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Liang Z, Tan K, Yin Li C, Kuang Y. Self-feedback loop-containing synthetic mRNA switches for controlled microRNA sensing. Bioorg Chem 2024; 144:107081. [PMID: 38232686 DOI: 10.1016/j.bioorg.2023.107081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/18/2023] [Accepted: 12/28/2023] [Indexed: 01/19/2024]
Abstract
Synthetic mRNA switches are powerful cell fate manipulation tools that sense cellular input molecules to directly control protein expression at the translational level. The lack of available switch designs that can mimic the natural sophisticated protein regulation is a fundamental issue that limits the application of synthetic mRNA switches. Here we report a new set of synthetic mRNA switches by incorporating self-feedback loop machineries to dynamically control protein expression levels upon sensing cellular microRNAs. We redesigned the coding region of the switch to express output protein along with mRNA regulatory proteins. RNA-binding proteins (RBPs) and RBP-binding RNA motifs (aptamers) guide the regulatory proteins to act on their own mRNAs, enhancing or flattening the effect of microRNA sensing. Importantly, we demonstrated that the switches with the positive feedback feature can enlarge a high-or-low microRNA effect into a nearly all-or-none pattern, substantially boosting the use of synthetic mRNA switches as high-performance microRNA sensors or binary cell regulation tools. We believe these novel mRNA switch designs provide new strategies to construct complex mRNA-based genetic circuits for future molecular sensing and cell engineering.
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Affiliation(s)
- Zhenghua Liang
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region
| | - Kaixin Tan
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region
| | - Cheuk Yin Li
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region
| | - Yi Kuang
- Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region.
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2
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Procknow SS, Kozel BA. Emerging mechanisms of elastin transcriptional regulation. Am J Physiol Cell Physiol 2022; 323:C666-C677. [PMID: 35816641 PMCID: PMC9448287 DOI: 10.1152/ajpcell.00228.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/06/2022] [Accepted: 07/06/2022] [Indexed: 11/22/2022]
Abstract
Elastin provides recoil to tissues that stretch such as the lung, blood vessels, and skin. It is deposited in a brief window starting in the prenatal period and extending to adolescence in vertebrates, and then slowly turns over. Elastin insufficiency is seen in conditions such as Williams-Beuren syndrome and elastin-related supravalvar aortic stenosis, which are associated with a range of vascular and connective tissue manifestations. Regulation of the elastin (ELN) gene occurs at multiple levels including promoter activation/inhibition, mRNA stability, interaction with microRNAs, and alternative splicing. However, these mechanisms are incompletely understood. Better understanding of the processes controlling ELN gene expression may improve medicine's ability to intervene in these rare conditions, as well as to replace age-associated losses by re-initiating elastin production. This review describes what is known about the ELN gene promoter structure, transcriptional regulation by cytokines and transcription factors, and posttranscriptional regulation via mRNA stability and micro-RNA and highlights new approaches that may influence regenerative medicine.
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Affiliation(s)
- Sara S Procknow
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Beth A Kozel
- Translational Vascular Medicine Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
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3
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Baud A, Derbis M, Tutak K, Sobczak K. Partners in crime: Proteins implicated in
RNA
repeat expansion diseases. WIRES RNA 2022; 13:e1709. [PMID: 35229468 PMCID: PMC9539487 DOI: 10.1002/wrna.1709] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/07/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Anna Baud
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Magdalena Derbis
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Katarzyna Tutak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
| | - Krzysztof Sobczak
- Department of Gene Expression Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University Poznan Poland
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4
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Estevez M, Li R, Paul B, Daneshvar K, Mullen AC, Romerio F, Addepalli B. Identification and mapping of post-transcriptional modifications on the HIV-1 antisense transcript Ast in human cells. RNA (NEW YORK, N.Y.) 2022; 28:697-710. [PMID: 35168996 PMCID: PMC9014878 DOI: 10.1261/rna.079043.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/29/2022] [Indexed: 05/03/2023]
Abstract
The human immunodeficiency virus type 1 (HIV-1) encodes multiple RNA molecules. Transcripts that originate from the proviral 5' long terminal repeat (LTR) function as messenger RNAs for the expression of 16 different mature viral proteins. In addition, HIV-1 expresses an antisense transcript (Ast) from the 3'LTR, which has both protein-coding and noncoding properties. While the mechanisms that regulate the coding and noncoding activities of Ast remain unknown, post-transcriptional modifications are known to influence RNA stability, interaction with protein partners, and translation capacity. Here, we report the nucleoside modification profile of Ast obtained through liquid chromatography coupled with mass spectrometry (LC-MS) analysis. The epitranscriptome includes a limited set of modified nucleosides but predominantly ribose methylations. A number of these modifications were mapped to specific positions of the sequence through RNA modification mapping procedures. The presence of modifications on Ast is consistent with the RNA-modifying enzymes interacting with Ast The identification and mapping of Ast post-transcriptional modifications is expected to elucidate the mechanisms through which this versatile molecule can carry out diverse activities in different cell compartments. Manipulation of post-transcriptional modifications on the Ast RNA may have therapeutic implications.
