel A, Varani G, Gagea M, Li C, Ajani JA, Calin GA. The Long Noncoding RNA CCAT2 Induces Chromosomal Instability Through BOP1-AURKB Signaling. Gastroenterology 2020; 159:2146-2162.e33. [PMID: 32805281 PMCID: PMC7725986 DOI: 10.1053/j.gastro.2020.08.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Chromosomal instability (CIN) is a carcinogenesis event that promotes metastasis and resistance to therapy by unclear mechanisms. Expression of the colon cancer-associated transcript 2 gene (CCAT2), which encodes a long noncoding RNA (lncRNA), associates with CIN, but little is known about how CCAT2 lncRNA regulates this cancer enabling characteristic. METHODS We performed cytogenetic analysis of colorectal cancer (CRC) cell lines (HCT116, KM12C/SM, and HT29) overexpressing CCAT2 and colon organoids from C57BL/6N mice with the CCAT2 transgene and without (controls). CRC cells were also analyzed by immunofluorescence microscopy, γ-H2AX, and senescence assays. CCAT2 transgene and control mice were given azoxymethane and dextran sulfate sodium to induce colon tumors. We performed gene expression array and mass spectrometry to detect downstream targets of CCAT2 lncRNA. We characterized interactions between CCAT2 with downstream proteins using MS2 pull-down, RNA immunoprecipitation, and selective 2'-hydroxyl acylation analyzed by primer extension analyses. Downstream proteins were overexpressed in CRC cells and analyzed for CIN. Gene expression levels were measured in CRC and non-tumor tissues from 5 cohorts, comprising more than 900 patients. RESULTS High expression of CCAT2 induced CIN in CRC cell lines and increased resistance to 5-fluorouracil and oxaliplatin. Mice that expressed the CCAT2 transgene developed chromosome abnormalities, and colon organoids derived from crypt cells of these mice had a higher percentage of chromosome abnormalities compared with organoids from control mice. The transgenic mice given azoxymethane and dextran sulfate sodium developed more and larger colon polyps than control mice given these agents. Microarray analysis and mass spectrometry indicated that expression of CCAT2 increased expression of genes involved in ribosome biogenesis and protein synthesis. CCAT2 lncRNA interacted directly with and stabilized BOP1 ribosomal biogenesis factor (BOP1). CCAT2 also increased expression of MYC, which activated expression of BOP1. Overexpression of BOP1 in CRC cell lines resulted in chromosomal missegregation errors, and increased colony formation, and invasiveness, whereas BOP1 knockdown reduced viability. BOP1 promoted CIN by increasing the active form of aurora kinase B, which regulates chromosomal segregation. BOP1 was overexpressed in polyp tissues from CCAT2 transgenic mice compared with healthy tissue. CCAT2 lncRNA and BOP1 mRNA or protein were all increased in microsatellite stable tumors (characterized by CIN), but not in tumors with microsatellite instability compared with nontumor tissues. Increased levels of CCAT2 lncRNA and BOP1 mRNA correlated with each other and with shorter survival times of patients. CONCLUSIONS We found that overexpression of CCAT2 in colon cells promotes CIN and carcinogenesis by stabilizing and inducing expression of BOP1 an activator of aurora kinase B. Strategies to target this pathway might be developed for treatment of patients with microsatellite stable colorectal tumors.
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Affiliation(s)
- Baoqing Chen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China,Department of Thoracic Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mihnea P. Dragomir
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of General Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Linda Fabris
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Recep Bayraktar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Xu Liu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Thoracic Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Changyan Tang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Yongfeng Li
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tadanobu Shimura
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, USA
| | - Tina Catela Ivkovic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Mireia Cruz De los Santos
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Simone Anfossi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Masayoshi Shimizu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maitri Y. Shah
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peng Shen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Asha S. Multani
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Pardini
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,present address: Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy.,present address: Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Jared K. Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lucas C. Reineke
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Longfei Huo
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Muddassir Syed
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden,Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Krithika Bhuvaneshwar
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Yuriy Gusev
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - David Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Subrata Sen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Takatoshi Matsuyama
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Hiroyuki Uetake
- Department of Specialized Surgeries, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Catalin Vasilescu
- Department of General Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,“Carol Davila University of Medicine and Pharmacy”, Bucharest, Romania
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jan Parker-Thornburg
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ayumu Taguchi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Samir M. Hanash
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Leonard Girnita
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institute and Karolinska University Hospital, SE-171 647 Stockholm, Sweden
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, USA.,present address: Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Mihai Gagea
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston Texas 77030, USA
| | - Chunlai Li
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Jaffer A. Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George A. Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Lead Contact
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11
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Zappi D, Ramma MM, Scognamiglio V, Antonacci A, Varani G, Giardi MT. High-Tech and Nature-Made Nanocomposites and Their Applications in the Field of Sensors and Biosensors for Gas Detection. Biosensors (Basel) 2020; 10:bios10110176. [PMID: 33203038 PMCID: PMC7696430 DOI: 10.3390/bios10110176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/25/2023]
Abstract
Gas sensors have been object of increasing attention by the scientific community in recent years. For the development of the sensing element, two major trends seem to have appeared. On one hand, the possibility of creating complex structures at the nanoscale level has given rise to ever more sensitive sensors based on metal oxides and metal-polymer combinations. On the other hand, gas biosensors have started to be developed, thanks to their intrinsic ability to be selective for the target analyte. In this review, we analyze the recent progress in both areas and underline their strength, current problems, and future perspectives.
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Affiliation(s)
- Daniele Zappi
- Istituto di Cristallografia, CNR Area Della Ricerca di Roma, 00015 Monterotondo Scalo Rome, Italy; (D.Z.); (V.S.); (A.A.)
| | - Matiss Martins Ramma
- Biosensor Srl, Via Degli Olmetti 44, 00060 Formello Rome, Italy; (M.M.R.); (G.V.)
| | - Viviana Scognamiglio
- Istituto di Cristallografia, CNR Area Della Ricerca di Roma, 00015 Monterotondo Scalo Rome, Italy; (D.Z.); (V.S.); (A.A.)
| | - Amina Antonacci
- Istituto di Cristallografia, CNR Area Della Ricerca di Roma, 00015 Monterotondo Scalo Rome, Italy; (D.Z.); (V.S.); (A.A.)
| | - Gabriele Varani
- Biosensor Srl, Via Degli Olmetti 44, 00060 Formello Rome, Italy; (M.M.R.); (G.V.)
| | - Maria Teresa Giardi
- Istituto di Cristallografia, CNR Area Della Ricerca di Roma, 00015 Monterotondo Scalo Rome, Italy; (D.Z.); (V.S.); (A.A.)
- Biosensor Srl, Via Degli Olmetti 44, 00060 Formello Rome, Italy; (M.M.R.); (G.V.)
- Correspondence:
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12
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Vitale C, Fedi A, Marrella A, Varani G, Fato M, Scaglione S. 3D Perfusable Hydrogel Recapitulating the Cancer Dynamic Environment to in Vitro Investigate Metastatic Colonization. Polymers (Basel) 2020; 12:E2467. [PMID: 33114344 PMCID: PMC7690854 DOI: 10.3390/polym12112467] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
Metastasis is a dynamic process involving the dissemination of circulating tumor cells (CTCs) through blood flow to distant tissues within the body. Nevertheless, the development of an in vitro platform that dissects the crucial steps of metastatic cascade still remains a challenge. We here developed an in vitro model of extravasation composed of (i) a single channel-based 3D cell laden hydrogel representative of the metastatic site, (ii) a circulation system recapitulating the bloodstream where CTCs can flow. Two polymers (i.e., fibrin and alginate) were tested and compared in terms of mechanical and biochemical proprieties. Computational fluid-dynamic (CFD) simulations were also performed to predict the fluid dynamics within the polymeric matrix and, consequently, the optimal culture conditions. Next, once the platform was validated through perfusion tests by fluidically connecting the hydrogels with the external circuit, highly metastatic breast cancer cells (MDA-MB-231) were injected and exposed to physiological wall shear stress (WSS) conditions (5 Dyn/cm2) to assess their migration toward the hydrogel. Results indicated that CTCs arrested and colonized the polymeric matrix, showing that this platform can be an effective fluidic system to model the first steps occurring during the metastatic cascade as well as a potential tool to in vitro elucidate the contribution of hemodynamics on cancer dissemination to a secondary site.