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Affiliation(s)
- Mariana Estevez
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, USA
| | - Rui Li
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Biplab Paul
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Kaveh Daneshvar
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Alan C Mullen
- Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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5
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Uppala JK, Ghosh C, Sabat G, Dey M. Pull-down of Biotinylated RNA and Associated Proteins. Bio Protoc 2022; 12:e4331. [PMID: 35340298 PMCID: PMC8899547 DOI: 10.21769/bioprotoc.4331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 10/28/2021] [Accepted: 01/05/2022] [Indexed: 09/23/2023] Open
Abstract
Mapping networks of RNA-protein interactions in cells is essential for understanding the inner workings of many biological processes, including RNA processing, trafficking, and translation. Current in vivo methods for studying protein-RNA interactions rely mostly on purification of poly(A) transcripts, which represent only ~2-3% of total RNAs (Figure 1). Alternate robust methods for tagging RNA molecules with an RNA aptamer (e.g., MS2-, U1A- and biotin-RNA aptamer) and capturing the RNA-protein complex by the respective aptamer-specific partner are not extensively studied. Here, we describe a protocol (Figure 2) in which a biotin-RNA aptamer, referred to as the RNA mimic of biotin (RMB), was conjugated separately to two small RNA secondary structures that contribute to trafficking and translating HAC1 mRNA in the budding yeast Saccharomyces cerevisiae. The RMB-tagged RNA was expressed in yeast cells from a constitutive promoter. The biotinylated RNA bound to proteins was pulled down from the cell lysate by streptavidin agarose beads. RNA was detected by RT-PCR (Figure 3) and associated proteins by mass spectrometry (Figure 4). Our findings show that an RNA aptamer tag to RNA molecule is an effective method to explore the functional roles of RNA-protein networks in vivo.
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Affiliation(s)
- Jagadeesh K. Uppala
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, 3209 N Maryland Ave, WI-53211, USA
| | - Chandrima Ghosh
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, 3209 N Maryland Ave, WI-53211, USA
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Madhusudan Dey
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, 3209 N Maryland Ave, WI-53211, USA
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6
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Malik I, Tseng Y, Wright SE, Zheng K, Ramaiyer P, Green KM, Todd PK. SRSF protein kinase 1 modulates RAN translation and suppresses CGG repeat toxicity. EMBO Mol Med 2021; 13:e14163. [PMID: 34542927 PMCID: PMC8573603 DOI: 10.15252/emmm.202114163] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 11/20/2022] Open
Abstract
Transcribed CGG repeat expansions cause neurodegeneration in Fragile X-associated tremor/ataxia syndrome (FXTAS). CGG repeat RNAs sequester RNA-binding proteins (RBPs) into nuclear foci and undergo repeat-associated non-AUG (RAN) translation into toxic peptides. To identify proteins involved in these processes, we employed a CGG repeat RNA-tagging system to capture repeat-associated RBPs by mass spectrometry in mammalian cells. We identified several SR (serine/arginine-rich) proteins that interact selectively with CGG repeats basally and under cellular stress. These proteins modify toxicity in a Drosophila model of FXTAS. Pharmacologic inhibition of serine/arginine protein kinases (SRPKs), which alter SRSF protein phosphorylation, localization, and activity, directly inhibits RAN translation of CGG and GGGGCC repeats (associated with C9orf72 ALS/FTD) and triggers repeat RNA retention in the nucleus. Lowering SRPK expression suppressed toxicity in both FXTAS and C9orf72 ALS/FTD model flies, and SRPK inhibitors suppressed CGG repeat toxicity in rodent neurons. Together, these findings demonstrate roles for CGG repeat RNA binding proteins in RAN translation and repeat toxicity and support further evaluation of SRPK inhibitors in modulating RAN translation associated with repeat expansion disorders.
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Affiliation(s)
- Indranil Malik
- Department of NeurologyUniversity of MichiganAnn ArborMIUSA
| | - Yi‐Ju Tseng
- Department of NeurologyUniversity of MichiganAnn ArborMIUSA
- Cellular and Molecular Biology Graduate ProgramUniversity of MichiganAnn ArborMIUSA
| | - Shannon E Wright
- Department of NeurologyUniversity of MichiganAnn ArborMIUSA
- Neuroscience Graduate ProgramUniversity of MichiganAnn ArborMIUSA
| | - Kristina Zheng
- Department of NeurologyUniversity of MichiganAnn ArborMIUSA
| | | | - Katelyn M Green
- Department of NeurologyUniversity of MichiganAnn ArborMIUSA
- Cellular and Molecular Biology Graduate ProgramUniversity of MichiganAnn ArborMIUSA
| | - Peter K Todd
- Department of NeurologyUniversity of MichiganAnn ArborMIUSA
- Ann Arbor Veterans Administration HealthcareAnn ArborMIUSA
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7
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Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochem Soc Trans 2021; 48:2399-2414. [PMID: 33196096 DOI: 10.1042/bst20190492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. The emerging theme from recent studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post-transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/post-transcriptional splicing are largely unknown, a few recent studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches.
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8
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Zhang Z, Liu T, Dong H, Li J, Sun H, Qian X, Qin W. An RNA tagging approach for system-wide RNA-binding proteome profiling and dynamics investigation upon transcription inhibition. Nucleic Acids Res 2021; 49:e65. [PMID: 33693821 PMCID: PMC8216453 DOI: 10.1093/nar/gkab156] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 02/17/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
RNA-protein interactions play key roles in epigenetic, transcriptional and posttranscriptional regulation. To reveal the regulatory mechanisms of these interactions, global investigation of RNA-binding proteins (RBPs) and monitor their changes under various physiological conditions are needed. Herein, we developed a psoralen probe (PP)-based method for RNA tagging and ribonucleic-protein complex (RNP) enrichment. Isolation of both coding and noncoding RNAs and mapping of 2986 RBPs including 782 unknown candidate RBPs from HeLa cells was achieved by PP enrichment, RNA-sequencing and mass spectrometry analysis. The dynamics study of RNPs by PP enrichment after the inhibition of RNA synthesis provides the first large-scale distribution profile of RBPs bound to RNAs with different decay rates. Furthermore, the remarkably greater decreases in the abundance of the RBPs obtained by PP-enrichment than by global proteome profiling suggest that PP enrichment after transcription inhibition offers a valuable way for large-scale evaluation of the candidate RBPs.
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Affiliation(s)
- Zheng Zhang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Tong Liu
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hangyan Dong
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jian Li
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Haofan Sun
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiaohong Qian
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China.,College of Basic Medicine, Anhui Medical University, Hefei 230032, China
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9
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Rosenblum SL, Lorenz DA, Garner AL. A live-cell assay for the detection of pre-microRNA-protein interactions. RSC Chem Biol 2021; 2:241-247. [PMID: 33817642 PMCID: PMC8006716 DOI: 10.1039/d0cb00055h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
Recent efforts in genome-wide sequencing and proteomics have revealed the fundamental roles that RNA-binding proteins (RBPs) play in the life cycle and function of coding and non-coding RNAs. While these methodologies provide a systems-level view of the networking of RNA and proteins, approaches to enable the cellular validation of discovered interactions are lacking. Leveraging the power of bioorthogonal chemistry- and split-luciferase-based assay technologies, we have devised a conceptually new assay for the live-cell detection of RNA-protein interactions (RPIs), RNA interaction with Protein-mediated Complementation Assay, or RiPCA. As proof-of-concept, we utilized the interaction of the pre-microRNA, pre-let-7, with its binding partner, Lin28. Using this system, we have demonstrated the selective detection of the pre-let-7-Lin28 RPI in both the cytoplasm and nucleus. Furthermore, we determined that this technology can be used to discern relative affinities for specific sequences as well as of individual RNA binding domains. Thus, RiPCA has the potential to serve as a useful tool in supporting the investigation of cellular RPIs.
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Affiliation(s)
- Sydney L Rosenblum
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , USA .
| | - Daniel A Lorenz
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , USA .
| | - Amanda L Garner
- Program in Chemical Biology , University of Michigan , 210 Washtenaw Avenue , Ann Arbor , Michigan 48109 , USA .
- Department of Medicinal Chemistry , College of Pharmacy , University of Michigan , 428 Church Street , Ann Arbor , Michigan 48109 , USA
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10
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RNA-protein interaction mapping via MS2- or Cas13-based APEX targeting. Proc Natl Acad Sci U S A 2020; 117:22068-22079. [PMID: 32839320 DOI: 10.1073/pnas.2006617117] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RNA-protein interactions underlie a wide range of cellular processes. Improved methods are needed to systematically map RNA-protein interactions in living cells in an unbiased manner. We used two approaches to target the engineered peroxidase APEX2 to specific cellular RNAs for RNA-centered proximity biotinylation of protein interaction partners. Both an MS2-MCP system and an engineered CRISPR-Cas13 system were used to deliver APEX2 to the human telomerase RNA hTR with high specificity. One-minute proximity biotinylation captured candidate binding partners for hTR, including more than a dozen proteins not previously linked to hTR. We validated the interaction between hTR and the N 6-methyladenosine (m6A) demethylase ALKBH5 and showed that ALKBH5 is able to erase the m6A modification on endogenous hTR. ALKBH5 also modulates telomerase complex assembly and activity. MS2- and Cas13-targeted APEX2 may facilitate the discovery of novel RNA-protein interactions in living cells.
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11
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Pouliquen DL, Boissard A, Coqueret O, Guette C. Biomarkers of tumor invasiveness in proteomics (Review). Int J Oncol 2020; 57:409-432. [PMID: 32468071 PMCID: PMC7307599 DOI: 10.3892/ijo.2020.5075] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022] Open
Abstract
Over the past two decades, quantitative proteomics has emerged as an important tool for deciphering the complex molecular events involved in cancers. The number of references involving studies on the cancer metastatic process has doubled since 2010, while the last 5 years have seen the development of novel technologies combining deep proteome coverage capabilities with quantitative consistency and accuracy. To highlight key findings within this huge amount of information, the present review identified a list of tumor invasive biomarkers based on both the literature and data collected on a biocollection of experimental cell lines, tumor models of increasing invasiveness and tumor samples from patients with colorectal or breast cancer. Crossing these different data sources led to 76 proteins of interest out of 1,245 mentioned in the literature. Information on these proteins can potentially be translated into clinical prospects, since they represent potential targets for the development and evaluation of innovative therapies, alone or in combination. Herein, a systematical review of the biology of each of these proteins, including their specific subcellular/extracellular or multiple localizations is presented. Finally, as an important advantage of quantitative proteomics is the ability to provide data on all these molecules simultaneously in cell pellets, body fluids or paraffin‑embedded sections of tumors/invaded tissues, the significance of some of their interconnections is discussed.