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Affiliation(s)
- Chiara Vitale
- National Research Council of Italy, Institute of Electronic, Computer and Telecommunications (IEIIT) Institute, 16149 Genoa, Italy; (C.V.); (A.F.); (G.V.); (M.F.); (S.S.)
| | - Arianna Fedi
- National Research Council of Italy, Institute of Electronic, Computer and Telecommunications (IEIIT) Institute, 16149 Genoa, Italy; (C.V.); (A.F.); (G.V.); (M.F.); (S.S.)
- Department of Computer Science, Bioengineering, Robotics and Systems Engineering, University of Genoa, 16126 Genoa, Italy
| | - Alessandra Marrella
- National Research Council of Italy, Institute of Electronic, Computer and Telecommunications (IEIIT) Institute, 16149 Genoa, Italy; (C.V.); (A.F.); (G.V.); (M.F.); (S.S.)
| | - Gabriele Varani
- National Research Council of Italy, Institute of Electronic, Computer and Telecommunications (IEIIT) Institute, 16149 Genoa, Italy; (C.V.); (A.F.); (G.V.); (M.F.); (S.S.)
| | - Marco Fato
- National Research Council of Italy, Institute of Electronic, Computer and Telecommunications (IEIIT) Institute, 16149 Genoa, Italy; (C.V.); (A.F.); (G.V.); (M.F.); (S.S.)
- Department of Computer Science, Bioengineering, Robotics and Systems Engineering, University of Genoa, 16126 Genoa, Italy
| | - Silvia Scaglione
- National Research Council of Italy, Institute of Electronic, Computer and Telecommunications (IEIIT) Institute, 16149 Genoa, Italy; (C.V.); (A.F.); (G.V.); (M.F.); (S.S.)
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13
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Jones AN, Pisignano G, Pavelitz T, White J, Kinisu M, Forino N, Albin D, Varani G. An evolutionarily conserved RNA structure in the functional core of the lincRNA Cyrano. RNA 2020; 26:1234-1246. [PMID: 32457084 PMCID: PMC7430676 DOI: 10.1261/rna.076117.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/18/2020] [Indexed: 05/08/2023]
Abstract
The wide prevalence and regulated expression of long noncoding RNAs (lncRNAs) highlight their functional roles, but the molecular basis for their activities and structure-function relationships remains to be investigated, with few exceptions. Among the relatively few lncRNAs conserved over significant evolutionary distances is the long intergenic noncoding RNA (lincRNA) Cyrano (orthologous to human OIP5-AS1), which contains a region of 300 highly conserved nucleotides within tetrapods, which in turn contains a functional stretch of 26 nt of deep conservation. This region binds to and facilitates the degradation of the microRNA miR-7, a short ncRNA with multiple cellular functions, including modulation of oncogenic expression. We probed the secondary structure of Cyrano in vitro and in cells using chemical and enzymatic probing, and validated the results using comparative sequence analysis. At the center of the functional core of Cyrano is a cloverleaf structure maintained over the >400 million years of divergent evolution that separates fish and primates. This strikingly conserved motif provides interaction sites for several RNA-binding proteins and masks a conserved recognition site for miR-7. Conservation in this region strongly suggests that the function of Cyrano depends on the formation of this RNA structure, which could modulate the rate and efficiency of degradation of miR-7.
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Affiliation(s)
- Alisha N Jones
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Giuseppina Pisignano
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR) and Oncology Institute of Southern Switzerland (IOSI), Bellinzona CH-6500, Switzerland
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom
| | - Thomas Pavelitz
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Jessica White
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Martin Kinisu
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Nicholas Forino
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Dreycey Albin
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195, USA
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14
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Sharma S, Varani G. NMR structure of Dengue West Nile viruses stem-loop B: A key cis-acting element for flavivirus replication. Biochem Biophys Res Commun 2020; 531:522-527. [PMID: 32807496 DOI: 10.1016/j.bbrc.2020.07.115] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 12/30/2022]
Abstract
Flaviviruses are major emerging human pathogenic viruses that pose a persistent and growing menace to global health. They are enveloped single-stranded RNA viruses with positive polarity transmitted by arthropod vectors like mosquitoes or ticks, responsible for a significant and growing number of human deaths and illnesses. The 5'- and 3'-untranslated regions (UTRs) are highly structured and contain conserved cis-acting RNA elements that participate in viral translation, replication and host adaptation. Despite their role in fiaviviruses replication, few high-resolution structural studies have investigated the RNA elements required for viral replication. Here we report the NMR structures of stem-loop B from WNV and DENV4 viruses. Because this element is required for cyclization of the genome and the activity of the replicative viral enzymes, viral replication rates are sensitive to even small changes in these RNAs. Therefore, this work provides structural insight into a new drug target to reduce flavivirus replication rates.
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Affiliation(s)
- Shrikant Sharma
- Department of Chemistry, University of Washington, Seattle, WA, USA, 98195
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA, USA, 98195.
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15
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Marrella A, Varani G, Aiello M, Vaccari I, Vitale C, Mojzisek M, Degrassi C, Scaglione S. 3D fluid-dynamic ovarian cancer model resembling systemic drug administration for efficacy assay. ALTEX 2020; 38:82-94. [PMID: 32754773 DOI: 10.14573/altex.2003131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/08/2020] [Indexed: 11/23/2022]
Abstract
Recently, 3D in vitro cancer models have become important alternatives to animal tests for establishing the efficacy of anticancer treatments. In this work, 3D SKOV-3 cell-laden alginate hydrogels were established as ovarian tumor models and cultured within a fluid-dynamic bioreactor (MIVO®) device able to mimic the capillary flow dynamics feeding the tumor. Cisplatin efficacy tests were performed within the device over time and compared with (i) the in vitro culture under static conditions and (ii) a xenograft mouse model with SKOV-3 cells, by monitoring and measuring cell proliferation or tumor regression, respectively, over time. After one week of treatment with 10 μM cisplatin, viability of cells within the 3D hydrogels cultured under static conditions remained above 80%. In contrast, the viability of cells within the 3D hydrogels cultured within dynamic MIVO® decreased by up to 50%, and very few proliferating Ki67-positive cells were observed through immunostaining. Analysis of drug diffusion, confirmed by computational analysis, explained that these results are due to different cisplatin diffusion mechanisms in the two culture conditions. Interestingly, the outcome of the drug efficacy test in the xenograft model was about 44% of tumor regression after 5 weeks, as predicted in a shorter time in the fluid-dynamic in vitro tests carried out in the MIVO® device. These results indicate that the in vivo-like dynamic environment provided by the MIVO® device allows to better model the 3D tumor environment and predict in vivo drug efficacy than a static in vitro model.
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Affiliation(s)
| | - Gabriele Varani
- CNR - National Research Council of Italy, IEIIT Institute, Genoa, Italy
| | | | - Ivan Vaccari
- CNR - National Research Council of Italy, IEIIT Institute, Genoa, Italy
| | - Chiara Vitale
- CNR - National Research Council of Italy, IEIIT Institute, Genoa, Italy
| | | | | | - Silvia Scaglione
- CNR - National Research Council of Italy, IEIIT Institute, Genoa, Italy.,React4life S.r.l, Genoa, Italy
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16
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Longo LM, Despotović D, Weil-Ktorza O, Walker MJ, Jabłońska J, Fridmann-Sirkis Y, Varani G, Metanis N, Tawfik DS. Primordial emergence of a nucleic acid-binding protein via phase separation and statistical ornithine-to-arginine conversion. Proc Natl Acad Sci U S A 2020; 117:15731-15739. [PMID: 32561643 PMCID: PMC7355028 DOI: 10.1073/pnas.2001989117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
De novo emergence demands a transition from disordered polypeptides into structured proteins with well-defined functions. However, can polypeptides confer functions of evolutionary relevance, and how might such polypeptides evolve into modern proteins? The earliest proteins present an even greater challenge, as they were likely based on abiotic, spontaneously synthesized amino acids. Here we asked whether a primordial function, such as nucleic acid binding, could emerge with ornithine, a basic amino acid that forms abiotically yet is absent in modern-day proteins. We combined ancestral sequence reconstruction and empiric deconstruction to unravel a gradual evolutionary trajectory leading from a polypeptide to a ubiquitous nucleic acid-binding protein. Intermediates along this trajectory comprise sequence-duplicated functional proteins built from 10 amino acid types, with ornithine as the only basic amino acid. Ornithine side chains were further modified into arginine by an abiotic chemical reaction, improving both structure and function. Along this trajectory, function evolved from phase separation with RNA (coacervates) to avid and specific double-stranded DNA binding. Our results suggest that phase-separating polypeptides may have been an evolutionary resource for the emergence of early proteins, and that ornithine, together with its postsynthesis modification to arginine, could have been the earliest basic amino acids.