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Affiliation(s)
| | - Alice Boissard
- Paul Papin ICO Cancer Center, CRCINA, Inserm, Université d'Angers, F‑44000 Nantes, France
| | | | - Catherine Guette
- Paul Papin ICO Cancer Center, CRCINA, Inserm, Université d'Angers, F‑44000 Nantes, France
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12
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Aptamers Against Live Targets: Is In Vivo SELEX Finally Coming to the Edge? MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:192-204. [PMID: 32585627 PMCID: PMC7321788 DOI: 10.1016/j.omtn.2020.05.025] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/18/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022]
Abstract
Targeted therapeutics underwent a revolution with the entry of monoclonal antibodies in the medical toolkit. Oligonucleotide aptamers form another family of target agents that have been lagging behind in reaching the clinical arena in spite of their potential clinical translation. Some of the reasons for this might be related to the challenge in identifying aptamers with optimal in vivo specificity, and the nature of their pharmacokinetics. Aptamers usually show exquisite specificity, but they are also molecules that display dynamic structures subject to changing environments. Temperature, ion atmosphere, pH, and other variables are factors that could determine the affinity and specificity of aptamers. Thus, it is important to tune the aptamer selection process to the conditions in which you want your final aptamer to function; ideally, for in vivo applications, aptamers should be selected in an in vivo-like system or, ultimately, in a whole in vivo organism. In this review we recapitulate the implementations in systematic evolution of ligands by exponential enrichment (SELEX) to obtain aptamers with the best in vivo activity.
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13
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Zhao X, Li D, Yang F, Lian H, Wang J, Wang X, Fang E, Song H, Hu A, Guo Y, Liu Y, Li H, Chen Y, Huang K, Zheng L, Tong Q. Long Noncoding RNA NHEG1 Drives β-Catenin Transactivation and Neuroblastoma Progression through Interacting with DDX5. Mol Ther 2020; 28:946-962. [PMID: 31982037 DOI: 10.1016/j.ymthe.2019.12.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 12/18/2019] [Accepted: 12/27/2019] [Indexed: 12/11/2022] Open
Abstract
Recent studies suggest that long noncoding RNAs (lncRNAs) play essential roles in tumor progression. However, the functional roles and underlying mechanisms of lncRNAs in neuroblastoma (NB), the most common malignant solid tumor in pediatric population, still remain elusive. Herein, through integrating analysis of a public RNA sequencing dataset, neuroblastoma highly expressed 1 (NHEG1) was identified as a risk-associated lncRNA, contributing to an unfavorable outcome of NB. Depletion of NHEG1 led to facilitated differentiation and decreased growth and aggressiveness of NB cells. Mechanistically, NHEG1 bound to and stabilized DEAD-box helicase 5 (DDX5) protein through repressing proteasome-mediated degradation, resulting in β-catenin transactivation that altered target gene expression associated with NB progression. We further determined a lymphoid enhancer binding factor 1 (LEF1)/transcription factor 7-like 2 (TCF7L2)/NHEG1/DDX5/β-catenin axis with a positive feedback loop and demonstrated that NHEG1 harbored oncogenic properties via its interplay with DDX5. Administration of small interfering RNAs against NHEG1 or DDX5 reduced tumor growth and prolonged survival of nude mice bearing xenografts. High NHEG1 or DDX5 expression was associated with poor survival of NB patients. These results indicate that lncRNA NHEG1 exhibits oncogenic activity that affects NB progression via stabilizing the DDX5 protein, which might serve as a potential therapeutic target for NB.
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Affiliation(s)
- Xiang Zhao
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Dan Li
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Feng Yang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Heng Lian
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Jianqun Wang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Xiaojing Wang
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Erhu Fang
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Huajie Song
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Anpei Hu
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Yanhua Guo
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Yang Liu
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Hongjun Li
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Yajun Chen
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Kai Huang
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China
| | - Liduan Zheng
- Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China; Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China.
| | - Qiangsong Tong
- Department of Pediatric Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China; Clinical Center of Human Genomic Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan 430022, Hubei Province, P.R. China.
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14
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Zaucker A, Nagorska A, Kumari P, Hecker N, Wang Y, Huang S, Cooper L, Sivashanmugam L, VijayKumar S, Brosens J, Gorodkin J, Sampath K. Translational co-regulation of a ligand and inhibitor by a conserved RNA element. Nucleic Acids Res 2019; 46:104-119. [PMID: 29059375 PMCID: PMC5758872 DOI: 10.1093/nar/gkx938] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/03/2017] [Indexed: 12/20/2022] Open
Abstract
In many organisms, transcriptional and post-transcriptional regulation of components of pathways or processes has been reported. However, to date, there are few reports of translational co-regulation of multiple components of a developmental signaling pathway. Here, we show that an RNA element which we previously identified as a dorsal localization element (DLE) in the 3'UTR of zebrafish nodal-related1/squint (ndr1/sqt) ligand mRNA, is shared by the related ligand nodal-related2/cyclops (ndr2/cyc) and the nodal inhibitors, lefty1 (lft1) and lefty2 mRNAs. We investigated the activity of the DLEs through functional assays in live zebrafish embryos. The lft1 DLE localizes fluorescently labeled RNA similarly to the ndr1/sqt DLE. Similar to the ndr1/sqt 3'UTR, the lft1 and lft2 3'UTRs are bound by the RNA-binding protein (RBP) and translational repressor, Y-box binding protein 1 (Ybx1), whereas deletions in the DLE abolish binding to Ybx1. Analysis of zebrafish ybx1 mutants shows that Ybx1 represses lefty1 translation in embryos. CRISPR/Cas9-mediated inactivation of human YBX1 also results in human NODAL translational de-repression, suggesting broader conservation of the DLE RNA element/Ybx1 RBP module in regulation of Nodal signaling. Our findings demonstrate translational co-regulation of components of a signaling pathway by an RNA element conserved in both sequence and structure and an RBP, revealing a 'translational regulon'.
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Affiliation(s)
- Andreas Zaucker
- Cell & Developmental Biology Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Agnieszka Nagorska
- Cell & Developmental Biology Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Pooja Kumari
- Cell & Developmental Biology Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Nikolai Hecker
- Center for non-coding RNAs in Technology and Health, Department of Veterinary and Animal Sciences, Faculty for Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark
| | - Yin Wang
- Cell & Developmental Biology Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Sizhou Huang
- Cell & Developmental Biology Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Ledean Cooper
- Cell & Developmental Biology Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Lavanya Sivashanmugam
- Cell & Developmental Biology Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Shruthi VijayKumar
- Cell & Developmental Biology Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Jan Brosens
- Cell & Developmental Biology Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Jan Gorodkin
- Center for non-coding RNAs in Technology and Health, Department of Veterinary and Animal Sciences, Faculty for Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark
| | - Karuna Sampath
- Cell & Developmental Biology Unit, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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15
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Leitner A, Dorn G, Allain FHT. Combining Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) Spectroscopy for Integrative Structural Biology of Protein-RNA Complexes. Cold Spring Harb Perspect Biol 2019; 11:a032359. [PMID: 31262947 PMCID: PMC6601463 DOI: 10.1101/cshperspect.a032359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Deciphering complex RNA-protein interactions on a (near-)atomic level is a hurdle that hinders advancing our understanding of fundamental processes in RNA metabolism and RNA-based gene regulation. To overcome challenges associated with individual structure determination methods, structural information derived from complementary biophysical methods can be combined in integrative structural biology approaches. Here, we review recent advances in such hybrid structural approaches with a focus on combining mass spectrometric analysis of cross-linked protein-RNA complexes and nuclear magnetic resonance (NMR) spectroscopy.
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Affiliation(s)
- Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Georg Dorn
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Frédéric H-T Allain
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
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16
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Han Y, Branon TC, Martell JD, Boassa D, Shechner D, Ellisman MH, Ting A. Directed Evolution of Split APEX2 Peroxidase. ACS Chem Biol 2019; 14:619-635. [PMID: 30848125 PMCID: PMC6548188 DOI: 10.1021/acschembio.8b00919] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
APEX is an engineered peroxidase that catalyzes the oxidation of a wide range of substrates, facilitating its use in a variety of applications from subcellular staining for electron microscopy to proximity biotinylation for spatial proteomics and transcriptomics. To further advance the capabilities of APEX, we used directed evolution to engineer a split APEX tool (sAPEX). A total of 20 rounds of fluorescence activated cell sorting (FACS)-based selections from yeast-displayed fragment libraries, using 3 different surface display configurations, produced a 200-amino-acid N-terminal fragment (with 9 mutations relative to APEX2) called "AP" and a 50-amino-acid C-terminal fragment called "EX". AP and EX fragments were each inactive on their own but were reconstituted to give peroxidase activity when driven together by a molecular interaction. We demonstrate sAPEX reconstitution in the mammalian cytosol, on engineered RNA motifs within a non-coding RNA scaffold, and at mitochondria-endoplasmic reticulum contact sites.
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Affiliation(s)
- Yisu Han
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - Tess Caroline Branon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Jeffrey D. Martell
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, California, USA
| | - Daniela Boassa
- Department of Neuroscience, University of California San Diego, La Jolla, California, USA
| | - David Shechner
- Department of Pharmacology, University of Washington, Seattle, Washington, USA
| | - Mark H. Ellisman
- Department of Neuroscience, University of California San Diego, La Jolla, California, USA
| | - Alice Ting
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Genetics, Stanford University, Stanford, California, USA
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Chemistry, Stanford University, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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17
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Gemmill D, D'souza S, Meier-Stephenson V, Patel TR. Current approaches for RNA-labelling to identify RNA-binding proteins. Biochem Cell Biol 2019; 98:31-41. [PMID: 30931575 DOI: 10.1139/bcb-2019-0041] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
RNA is involved in all domains of life, playing critical roles in a host of gene expression processes, host-defense mechanisms, cell proliferation, and diseases. A critical component in many of these events is the ability for RNA to interact with proteins. Over the past few decades, our understanding of such RNA-protein interactions and their importance has driven the search and development of new techniques for the identification of RNA-binding proteins. In determining which proteins bind to the RNA of interest, it is often useful to use the approach where the RNA molecule is the "bait" and allow it to capture proteins from a lysate or other relevant solution. Here, we review a collection of methods for modifying RNA to capture RNA-binding proteins. These include small-molecule modification, the addition of aptamers, DNA-anchoring, and nucleotide substitution. With each, we provide examples of their application, as well as highlight their advantages and potential challenges.