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Affiliation(s)
- Liam M Longo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dragana Despotović
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orit Weil-Ktorza
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Matthew J Walker
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Jagoda Jabłońska
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yael Fridmann-Sirkis
- Life Sciences Core Facility, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Norman Metanis
- Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel;
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17
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Walker MJ, Shortridge MD, Albin DD, Cominsky LY, Varani G. Structure of the RNA Specialized Translation Initiation Element that Recruits eIF3 to the 5'-UTR of c-Jun. J Mol Biol 2020; 432:1841-1855. [PMID: 31953146 PMCID: PMC7225069 DOI: 10.1016/j.jmb.2020.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/10/2019] [Accepted: 01/02/2020] [Indexed: 02/05/2023]
Abstract
Specialized translation initiation is a novel form of regulation of protein synthesis, whereby RNA structures within the 5'-UTR regulate translation rates of specific mRNAs. Similar to internal ribosome entry sites (IRESs), specialized translation initiation requires the recruitment of eukaryotic initiation factor 3 (eIF3), but also requires cap recognition by eIF3d, a new 5'-m7GTP recognizing protein. How these RNA structures mediate eIF3 recruitment to affect translation of specific mRNAs remains unclear. Here, we report the nuclear magnetic resonance (NMR) structure of a stem-loop within the c-JUN 5' UTR recognized by eIF3 and essential for specialized translation initiation of this well-known oncogene. The structure exhibits similarity to eIF3 recognizing motifs found in hepatitis C virus (HCV)-like IRESs, suggesting mechanistic similarities. This work establishes the RNA structural features involved in c-JUN specialized translation initiation and provides a basis to search for small molecule inhibitors of aberrant expression of the proto-oncogenic c-JUN.
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Affiliation(s)
- Matthew J Walker
- Department of Chemistry, University of Washington, Seattle, WA, USA 98195
| | | | - Dreycey D Albin
- Department of Chemistry, University of Washington, Seattle, WA, USA 98195
| | - Lauren Y Cominsky
- Department of Chemistry, University of Washington, Seattle, WA, USA 98195
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA, USA 98195.
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18
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Pacelli S, Paolicelli P, Petralito S, Subham S, Gilmore D, Varani G, Yang G, Lin D, Casadei MA, Paul A. Investigating the Role of Polydopamine to Modulate Stem Cell Adhesion and Proliferation on Gellan Gum-Based Hydrogels. ACS Appl Bio Mater 2020; 3:945-951. [DOI: 10.1021/acsabm.9b00989] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Settimio Pacelli
- Department of Chemical and Petroleum Engineering, BioIntel Research Laboratory, University of Kansas, Lawrence, Kansas 66045, United States
| | - Patrizia Paolicelli
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Stefania Petralito
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Siddharth Subham
- Department of Chemical and Petroleum Engineering, BioIntel Research Laboratory, University of Kansas, Lawrence, Kansas 66045, United States
| | - Drake Gilmore
- Department of Chemical and Petroleum Engineering, BioIntel Research Laboratory, University of Kansas, Lawrence, Kansas 66045, United States
| | - Gabriele Varani
- CNR National Research Council of Italy, IEIIT Institute, Via de Marini 6, 16149, Genoa, Italy
| | - Guang Yang
- Department of Industrial and Manufacturing Systems Engineering, Kansas State University, 2080 Rathbone Hall, 1701 D Platt Street, Manhattan, Kansas 66506, United States
| | - Dong Lin
- Department of Industrial and Manufacturing Systems Engineering, Kansas State University, 2080 Rathbone Hall, 1701 D Platt Street, Manhattan, Kansas 66506, United States
| | - Maria Antonietta Casadei
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Arghya Paul
- Department of Chemical and Biochemical Engineering and Department of Chemistry, The University of Western Ontario, London, ON N6A 5B9, Canada
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19
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Smith KN, Miller SC, Varani G, Calabrese JM, Magnuson T. Multimodal Long Noncoding RNA Interaction Networks: Control Panels for Cell Fate Specification. Genetics 2019; 213:1093-1110. [PMID: 31796550 PMCID: PMC6893379 DOI: 10.1534/genetics.119.302661] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
Lineage specification in early development is the basis for the exquisitely precise body plan of multicellular organisms. It is therefore critical to understand cell fate decisions in early development. Moreover, for regenerative medicine, the accurate specification of cell types to replace damaged/diseased tissue is strongly dependent on identifying determinants of cell identity. Long noncoding RNAs (lncRNAs) have been shown to regulate cellular plasticity, including pluripotency establishment and maintenance, differentiation and development, yet broad phenotypic analysis and the mechanistic basis of their function remains lacking. As components of molecular condensates, lncRNAs interact with almost all classes of cellular biomolecules, including proteins, DNA, mRNAs, and microRNAs. With functions ranging from controlling alternative splicing of mRNAs, to providing scaffolding upon which chromatin modifiers are assembled, it is clear that at least a subset of lncRNAs are far from the transcriptional noise they were once deemed. This review highlights the diversity of lncRNA interactions in the context of cell fate specification, and provides examples of each type of interaction in relevant developmental contexts. Also highlighted are experimental and computational approaches to study lncRNAs.
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Affiliation(s)
- Keriayn N Smith
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Sarah C Miller
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195
| | - J Mauro Calabrese
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Terry Magnuson
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
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20
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Abstract
Regulation of protein-DNA binding specificity occurs through myriad mechanisms. Boudet et al. discover yet a new form of specificity through allosteric regulation, an ATP-induced structural switch that mediates specific DNA recognition in an archaeoeukaryotic primase.
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Affiliation(s)
- Matthew J Walker
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
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21
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Abstract
The world of noncoding RNAs (ncRNAs) is composed of an enormous and growing number of transcripts, ranging in length from tens of bases to tens of kilobases, involved in all biological processes and altered in expression and/or function in many types of human disorders. The premise of this review is the concept that ncRNAs, like many large proteins, have a multidomain architecture that organizes them spatially and functionally. As ncRNAs are beginning to be imprecisely classified into functional families, we review here how their structural properties might inform their functions with focus on structural architecture–function relationships. We will describe the properties of “interactor elements” (IEs) involved in direct physical interaction with nucleic acids, proteins, or lipids and of “structural elements” (SEs) directing their wiring within the “ncRNA interactor networks” through the emergence of secondary and/or tertiary structures. We suggest that spectrums of “letters” (ncRNA elements) are assembled into “words” (ncRNA domains) that are further organized into “phrases” (complete ncRNA structures) with functional meaning (signaling output) through complex “sentences” (the ncRNA interactor networks). This semiotic analogy can guide the exploitation of ncRNAs as new therapeutic targets through the development of IE-blockers and/or SE-lockers that will change the interactor partners’ spectrum of proteins, RNAs, DNAs, or lipids and consequently influence disease phenotypes.