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Affiliation(s)
- Darren Gemmill
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Simmone D'souza
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Vanessa Meier-Stephenson
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada.,Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Trushar R Patel
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada.,Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.,Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, AB T6G 2E1, Canada
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18
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Cao M, Zhao J, Hu G. Genome-wide methods for investigating long noncoding RNAs. Biomed Pharmacother 2019; 111:395-401. [PMID: 30594777 PMCID: PMC6401243 DOI: 10.1016/j.biopha.2018.12.078] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/27/2018] [Accepted: 12/17/2018] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are large RNA transcripts that do not code for proteins but exert their effects in the form of RNA. To date many thousands of lncRNAs have been identified, their molecular functions and mechanisms of action however are largely unknown. The development of high-throughput experimental technologies, such as ChIRP (Chromatin isolation by RNA purification), CHART (Capture Hybridization Analysis of RNA Targets), RAP (RNA antisense purification), RIP (RNA Immunoprecipitation), CLIP (cross-linking and immunoprecipitation) and RNA pull-down, has led to a rapid expansion of lncRNA research and resulted in many publicly-available databases. This review provides an overview of the current methodologies available for discovering and investigating functions of lncRNAs in various human diseases. A comparison and application of these methods are also included. Finally, this paper surveys current databases containing annotations, interactome networks and functions of lncRNAs. The appropriate use of these methods and databases will provide not only high-resolution functional features of lncRNAs, but also enhance our understanding of the underlying mechanisms by which lncRNAs regulate a variety of biological processes.
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Affiliation(s)
- Mei Cao
- Core Laboratory, School of Medicine, Sichuan Provincial People's Hospital Affiliated to University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
| | - Jian Zhao
- Key Laboratory of Biological Resource and Ecological Environment of Chinese Education Ministry, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610064, People's Republic of China.
| | - Guoku Hu
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA.
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19
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RNA-Based Therapy Utilizing Oculopharyngeal Muscular Dystrophy Transcript Knockdown and Replacement. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 15:12-25. [PMID: 30831428 PMCID: PMC6403420 DOI: 10.1016/j.omtn.2019.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 02/08/2019] [Accepted: 02/10/2019] [Indexed: 11/23/2022]
Abstract
Oculopharyngeal muscular dystrophy (OPMD) is caused by a small expansion of a short polyalanine (polyAla) tract in the poly(A)-binding protein nuclear 1 protein (PABPN1). Despite the monogenic nature of OPMD, no treatment is currently available. Here we report an RNA replacement strategy that has therapeutic potential in cell and C. elegans OPMD models. We develop selective microRNAs (miRNAs) against PABPN1, and we report that miRNAs and our previously developed hammerhead ribozymes (hhRzs) are capable of reducing the expression of both the mRNA and protein levels of PABPN1 by as much as 90%. Since OPMD derives from a very small expansion of GCG within the polyAla tract, our hhRz and miRNA molecules cannot distinguish between the wild-type and mutant mRNAs of PABPN1. Therefore, we designed an optimized-codon wild-type PABPN1 (opt-PABPN1) that is resistant to cleavage by hhRzs and miRNAs. Co-expression of opt-PABPN1 with either our hhRzs or miRNAs restored the level of PABPN1, concomitantly with a reduction in expanded PABPN1-associated cell death in a stable C2C12 OPMD model. Interestingly, knockdown of the PABPN1 by selective hhRzs in the C. elegans OPMD model significantly improved the motility of the PABPN1-13Ala worms. Taken together, RNA replacement therapy represents an exciting approach for OPMD treatment.
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20
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Giambruno R, Mihailovich M, Bonaldi T. Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World. Front Mol Biosci 2018; 5:90. [PMID: 30467545 PMCID: PMC6236024 DOI: 10.3389/fmolb.2018.00090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/15/2018] [Indexed: 01/03/2023] Open
Abstract
The interaction between non-coding RNAs (ncRNAs) and proteins is crucial for the stability, localization and function of the different classes of ncRNAs. Although ncRNAs, when embedded in various ribonucleoprotein (RNP) complexes, control the fundamental processes of gene expression, their biological functions and mechanisms of action are still largely unexplored. Mass Spectrometry (MS)-based proteomics has emerged as powerful tool to study the ncRNA world: on the one hand, by identifying the proteins interacting with distinct ncRNAs; on the other hand, by measuring the impact of ncRNAs on global protein levels. Here, we will first provide a concise overview on the basic principles of MS-based proteomics for systematic protein identification and quantification; then, we will recapitulate the main approaches that have been implemented for the screening of ncRNA interactors and the dissection of ncRNA-protein complex composition. Finally, we will describe examples of various proteomics strategies developed to characterize the effect of ncRNAs on gene expression, with a focus on the systematic identification of microRNA (miRNA) targets.
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Affiliation(s)
| | | | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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21
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Conserved Pbp1/Ataxin-2 regulates retrotransposon activity and connects polyglutamine expansion-driven protein aggregation to lifespan-controlling rDNA repeats. Commun Biol 2018; 1:187. [PMID: 30417124 PMCID: PMC6218562 DOI: 10.1038/s42003-018-0187-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/09/2018] [Indexed: 12/17/2022] Open
Abstract
Ribosomal DNA (rDNA) repeat instability and protein aggregation are thought to be two major and independent drivers of cellular aging. Pbp1, the yeast ortholog of human ATXN2, maintains rDNA repeat stability and lifespan via suppression of RNA-DNA hybrids. ATXN2 polyglutamine expansion drives neurodegeneration causing spinocerebellar ataxia type 2 and promoting amyotrophic lateral sclerosis. Here, molecular characterization of Pbp1 revealed that its knockout or subjection to disease-modeling polyQ expansion represses Ty1 (Transposons of Yeast) retrotransposons by respectively promoting Trf4-depedendent RNA turnover and Ty1 Gag protein aggregation. This aggregation, but not its impact on retrotransposition, compromises rDNA repeat stability and shortens lifespan by hyper-activating Trf4-dependent turnover of intergenic ncRNA within the repeats. We uncover a function for the conserved Pbp1/ATXN2 proteins in the promotion of retrotransposition, create and describe powerful yeast genetic models of ATXN2-linked neurodegenerative diseases, and connect the major aging mechanisms of rDNA instability and protein aggregation.