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Affiliation(s)
- Muller Fabbri
- University of Hawaii Cancer Center, Cancer Biology Program, Honolulu, Hawaii 96813, USA
| | - Leonard Girnita
- Department of Oncology-Pathology, Cellular and Molecular Tumor Pathology, Karolinska Institute, and Karolinska University Hospital, Stockholm, 17164 Sweden
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - George A Calin
- Department of Experimental Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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22
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Shortridge MD, Wille PT, Jones AN, Davidson A, Bogdanovic J, Arts E, Karn J, Robinson JA, Varani G. An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb. Nucleic Acids Res 2019; 47:1523-1531. [PMID: 30481318 PMCID: PMC6379670 DOI: 10.1093/nar/gky1197] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/09/2018] [Accepted: 11/23/2018] [Indexed: 12/16/2022] Open
Abstract
The HIV-1 trans-activator protein Tat binds the trans-activation response element (TAR) to facilitate recruitment of the super elongation complex (SEC) to enhance transcription of the integrated pro-viral genome. The Tat–TAR interaction is critical for viral replication and the emergence of the virus from the latent state, therefore, inhibiting this interaction has long been pursued to discover new anti-viral or latency reversal agents. However, discovering active compounds that directly target RNA with high affinity and selectivity remains a significant challenge; limiting pre-clinical development. Here, we report the rational design of a macrocyclic peptide mimic of the arginine rich motif of Tat, which binds to TAR with low pM affinity and 100-fold selectivity against closely homologous RNAs. Despite these unprecedented binding properties, the new ligand (JB181) only moderately inhibits Tat-dependent reactivation in cells and recruitment of positive transcription elongation factor (P-TEFb) to TAR. The NMR structure of the JB181–TAR complex revealed that the ligand induces a structure in the TAR loop that closely mimics the P-TEFb/Tat1:57/AFF4/TAR complex. These results strongly suggest that high-affinity ligands which bind the UCU bulge are not likely to inhibit recruitment of the SEC and suggest that targeting of the TAR loop will be an essential feature of effective Tat inhibitors.
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Affiliation(s)
- Matthew D Shortridge
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Paul T Wille
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - Alisha N Jones
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Amy Davidson
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Jasmina Bogdanovic
- Department of Chemistry, University of Zurich, Zurich, Switzerland CH-8057
| | - Eric Arts
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - John A Robinson
- Department of Chemistry, University of Zurich, Zurich, Switzerland CH-8057
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
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Yang W, Hsu PL, Yang F, Song JE, Varani G. Reconstitution of the CstF complex unveils a regulatory role for CstF-50 in recognition of 3'-end processing signals. Nucleic Acids Res 2019; 46:493-503. [PMID: 29186539 PMCID: PMC5778602 DOI: 10.1093/nar/gkx1177] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/13/2017] [Indexed: 01/18/2023] Open
Abstract
Cleavage stimulation factor (CstF) is a highly conserved protein complex composed of three subunits that recognizes G/U-rich sequences downstream of the polyadenylation signal of eukaryotic mRNAs. While CstF has been identified over 25 years ago, the architecture and contribution of each subunit to RNA recognition have not been fully understood. In this study, we provide a structural basis for the recruitment of CstF-50 to CstF via interaction with CstF-77 and establish that the hexameric assembly of CstF creates a high affinity platform to target various G/U-rich sequences. We further demonstrate that CstF-77 boosts the affinity of the CstF-64 RRM to the RNA targets and CstF-50 fine tunes the ability of the complex to recognize G/U sequences of certain lengths and content.
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Affiliation(s)
- Wen Yang
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Peter L Hsu
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Fan Yang
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Jae-Eun Song
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
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24
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Abstract
RNA structures play a pivotal role in many biological processes and the progression of human disease, making them an attractive target for therapeutic development. Often RNA structures operate through the formation of complexes with RNA-binding proteins, however, much like protein-protein interactions, RNA-protein interactions span large surface areas and often lack traditional druggable properties, making it challenging to target them with small molecules. Peptides provide much greater surface areas and therefore greater potential for forming specific and high affinity interactions with RNA. In this chapter, we discuss our approach for engineering peptides that bind to structured RNAs by highlighting methods and design strategies from previous successful projects aimed at inhibiting the HIV Tat-TAR interaction and the biogenesis of oncogenic microRNAs.
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Affiliation(s)
- Matthew J Walker
- Department of Chemistry, University of Washington, Seattle, WA, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA, United States.
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25
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Sun YT, Shortridge MD, Varani G. A Small Cyclic β-Hairpin Peptide Mimics the Rbfox2 RNA Recognition Motif and Binds to the Precursor miRNA 20b. Chembiochem 2019; 20:931-939. [PMID: 30537200 DOI: 10.1002/cbic.201800645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Indexed: 12/22/2022]
Abstract
The RNA recognition motif (RRM), which is the most abundant RNA-binding motif in eukaryotes, is a well-structured domain of about 90 amino acids, yet the β2β3 hairpin, corresponding to strands 2 and 3 of the β-sheet, and the intervening loop make essential interactions with RNA in many RRM complexes. A series of small cyclic peptide mimics of the β2β3 hairpin of Rbfox2 protein that recognize the terminal loop of precursor miR-20b have been designed to investigate whether the full RNA-binding protein can be mimicked with a minimal structurally preorganized peptide. Within a small library of seven cyclic peptides, a peptide with low-micromolar affinity for the miR-20b precursor was found. NMR spectroscopy titration data suggest that this peptide specifically targets the apical loop of pre-miR-20b. This work shows that it is possible to mimic RNA-binding proteins with designed stable peptides, which provide a starting point for designing or evolving small peptide mimetics of RRM proteins.
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Affiliation(s)
- Yi-Ting Sun
- Department of Chemistry, University of Washington, 4000 15th Ave NE, Bagley Hall, Seattle, WA, 98195-1700, USA
| | - Matthew D Shortridge
- Department of Chemistry, University of Washington, 4000 15th Ave NE, Bagley Hall, Seattle, WA, 98195-1700, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, 4000 15th Ave NE, Bagley Hall, Seattle, WA, 98195-1700, USA
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26
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Bochicchio A, Krepl M, Yang F, Varani G, Sponer J, Carloni P. Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study. PLoS Comput Biol 2018; 14:e1006642. [PMID: 30521520 PMCID: PMC6307825 DOI: 10.1371/journal.pcbi.1006642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 12/27/2018] [Accepted: 11/13/2018] [Indexed: 12/25/2022] Open
Abstract
The RNA recognition motif (RRM) is the most common RNA binding domain across eukaryotic proteins. It is therefore of great value to engineer its specificity to target RNAs of arbitrary sequence. This was recently achieved for the RRM in Rbfox protein, where four mutations R118D, E147R, N151S, and E152T were designed to target the precursor to the oncogenic miRNA 21. Here, we used a variety of molecular dynamics-based approaches to predict specific interactions at the binding interface. Overall, we have run approximately 50 microseconds of enhanced sampling and plain molecular dynamics simulations on the engineered complex as well as on the wild-type Rbfox·pre-miRNA 20b from which the mutated systems were designed. Comparison with the available NMR data on the wild type molecules (protein, RNA, and their complex) served to establish the accuracy of the calculations. Free energy calculations suggest that further improvements in affinity and selectivity are achieved by the S151T replacement. RNA is an outstanding target for oncological intervention. Engineering the most common RNA binding motif in human proteins (called RRM) so as to bind to a specific RNA has an enormous pharmacological potential. Yet, it is highly non trivial to design RRM-bearing protein variants with RNA selectivity and affinity sufficiently high for clinical applications. Here we present an extensive molecular simulation study which shed light on the exquisite molecular recognition of the empirically-engineered complex between the RRM-bearing protein Rbfox and its RNA target pre-miR21. The simulations allow predicting a variant, the S151T, which may lead to further enhancement of selectivity and affinity for pre-miR21.
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Affiliation(s)
- Anna Bochicchio
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- * E-mail: (MK); (PC)
| | - Fan Yang
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, Olomouc, Czech Republic
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
- JARA-HPC, Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, Jülich, Germany
- * E-mail: (MK); (PC)
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Adrover A, Varani G, Paolicelli P, Petralito S, Di Muzio L, Casadei MA, Tho I. Experimental and Modeling Study of Drug Release from HPMC-Based Erodible Oral Thin Films. Pharmaceutics 2018; 10:pharmaceutics10040222. [PMID: 30423941 PMCID: PMC6320981 DOI: 10.3390/pharmaceutics10040222] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 12/13/2022] Open
Abstract
In this work hydroxypropyl methylcellulose (HPMC) fast-dissolving thin films for oral administration are investigated. Furosemide (Class IV of the Biopharmaceutical Classification System) has been used as a model drug for in vitro release tests using three different set-ups: the Franz cell, the millifluidic flow-through device, and the paddle type dissolution apparatus (USP II). In order to enable drug incorporation within HPMC films, a multifunctional excipient, hydroxypropyl-β-cyclodextrin (HP-β-CD) has been included in the formulation, and the influence of HP-β-CD on film swelling, erosion, and release properties has been investigated. Mathematical models capable of describing the swelling and release processes from HPMC erodible thin films in different apparatuses have been developed. In particular, we propose a new model for the description of drug transport and release in a Franz cell that accounts for the effect of the unavoidable imperfect mixing of the receptor chamber.