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22
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Huang R, Han M, Meng L, Chen X. Capture and Identification of RNA-binding Proteins by Using Click Chemistry-assisted RNA-interactome Capture (CARIC) Strategy. J Vis Exp 2018. [PMID: 30394395 DOI: 10.3791/58580] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A comprehensive identification of RNA-binding proteins (RBPs) is key to understanding the posttranscriptional regulatory network in cells. A widely used strategy for RBP capture exploits the polyadenylation [poly(A)] of target RNAs, which mostly occurs on eukaryotic mature mRNAs, leaving most binding proteins of non-poly(A) RNAs unidentified. Here we describe the detailed procedures of a recently reported method termed click chemistry-assisted RNA-interactome capture (CARIC), which enables the transcriptome-wide capture of both poly(A) and non-poly(A) RBPs by combining the metabolic labeling of RNAs, in vivo UV cross-linking, and bioorthogonal tagging.
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Affiliation(s)
- Rongbing Huang
- College of Chemistry and Molecular Engineering, Peking University; Beijing National Laboratory for Molecular Sciences, Peking University
| | - Mengting Han
- College of Chemistry and Molecular Engineering, Peking University; Beijing National Laboratory for Molecular Sciences, Peking University
| | - Liying Meng
- College of Chemistry and Molecular Engineering, Peking University; Peking-Tsinghua Center for Life Sciences, Peking University
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University; Beijing National Laboratory for Molecular Sciences, Peking University; Peking-Tsinghua Center for Life Sciences, Peking University; Synthetic and Functional Biomolecules Center, Peking University; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University;
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23
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Transcriptome-wide discovery of coding and noncoding RNA-binding proteins. Proc Natl Acad Sci U S A 2018; 115:E3879-E3887. [PMID: 29636419 DOI: 10.1073/pnas.1718406115] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Transcriptome-wide identification of RNA-binding proteins (RBPs) is a prerequisite for understanding the posttranscriptional gene regulation networks. However, proteomic profiling of RBPs has been mostly limited to polyadenylated mRNA-binding proteins, leaving RBPs on nonpoly(A) RNAs, including most noncoding RNAs (ncRNAs) and pre-mRNAs, largely undiscovered. Here we present a click chemistry-assisted RNA interactome capture (CARIC) strategy, which enables unbiased identification of RBPs, independent of the polyadenylation state of RNAs. CARIC combines metabolic labeling of RNAs with an alkynyl uridine analog and in vivo RNA-protein photocross-linking, followed by click reaction with azide-biotin, affinity enrichment, and proteomic analysis. Applying CARIC, we identified 597 RBPs in HeLa cells, including 130 previously unknown RBPs. These newly discovered RBPs can likely bind ncRNAs, thus uncovering potential involvement of ncRNAs in processes previously unknown to be ncRNA-related, such as proteasome function and intermediary metabolism. The CARIC strategy should be broadly applicable across various organisms to complete the census of RBPs.
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24
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Stastna M, Gottlieb RA, Van Eyk JE. Exploring ribosome composition and newly synthesized proteins through proteomics and potential biomedical applications. Expert Rev Proteomics 2017; 14:529-543. [PMID: 28532181 DOI: 10.1080/14789450.2017.1333424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Protein synthesis is the outcome of tightly regulated gene expression which is responsive to a variety of conditions. Efforts are ongoing to monitor individual stages of protein synthesis to ensure maximum efficiency and accuracy. Due to post-transcriptional regulation mechanisms, the correlation between translatome and proteome is higher than between transcriptome and proteome. However, the most accurate approach to assess the key modulators and final protein expression is directly by using proteomics. Areas covered: This review covers various proteomic strategies that were used to better understand post-transcriptional regulation, specifically during and early after translation. The methods that identify both regulatory proteins associated with translational components and newly synthesized proteins are discussed. Expert commentary: Emerging proteomic approaches make it possible to monitor protein dynamics in cells, tissues and whole animals. The ability to detect alteration in protein abundance soon after their synthesis enables earlier recognition of disease causing factors and candidates to prevent/rectify disease phenotype.
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Affiliation(s)
- Miroslava Stastna
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,c Institute of Analytical Chemistry of the Czech Academy of Sciences, v. v. i ., Brno , Czech Republic
| | - Roberta A Gottlieb
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Jennifer E Van Eyk
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
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25
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Morriss GR, Cooper TA. Protein sequestration as a normal function of long noncoding RNAs and a pathogenic mechanism of RNAs containing nucleotide repeat expansions. Hum Genet 2017; 136:1247-1263. [PMID: 28484853 DOI: 10.1007/s00439-017-1807-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 04/28/2017] [Indexed: 12/12/2022]
Abstract
An emerging class of long noncoding RNAs (lncRNAs) function as decoy molecules that bind and sequester proteins thereby inhibiting their normal functions. Titration of proteins by lncRNAs has wide-ranging effects affecting nearly all steps in gene expression. While decoy lncRNAs play a role in normal physiology, RNAs expressed from alleles containing nucleotide repeat expansions can be pathogenic due to protein sequestration resulting in disruption of normal functions. This review focuses on commonalities between decoy lncRNAs that regulate gene expression by competitive inhibition of protein function through sequestration and specific examples of nucleotide repeat expansion disorders mediated by toxic RNA that sequesters RNA-binding proteins and impedes their normal functions. Understanding how noncoding RNAs compete with various RNA and DNA molecules for binding of regulatory proteins will provide insight into how similar mechanisms contribute to disease pathogenesis.