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Affiliation(s)
- Alessandra Adrover
- Dipartimento di Ingegneria Chimica, Materiali e Ambiente, Sapienza Universitá di Roma, Via Eudossiana 18, 00184 Rome, Italy.
| | - Gabriele Varani
- Dipartimento di Ingegneria Chimica, Materiali e Ambiente, Sapienza Universitá di Roma, Via Eudossiana 18, 00184 Rome, Italy.
| | - Patrizia Paolicelli
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Universitá di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Stefania Petralito
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Universitá di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Laura Di Muzio
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Universitá di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Maria Antonietta Casadei
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Universitá di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Ingunn Tho
- Section of Pharmaceutics and Social Pharmacy, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316 Oslo, Norway.
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Pacelli S, Paolicelli P, Avitabile M, Varani G, Di Muzio L, Cesa S, Tirillò J, Bartuli C, Nardoni M, Petralito S, Adrover A, Casadei MA. Design of a tunable nanocomposite double network hydrogel based on gellan gum for drug delivery applications. Eur Polym J 2018. [DOI: 10.1016/j.eurpolymj.2018.04.034] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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29
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Hosseinzadeh P, Bhardwaj G, Mulligan VK, Shortridge MD, Craven TW, Pardo-Avila F, Rettie SA, Kim DE, Silva DA, Ibrahim YM, Webb IK, Cort JR, Adkins JN, Varani G, Baker D. Comprehensive computational design of ordered peptide macrocycles. Science 2017; 358:1461-1466. [PMID: 29242347 PMCID: PMC5860875 DOI: 10.1126/science.aap7577] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Accepted: 11/15/2017] [Indexed: 12/31/2022]
Abstract
Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with l-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of l- and d-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods.
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Affiliation(s)
- Parisa Hosseinzadeh
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Gaurav Bhardwaj
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Vikram Khipple Mulligan
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | | | - Timothy W. Craven
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Fátima Pardo-Avila
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stephen A. Rettie
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - David E. Kim
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Daniel-Adriano Silva
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ian K. Webb
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - John R. Cort
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Joshua N. Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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Paolicelli P, Varani G, Pacelli S, Ogliani E, Nardoni M, Petralito S, Adrover A, Casadei MA. DESIGN AND CHARACTERIZATION OF A BIOCOMPATIBLE PHYSICAL HYDROGEL BASED ON SCLEROGLUCAN FOR TOPICAL DRUG DELIVERY. Carbohydr Polym 2017; 174:960-969. [DOI: 10.1016/j.carbpol.2017.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 06/14/2017] [Accepted: 07/04/2017] [Indexed: 10/19/2022]
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31
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Shortridge MD, Walker MJ, Pavelitz T, Chen Y, Yang W, Varani G. A Macrocyclic Peptide Ligand Binds the Oncogenic MicroRNA-21 Precursor and Suppresses Dicer Processing. ACS Chem Biol 2017; 12:1611-1620. [PMID: 28437065 DOI: 10.1021/acschembio.7b00180] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) help orchestrate cellular growth and survival through post-transcriptional mechanisms. The dysregulation of miRNA biogenesis can lead to cellular growth defects and chemotherapeutic resistance and plays a direct role in the development of many chronic diseases. Among these RNAs, miR-21 is consistently overexpressed in most human cancers, leading to the down-regulation of key tumor-suppressing and pro-apoptotic factors, suggesting that inhibition of miR-21 biogenesis could reverse these negative effects. However, targeted inhibition of miR-21 using small molecules has had limited success. To overcome difficulties in targeting RNA secondary structure with small molecules, we developed a class of cyclic β-hairpin peptidomimetics which bind to RNA stem-loop structures, such as miRNA precursors, with potent affinity and specificity. We screened an existing cyclic peptide library and discovered a lead structure which binds to pre-miR21 with KD = 200 nM and prefers it over other pre-miRNAs. The NMR structure of the complex shows that the peptide recognizes the Dicer cleavage site and alters processing of the precursor to the mature miRNA in vitro and in cultured cells. The structure provides a rationale for the peptide binding activity and clear guidance for further improvements in affinity and targeting.
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Affiliation(s)
- Matthew D. Shortridge
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Matthew J. Walker
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Tom Pavelitz
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Yu Chen
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Box
351700, Seattle, Washington 98195, United States
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32
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Pisignano G, Napoli S, Magistri M, Mapelli SN, Pastori C, Di Marco S, Civenni G, Albino D, Enriquez C, Allegrini S, Mitra A, D'Ambrosio G, Mello-Grand M, Chiorino G, Garcia-Escudero R, Varani G, Carbone GM, Catapano CV. A promoter-proximal transcript targeted by genetic polymorphism controls E-cadherin silencing in human cancers. Nat Commun 2017; 8:15622. [PMID: 28555645 PMCID: PMC5459991 DOI: 10.1038/ncomms15622] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 04/12/2017] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs are emerging players in the epigenetic machinery with key roles in development and diseases. Here we uncover a complex network comprising a promoter-associated noncoding RNA (paRNA), microRNA and epigenetic regulators that controls transcription of the tumour suppressor E-cadherin in epithelial cancers. E-cadherin silencing relies on the formation of a complex between the paRNA and microRNA-guided Argonaute 1 that, together, recruit SUV39H1 and induce repressive chromatin modifications in the gene promoter. A single nucleotide polymorphism (rs16260) linked to increased cancer risk alters the secondary structure of the paRNA, with the risk allele facilitating the assembly of the microRNA-guided Argonaute 1 complex and gene silencing. Collectively, these data demonstrate the role of a paRNA in E-cadherin regulation and the impact of a noncoding genetic variant on its function. Deregulation of paRNA-based epigenetic networks may contribute to cancer and other diseases making them promising targets for drug discovery.
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Affiliation(s)
- Giuseppina Pisignano
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Sara Napoli
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Marco Magistri
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Sarah N Mapelli
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Chiara Pastori
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Stefano Di Marco
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Gianluca Civenni
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Domenico Albino
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Claudia Enriquez
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Sara Allegrini
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Abhishek Mitra
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | | | | | - Giovanna Chiorino
- Laboratory of Cancer Genomics, Fondo Edo Tempia, Biella 13900, Italy
| | - Ramon Garcia-Escudero
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland.,Molecular Oncology Unit, CIEMAT and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid 28040, Spain
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - Giuseppina M Carbone
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland
| | - Carlo V Catapano
- Tumor Biology and Experimental Therapeutics Program, Institute of Oncology Research (IOR), and Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland.,Department of Oncology, Faculty of Biology and Medicine, University of Lausanne, Lausanne 1066, Switzerland
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Yang F, Hsu P, Lee SD, Yang W, Hoskinson D, Xu W, Moore C, Varani G. The C terminus of Pcf11 forms a novel zinc-finger structure that plays an essential role in mRNA 3'-end processing. RNA 2017; 23:98-107. [PMID: 27780845 PMCID: PMC5159653 DOI: 10.1261/rna.058354.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/16/2016] [Indexed: 05/22/2023]
Abstract
3'-End processing of pre-mRNAs prior to packaging and export to the cytoplasm of the mature transcript is a highly regulated process executed by several tens of protein factors that recognize poorly conserved RNA signals. Among them is Pcf11, a highly conserved, multidomain protein that links transcriptional elongation, 3'-end processing, and transcription termination. Here we report the structure and biochemical function of Pcf11's C-terminal domain, which is conserved from yeast to humans. We identify a novel zinc-finger fold, resembling a trillium flower. Structural, biochemical, and genetic analyses reveal a highly conserved surface that plays a critical role in both cleavage and polyadenylation. These findings provide further insight into this important protein and its multiple functional roles during cotranscriptional RNA processing.
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Affiliation(s)
- Fan Yang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Peter Hsu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Susan D Lee
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Derick Hoskinson
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Weihao Xu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Claire Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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Abstract
Intrinsic motions may allow HIV-1 transactivation response (TAR) RNA to change its conformation to form a functional complex with the Tat protein, which is essential for viral replication. Understanding the dynamic properties of TAR necessitates determining motion on the intermediate nanosecond-to-microsecond time scale. To this end, we performed solid-state deuterium NMR line-shape and T1Z relaxation-time experiments to measure intermediate motions for two uridine residues, U40 and U42, within the lower helix of TAR. We infer global motions at rates of ∼105 s-1 in the lower helix, which are much slower than those in the upper helix (∼106 s-1), indicating that the two helical domains reorient independently of one another in the solid-state sample. These results contribute to the aim of fully describing the properties of functional motions in TAR RNA.
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Affiliation(s)
- Wei Huang
- Department of Chemistry, University of Washington , Box 351700, Seattle 98195, United States
| | - Prashant S Emani
- Department of Chemistry, University of Washington , Box 351700, Seattle 98195, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington , Box 351700, Seattle 98195, United States
| | - Gary P Drobny
- Department of Chemistry, University of Washington , Box 351700, Seattle 98195, United States
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Barnwal RP, Loh E, Godin KS, Yip J, Lavender H, Tang CM, Varani G. Structure and mechanism of a molecular rheostat, an RNA thermometer that modulates immune evasion by Neisseria meningitidis. Nucleic Acids Res 2016; 44:9426-9437. [PMID: 27369378 PMCID: PMC5100586 DOI: 10.1093/nar/gkw584] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/24/2016] [Accepted: 06/18/2016] [Indexed: 11/15/2022] Open
Abstract
Neisseria meningitidis causes bacterial meningitis and septicemia. It evades the host complement system by upregulating expression of immune evasion factors in response to changes in temperature. RNA thermometers within mRNAs control expression of bacterial immune evasion factors, including CssA, in the 5'-untranslated region of the operon for capsule biosynthesis. We dissect the molecular mechanisms of thermoregulation and report the structure of the CssA thermometer. We show that the RNA thermometer acts as a rheostat, whose stability is optimized to respond in a small temperature range around 37°C as occur within the upper airways during infection. Small increases in temperature gradually open up the structure to allow progressively increased access to the ribosome binding site. Even small changes in stability induced by mutations of imperfect base pairs, as in naturally occurring polymorphisms, shift the thermometer response outside of the desired temperature range, suggesting that its activity could be modulated by pharmacological intervention.
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Affiliation(s)
| | - Edmund Loh
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Department of Microbiology, Tumor and Cell Biology (MTC), Mikrobiell Patogenes, Gustaf V, Karolinska Sjukhuset 171 76 Stockholm, Sweden
| | - Katherine S Godin
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Jordan Yip
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Hayley Lavender
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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36
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Chen Y, Yang F, Zubovic L, Pavelitz T, Yang W, Godin K, Walker M, Zheng S, Macchi P, Varani G. Targeted inhibition of oncogenic miR-21 maturation with designed RNA-binding proteins. Nat Chem Biol 2016; 12:717-23. [PMID: 27428511 PMCID: PMC4990487 DOI: 10.1038/nchembio.2128] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 05/02/2016] [Indexed: 02/07/2023]
Abstract
The RNA Recognition Motif (RRM) is the largest family of eukaryotic RNA-binding proteins. Engineered RRMs with new specificity would provide valuable tools and an exacting test of our understanding of specificity. We have achieved the first successful re-design of the specificity of an RRM using rational methods and demonstrated re-targeting of activity in cells. We engineered the conserved RRM of human Rbfox proteins to specifically bind to the terminal loop of miR-21 precursor with high affinity and inhibit its processing by Drosha and Dicer. We further engineered Giardia Dicer by replacing its PAZ domain with the designed RRM. The reprogrammed enzyme degrades pre-miR-21 specifically in vitro and suppresses mature miR-21 levels in cells, which results in increased expression of PDCD4 and significantly decreased viability for cancer cells. The results demonstrate the feasibility of engineering the sequence-specificity of RRMs and of using this ubiquitous platform for diverse biological applications.
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Affiliation(s)
- Yu Chen
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Fan Yang
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Lorena Zubovic
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Tom Pavelitz
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Katherine Godin
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Matthew Walker
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Suxin Zheng
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Paolo Macchi
- Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington, USA
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37
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Borkar AN, Bardaro MF, Camilloni C, Aprile FA, Varani G, Vendruscolo M. Structure of a low-population binding intermediate in protein-RNA recognition. Proc Natl Acad Sci U S A 2016; 113:7171-6. [PMID: 27286828 PMCID: PMC4932932 DOI: 10.1073/pnas.1521349113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interaction of the HIV-1 protein transactivator of transcription (Tat) and its cognate transactivation response element (TAR) RNA transactivates viral transcription and represents a paradigm for the widespread occurrence of conformational rearrangements in protein-RNA recognition. Although the structures of free and bound forms of TAR are well characterized, the conformations of the intermediates in the binding process are still unknown. By determining the free energy landscape of the complex using NMR residual dipolar couplings in replica-averaged metadynamics simulations, we observe two low-population intermediates. We then rationally design two mutants, one in the protein and another in the RNA, that weaken specific nonnative interactions that stabilize one of the intermediates. By using surface plasmon resonance, we show that these mutations lower the release rate of Tat, as predicted. These results identify the structure of an intermediate for RNA-protein binding and illustrate a general strategy to achieve this goal with high resolution.
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Affiliation(s)
- Aditi N Borkar
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michael F Bardaro
- Department of Chemistry, University of Washington, Seattle, WA 98197-1700
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Francesco A Aprile
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98197-1700
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
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Chen Y, Zubovic L, Yang F, Godin K, Pavelitz T, Castellanos J, Macchi P, Varani G. Rbfox proteins regulate microRNA biogenesis by sequence-specific binding to their precursors and target downstream Dicer. Nucleic Acids Res 2016; 44:4381-95. [PMID: 27001519 PMCID: PMC4872098 DOI: 10.1093/nar/gkw177] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/26/2016] [Accepted: 03/07/2016] [Indexed: 12/26/2022] Open
Abstract
Rbfox proteins regulate tissue-specific splicing by targeting a conserved GCAUG sequence within pre-mRNAs. We report here that sequence-specific binding of the conserved Rbfox RRM to miRNA precursors containing the same sequence motif in their terminal loops, including miR-20b and miR-107, suppresses their nuclear processing. The structure of the complex between precursor miR-20b and Rbfox RRM shows the molecular basis for recognition, and reveals changes in the stem-loop upon protein binding. In mammalian cells, Rbfox2 downregulates mature miR-20b and miR-107 levels and increases the expression of their downstream targets PTEN and Dicer, respectively, suggesting that Rbfox2 indirectly regulates many more cellular miRNAs. Thus, some of the widespread cellular functions of Rbfox2 protein are attributable to regulation of miRNA biogenesis, and might include the mis-regulation of miR-20b and miR-107 in cancer and neurodegeneration.
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Affiliation(s)
- Yu Chen
- Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
| | - Lorena Zubovic
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Fan Yang
- Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
| | - Katherine Godin
- Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
| | - Tom Pavelitz
- Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
| | - Javier Castellanos
- Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
| | - Paolo Macchi
- Department of Chemistry, University of Washington, Seattle, WA 98195-1700, USA
| | - Gabriele Varani
- Center for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento (TN), Italy
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39
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Affiliation(s)
- Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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40
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Bottini A, De SK, Wu B, Tang C, Varani G, Pellecchia M. Targeting Influenza A Virus RNA Promoter. Chem Biol Drug Des 2015; 86:663-73. [PMID: 25676805 DOI: 10.1111/cbdd.12534] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/08/2015] [Accepted: 01/23/2015] [Indexed: 12/24/2022]
Abstract
The emergence of drug-resistant strains of influenza virus makes exploring new classes of inhibitors that target universally conserved viral targets a highly important goal. The influenza A viral genome is made up of eight single-stranded RNA-negative segments. The RNA promoter, consisting of the conserved sequences at the 3' and 5' end of each RNA genomic segment, is universally conserved among influenza A virus strains and in all segments. Previously, we reported on the identification and NMR structure of DPQ (6,7-dimethoxy-2-(1-piperazinyl)-4-quinazolinamine) (compound 1) in complex with the RNA promoter. Here, we report on additional screening and SAR studies with compound 1, including ex vivo anti-influenza activity assays, resulted in improved cellular activity against influenza A virus in the micromolar range.