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Affiliation(s)
- Ginny R Morriss
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Thomas A Cooper
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA.
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26
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Ciesiolka A, Jazurek M, Drazkowska K, Krzyzosiak WJ. Structural Characteristics of Simple RNA Repeats Associated with Disease and their Deleterious Protein Interactions. Front Cell Neurosci 2017; 11:97. [PMID: 28442996 PMCID: PMC5387085 DOI: 10.3389/fncel.2017.00097] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/21/2017] [Indexed: 12/14/2022] Open
Abstract
Short Tandem Repeats (STRs) are frequent entities in many transcripts, however, in some cases, pathological events occur when a critical repeat length is reached. This phenomenon is observed in various neurological disorders, such as myotonic dystrophy type 1 (DM1), fragile X-associated tremor/ataxia syndrome, C9orf72-related amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), and polyglutamine diseases, such as Huntington's disease (HD) and spinocerebellar ataxias (SCA). The pathological effects of these repeats are triggered by mutant RNA transcripts and/or encoded mutant proteins, which depend on the localization of the expanded repeats in non-coding or coding regions. A growing body of recent evidence revealed that the RNA structures formed by these mutant RNA repeat tracts exhibit toxic effects on cells. Therefore, in this review article, we present existing knowledge on the structural aspects of different RNA repeat tracts as revealed mainly using well-established biochemical and biophysical methods. Furthermore, in several cases, it was shown that these expanded RNA structures are potent traps for a variety of RNA-binding proteins and that the sequestration of these proteins from their normal intracellular environment causes alternative splicing aberration, inhibition of nuclear transport and export, or alteration of a microRNA biogenesis pathway. Therefore, in this review article, we also present the most studied examples of abnormal interactions that occur between mutant RNAs and their associated proteins.
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Affiliation(s)
- Adam Ciesiolka
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Magdalena Jazurek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Karolina Drazkowska
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
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27
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Urbanek MO, Fiszer A, Krzyzosiak WJ. Reduction of Huntington's Disease RNA Foci by CAG Repeat-Targeting Reagents. Front Cell Neurosci 2017; 11:82. [PMID: 28400719 PMCID: PMC5368221 DOI: 10.3389/fncel.2017.00082] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/09/2017] [Indexed: 12/14/2022] Open
Abstract
In several human polyglutamine diseases caused by expansions of CAG repeats in the coding sequence of single genes, mutant transcripts are detained in nuclear RNA foci. In polyglutamine disorders, unlike other repeat-associated diseases, both RNA and proteins exert pathogenic effects; therefore, decreases of both RNA and protein toxicity need to be addressed in proposed treatments. A variety of oligonucleotide-based therapeutic approaches have been developed for polyglutamine diseases, but concomitant assays for RNA foci reduction are lacking. Here, we show that various types of oligonucleotide-based reagents affect RNA foci number in Huntington’s disease cells. We analyzed the effects of reagents targeting either CAG repeat tracts or specific HTT sequences in fibroblasts derived from patients. We tested reagents that either acted as translation blockers or triggered mRNA degradation via the RNA interference pathway or RNase H activation. We also analyzed the effect of chemical modifications of CAG repeat-targeting siRNAs on their efficiency in the foci decline. Our results suggest that the decrease of RNA foci number may be considered as a readout of treatment outcomes for oligonucleotide reagents.
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Affiliation(s)
- Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan, Poland
| | - Agnieszka Fiszer
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry Polish Academy of Sciences Poznan, Poland
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28
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Mihailovic MK, Chen A, Gonzalez-Rivera JC, Contreras LM. Defective Ribonucleoproteins, Mistakes in RNA Processing, and Diseases. Biochemistry 2017; 56:1367-1382. [PMID: 28206738 DOI: 10.1021/acs.biochem.6b01134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ribonucleoproteins (RNPs) are vital to many cellular events. To this end, many neurodegenerative diseases and cancers have been linked to RNP malfunction, particularly as this relates to defective processing of cellular RNA. The connection of RNPs and diseases has also propagated a shift of focus onto RNA targeting from traditional protein targeting treatments. However, therapeutic development in this area has been limited by incomplete molecular insight into the specific contributions of RNPs to disease. This review outlines the role of several RNPs in diseases, focusing on molecular defects in processes that affect proper RNA handling in the cell. This work also evaluates the contributions of recently developed methods to understanding RNP association and function. We review progress in this area by focusing on molecular malfunctions of RNPs associated with the onset and progression of several neurodegenerative diseases and cancer and conclude with a brief discussion of RNA-based therapeutic efforts.
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Affiliation(s)
- Mia K Mihailovic
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Angela Chen
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Juan C Gonzalez-Rivera
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
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