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Affiliation(s)
- Angel Bottini
- Infectious and Inflammatory Disease Center and Cancer Center, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA.,Sanford Burnham Graduate School of Biomedical Sciences, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Surya K De
- Infectious and Inflammatory Disease Center and Cancer Center, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Bainan Wu
- Infectious and Inflammatory Disease Center and Cancer Center, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Changyan Tang
- Department of Chemistry, University of Washington, Seattle, WA, 98195-1700, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA, 98195-1700, USA
| | - Maurizio Pellecchia
- Infectious and Inflammatory Disease Center and Cancer Center, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
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41
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Shortridge MD, Varani G. Structure based approaches for targeting non-coding RNAs with small molecules. Curr Opin Struct Biol 2015; 30:79-88. [PMID: 25687935 PMCID: PMC4416997 DOI: 10.1016/j.sbi.2015.01.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/19/2015] [Accepted: 01/28/2015] [Indexed: 12/22/2022]
Abstract
The increasing appreciation of the central role of non-coding RNAs (miRNAs and long non-coding RNAs) in chronic and degenerative human disease makes them attractive therapeutic targets. This would not be unprecedented: the bacterial ribosomal RNA is a mainstay for antibacterial treatment, while the conservation and functional importance of viral RNA regulatory elements has long suggested they would constitute attractive targets for new antivirals. Oligonucleotide-based chemistry has obvious appeals but also considerable pharmacological limitations that are yet to be addressed satisfactorily. Recent studies identifying small molecules targeting non-coding RNAs may provide an alternative approach to oligonucleotide methods. Here we review recent work investigating new structural and chemical principles for targeting RNA with small molecules.
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Affiliation(s)
- Matthew D Shortridge
- Department of Chemistry, University of Washington, Seattle, Box 351700, Seattle 98195, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Box 351700, Seattle 98195, USA.
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42
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Smith-Kinnaman WR, Berna MJ, Hunter GO, True JD, Hsu P, Cabello GI, Fox MJ, Varani G, Mosley AL. The interactome of the atypical phosphatase Rtr1 in Saccharomyces cerevisiae. Mol Biosyst 2015; 10:1730-41. [PMID: 24671508 DOI: 10.1039/c4mb00109e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The phosphatase Rtr1 has been implicated in dephosphorylation of the RNA Polymerase II (RNAPII) C-terminal domain (CTD) during transcription elongation and in regulation of nuclear import of RNAPII. Although it has been shown that Rtr1 interacts with RNAPII in yeast and humans, the specific mechanisms that underlie Rtr1 recruitment to RNAPII have not been elucidated. To address this, we have performed an in-depth proteomic analysis of Rtr1 interacting proteins in yeast. Our studies revealed that hyperphosphorylated RNAPII is the primary interacting partner for Rtr1. To extend these findings, we performed quantitative proteomic analyses of Rtr1 interactions in yeast strains deleted for CTK1, the gene encoding the catalytic subunit of the CTD kinase I (CTDK-I) complex. Interestingly, we found that the interaction between Rtr1 and RNAPII is decreased in ctk1Δ strains. We hypothesize that serine-2 CTD phosphorylation is required for Rtr1 recruitment to RNAPII during transcription elongation.
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Affiliation(s)
- Whitney R Smith-Kinnaman
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.
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Musiani F, Rossetti G, Capece L, Gerger TM, Micheletti C, Varani G, Carloni P. Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA. J Am Chem Soc 2014; 136:15631-7. [PMID: 25313638 PMCID: PMC5521259 DOI: 10.1021/ja507812v] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The HIV-1 Tat protein and several small molecules bind to HIV-1 transactivation responsive RNA (TAR) by selecting sparsely populated but pre-existing conformations. Thus, a complete characterization of TAR conformational ensemble and dynamics is crucial to understand this paradigmatic system and could facilitate the discovery of new antivirals targeting this essential regulatory element. We show here that molecular dynamics simulations can be effectively used toward this goal by bridging the gap between functionally relevant time scales that are inaccessible to current experimental techniques. Specifically, we have performed several independent microsecond long molecular simulations of TAR based on one of the most advanced force fields available for RNA, the parmbsc0 AMBER. Our simulations are first validated against available experimental data, yielding an excellent agreement with measured residual dipolar couplings and order parameter S(2). This contrast with previous molecular dynamics simulations (Salmon et al., J. Am. Chem. Soc. 2013 135, 5457-5466) based on the CHARMM36 force field, which could achieve only modest accord with the experimental RDC values. Next, we direct the computation toward characterizing the internal dynamics of TAR over the microsecond time scale. We show that the conformational fluctuations observed over this previously elusive time scale have a strong functionally oriented character in that they are primed to sustain and assist ligand binding.
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Affiliation(s)
- Francesco Musiani
- Scuola Internazionale Superiore di Studi Avanzati (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
- Institute of Neuroscience and Medicine INM-9 and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Giulia Rossetti
- Institute of Neuroscience and Medicine INM-9 and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Luciana Capece
- International Centre for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Thomas Martin Gerger
- Institute of Neuroscience and Medicine INM-9 and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Gabriele Varani
- Department of Chemistry and Department of Biochemistry, University of Washington, Seattle, 98195 WA, USA
| | - Paolo Carloni
- Institute of Neuroscience and Medicine INM-9 and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
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Hsu PL, Yang F, Smith-Kinnaman W, Yang W, Song JE, Mosley AL, Varani G. Rtr1 is a dual specificity phosphatase that dephosphorylates Tyr1 and Ser5 on the RNA polymerase II CTD. J Mol Biol 2014; 426:2970-81. [PMID: 24951832 PMCID: PMC4119023 DOI: 10.1016/j.jmb.2014.06.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 06/11/2014] [Accepted: 06/12/2014] [Indexed: 01/07/2023]
Abstract
The phosphorylation state of heptapeptide repeats within the C-terminal domain (CTD) of the largest subunit of RNA polymerase II (PolII) controls the transcription cycle and is maintained by the competing action of kinases and phosphatases. Rtr1 was recently proposed to be the enzyme responsible for the transition of PolII into the elongation and termination phases of transcription by removing the phosphate marker on serine 5, but this attribution was questioned by the apparent lack of enzymatic activity. Here we demonstrate that Rtr1 is a phosphatase of new structure that is auto-inhibited by its own C-terminus. The enzymatic activity of the protein in vitro is functionally important in vivo as well: a single amino acid mutation that reduces activity leads to the same phenotype in vivo as deletion of the protein-coding gene from yeast. Surprisingly, Rtr1 dephosphorylates not only serine 5 on the CTD but also the newly described anti-termination tyrosine 1 marker, supporting the hypothesis that Rtr1 and its homologs promote the transition from transcription to termination.
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Affiliation(s)
- Peter L. Hsu
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Fan Yang
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Whitney Smith-Kinnaman
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Jae-Eun Song
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Amber L. Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington, USA,Corresponding author. , telephone (206) 543-7113
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Hopping G, Kellock J, Barnwal RP, Law P, Bryers J, Varani G, Caughey B, Daggett V. Designed α-sheet peptides inhibit amyloid formation by targeting toxic oligomers. eLife 2014; 3:e01681. [PMID: 25027691 PMCID: PMC4091096 DOI: 10.7554/elife.01681] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Previous studies suggest that the toxic soluble-oligomeric form of different amyloid proteins share a common backbone conformation, but the amorphous nature of this oligomer prevents its structural characterization by experiment. Based on molecular dynamics simulations we proposed that toxic intermediates of different amyloid proteins adopt a common, nonstandard secondary structure, called α-sheet. Here we report the experimental characterization of peptides designed to be complementary to the α-sheet conformation observed in the simulations. We demonstrate inhibition of aggregation in two different amyloid systems, β-amyloid peptide (Aβ) and transthyretin, by these designed α-sheet peptides. When immobilized the α-sheet designs preferentially bind species from solutions enriched in the toxic conformer compared with non-aggregated, nontoxic species or mature fibrils. The designs display characteristic spectroscopic signatures distinguishing them from conventional secondary structures, supporting α-sheet as a structure involved in the toxic oligomer stage of amyloid formation and paving the way for novel therapeutics and diagnostics. DOI:http://dx.doi.org/10.7554/eLife.01681.001 The build up of very thin fibres called amyloid fibrils is known to lead to more than 40 different human diseases, including Parkinson’s disease and rheumatoid arthritis. These diseases involve soluble proteins or peptides joining other proteins or peptides to form the fibrils, which are not soluble. However, the damage is done by the time the fibrils form because soluble intermediate structures formed by the proteins and peptides are toxic. The development of methods that can detect these toxic intermediate structures could lead to earlier interventions before significant damage. Amyloid fibrils are known to have a beta-sheet structure that is found in many protein systems. In 2004, based on computer simulations, researchers predicted that proteins and peptides that go on to form amyloid fibrils would pass through a related but less stable structure called an alpha-sheet, and that this structure would be toxic. Now Hopping et al., including some of the researchers involved in the 2004 work, have confirmed that the alpha-sheet structure is indeed involved in the formation of amyloid fibrils. To do this Hopping et al. designed peptides with alpha-sheet structures that could bind to the alpha-sheet structures predicted by their simulations. When these complementary designed peptides were added to a solution of peptide that causes Alzheimer’s Disease, or a protein that causes systemic amyloid disease, the designed peptides bound the toxic peptides or proteins and prevented the formation of fibrils. The results of Hopping et al. suggest that designed alpha-sheet compounds might be able to capture peptides and proteins that are implicated in a wide variety of amyloid diseases, independent of their composition and native structure, by targeting the intermediate alpha-sheet structure. Future challenges include showing that most proteins and peptides pass through this intermediate structure as they form fibrils, and improving the sensitivity of the binding in the hope of developing diagnostics for amyloid diseases. DOI:http://dx.doi.org/10.7554/eLife.01681.002
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Affiliation(s)
- Gene Hopping
- Department of Bioengineering, University of Washington, Seattle, United States
| | - Jackson Kellock
- Department of Bioengineering, University of Washington, Seattle, United States
| | | | - Peter Law
- Department of Bioengineering, University of Washington, Seattle, United States
| | - James Bryers
- Department of Bioengineering, University of Washington, Seattle, United States
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, United States
| | - Byron Caughey
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, United States
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, United States
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Sperber H, Beem A, Shannon S, Jones R, Banik P, Chen Y, Ku S, Varani G, Yao S, Ruohola-Baker H. miRNA sensitivity to Drosha levels correlates with pre-miRNA secondary structure. RNA 2014; 20:621-631. [PMID: 24677349 PMCID: PMC3988564 DOI: 10.1261/rna.043943.113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 01/25/2014] [Indexed: 05/29/2023]
Abstract
microRNAs (miRNAs) are crucial for cellular development and homeostasis. In order to better understand regulation of miRNA biosynthesis, we studied cleavage of primary miRNAs by Drosha. While Drosha knockdown triggers an expected decrease of many mature miRNAs in human embryonic stem cells (hESC), a subset of miRNAs are not reduced. Statistical analysis of miRNA secondary structure and fold change of expression in response to Drosha knockdown showed that absence of mismatches in the central region of the hairpin, 5 and 9-12 nt from the Drosha cutting site conferred decreased sensitivity to Drosha knockdown. This suggests that, when limiting, Drosha processes miRNAs without mismatches more efficiently than mismatched miRNAs. This is important because Drosha expression changes over cellular development and the fold change of expression for miRNAs with mismatches in the central region correlates with Drosha levels. To examine the biochemical relationship directly, we overexpressed structural variants of miRNA-145, miRNA-137, miRNA-9, and miRNA-200b in HeLa cells with and without Drosha knockdown; for these miRNAs, elimination of mismatches in the central region increased, and addition of mismatches decreased their expression in an in vitro assay and in cells with low Drosha expression. Change in Drosha expression can be a biologically relevant mechanism by which eukaryotic cells control miRNA profiles. This phenomenon may explain the impact of point mutations outside the seed region of certain miRNAs.
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Affiliation(s)
- Henrik Sperber
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, UW Medicine at South Lake Union, Seattle, Washington 98109, USA
| | - Alan Beem
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, UW Medicine at South Lake Union, Seattle, Washington 98109, USA
- Department of Economics, University of Washington, Seattle, Washington 98195, USA
- Undergraduate Program in Neurobiology, University of Washington, Seattle, Washington 98195, USA
| | - Sandra Shannon
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, UW Medicine at South Lake Union, Seattle, Washington 98109, USA
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
| | - Ross Jones
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, UW Medicine at South Lake Union, Seattle, Washington 98109, USA
| | - Pratyusha Banik
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, UW Medicine at South Lake Union, Seattle, Washington 98109, USA
| | - Yu Chen
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Sherman Ku
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Shuyuan Yao
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, UW Medicine at South Lake Union, Seattle, Washington 98109, USA
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
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Emani PS, Bardaro MF, Huang W, Aragon S, Varani G, Drobny GP. Elucidating molecular motion through structural and dynamic filters of energy-minimized conformer ensembles. J Phys Chem B 2014; 118:1726-42. [PMID: 24479561 PMCID: PMC3983377 DOI: 10.1021/jp409386t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Complex RNA structures are constructed
from helical segments connected
by flexible loops that move spontaneously and in response to binding
of small molecule ligands and proteins. Understanding the conformational
variability of RNA requires the characterization of the coupled time
evolution of interconnected flexible domains. To elucidate the collective
molecular motions and explore the conformational landscape of the
HIV-1 TAR RNA, we describe a new methodology that utilizes energy-minimized
structures generated by the program “Fragment Assembly of RNA
with Full-Atom Refinement (FARFAR)”. We apply structural filters
in the form of experimental residual dipolar couplings (RDCs) to select
a subset of discrete energy-minimized conformers and carry out principal
component analyses (PCA) to corroborate the choice of the filtered
subset. We use this subset of structures to calculate solution T1 and T1ρ relaxation times for 13C spins in multiple residues in different domains of the molecule
using two simulation protocols that we previously published. We match
the experimental T1 times to within 2% and the T1ρ times to within less than 10% for helical residues. These results
introduce a protocol to construct viable dynamic trajectories for
RNA molecules that accord well with experimental NMR data and support
the notion that the motions of the helical portions of this small
RNA can be described by a relatively small number of discrete conformations
exchanging over time scales longer than 1 μs.
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Affiliation(s)
- Prashant S Emani
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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Lee MK, Bottini A, Kim M, Bardaro MF, Zhang Z, Pellecchia M, Choi BS, Varani G. Correction: A novel small-molecule binds to the influenza A virus RNA promoter and inhibits viral replication. Chem Commun (Camb) 2014. [DOI: 10.1039/c4cc90361g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lee MK, Bottini A, Kim M, Bardaro MF, Zhang Z, Pellecchia M, Choi BS, Varani G. A novel small-molecule binds to the influenza A virus RNA promoter and inhibits viral replication. Chem Commun (Camb) 2013; 50:368-70. [PMID: 24247110 DOI: 10.1039/c3cc46973e] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Through screening by NMR spectroscopy, we discovered a novel scaffold (DPQ: 6,7-dimethoxy-2-(1-piperazinyl)-4-quinazolinamine) that binds specifically to the influenza A virus RNA promoter. The solution structure of the RNA-DPQ complex reported here demonstrates that the internal loop is the binding site of DPQ. The scaffold exhibits antiviral activity against influenza viruses.
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Affiliation(s)
- Mi-Kyung Lee
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195, USA.
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Abstract
RNA-binding proteins play essential roles in the regulation of gene expression. Many have modular structures and combine relatively few common domains in various arrangements to recognize RNA sequences and/or structures. Recent progress in engineering the specificity of the PUF class RNA-binding proteins has shown that RNA-binding domains may be combined with various effector or functional domains to regulate the metabolism of targeted RNAs. Designer RNA-binding proteins with tailored sequence specificity will provide valuable tools for biochemical research as well as potential therapeutic applications. In this review, we discuss the suitability of various RNA-binding domains for engineering RNA-binding specificity, based on the structural basis for their recognition. We also compare various protein engineering and design methods applied to RNA-binding proteins, and discuss future applications of these proteins.
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Affiliation(s)
- Yu Chen
- Department of Biochemistry, University of Washington, Seattle, WA 98195-1700, USA.
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