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Ying B, Kawabe Y, Zheng F, Amamoto Y, Kamihira M. High-Level Production of scFv-Fc Antibody Using an Artificial Promoter System with Transcriptional Positive Feedback Loop of Transactivator in CHO Cells. Cells 2023; 12:2638. [PMID: 37998372 PMCID: PMC10670205 DOI: 10.3390/cells12222638] [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: 10/17/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
With the increasing demand for therapeutic antibodies, CHO cells have become the de facto standard as producer host cells for biopharmaceutical production. High production yields are required for antibody production, and developing a high-titer production system is increasingly crucial. This study was established to develop a high-production system using a synthetic biology approach by designing a gene expression system based on an artificial transcription factor that can strongly induce the high expression of target genes in CHO cells. To demonstrate the functionality of this artificial gene expression system and its ability to induce the high expression of target genes in CHO cells, a model antibody (scFv-Fc) was produced using this system. Excellent results were obtained with the plate scale, and when attempting continuous production in semi-continuous cultures using bioreactor tubes with high-cell-density suspension culture using a serum-free medium, high-titer antibody production at the gram-per-liter level was achieved. Shifting the culture temperature to a low temperature of 33 °C achieved scFv-Fc concentrations of up to 5.5 g/L with a specific production rate of 262 pg/(cell∙day). This artificial gene expression system should be a powerful tool for CHO cell engineering aimed at constructing high-yield production systems.
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Affiliation(s)
| | | | | | | | - Masamichi Kamihira
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; (B.Y.); (Y.K.); (F.Z.); (Y.A.)
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Joly-Smith E, Wang ZJ, Hilfinger A. Inferring gene regulation dynamics from static snapshots of gene expression variability. Phys Rev E 2021; 104:044406. [PMID: 34781497 DOI: 10.1103/physreve.104.044406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 08/27/2021] [Indexed: 11/07/2022]
Abstract
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data obtained from single-cell sequencing or flow-cytometry experiments into regulatory dynamics. We show how static population snapshots of covariability can be exploited to rigorously infer properties of gene expression dynamics when gene expression reporters probe their upstream dynamics on separate timescales. This can be experimentally exploited in dual-reporter experiments with fluorescent proteins of unequal maturation times, thus turning an experimental bug into an analysis feature. We derive correlation conditions that detect the presence of closed-loop feedback regulation in gene regulatory networks. Furthermore, we show how genes with cell-cycle-dependent transcription rates can be identified from the variability of coregulated fluorescent proteins. Similar correlation constraints might prove useful in other areas of science in which static correlation snapshots are used to infer causal connections between dynamically interacting components.
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Affiliation(s)
- Euan Joly-Smith
- Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario, Canada M5S 1A7
| | - Zitong Jerry Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Andreas Hilfinger
- Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario, Canada M5S 1A7.,Department of Mathematics, University of Toronto, 40 St. George Street, Toronto, Ontario, Canada M5S 2E4.,Department of Cell & Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario, Canada M5S 3G5
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Derksen A, Shih HY, Forget D, Darbelli L, Tran LT, Poitras C, Guerrero K, Tharun S, Alkuraya FS, Kurdi WI, Nguyen CTE, Laberge AM, Si Y, Gauthier MS, Bonkowsky JL, Coulombe B, Bernard G. Variants in LSM7 impair LSM complexes assembly, neurodevelopment in zebrafish and may be associated with an ultra-rare neurological disease. HGG ADVANCES 2021; 2:100034. [PMID: 35047835 PMCID: PMC8756503 DOI: 10.1016/j.xhgg.2021.100034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 04/28/2021] [Indexed: 11/15/2022] Open
Abstract
Leukodystrophies, genetic neurodevelopmental and/or neurodegenerative disorders of cerebral white matter, result from impaired myelin homeostasis and metabolism. Numerous genes have been implicated in these heterogeneous disorders; however, many individuals remain without a molecular diagnosis. Using whole-exome sequencing, biallelic variants in LSM7 were uncovered in two unrelated individuals, one with a leukodystrophy and the other who died in utero. LSM7 is part of the two principle LSM protein complexes in eukaryotes, namely LSM1-7 and LSM2-8. Here, we investigate the molecular and functional outcomes of these LSM7 biallelic variants in vitro and in vivo. Affinity purification-mass spectrometry of the LSM7 variants showed defects in the assembly of both LSM complexes. Lsm7 knockdown in zebrafish led to central nervous system defects, including impaired oligodendrocyte development and motor behavior. Our findings demonstrate that variants in LSM7 cause misassembly of the LSM complexes, impair neurodevelopment of the zebrafish, and may be implicated in human disease. The identification of more affected individuals is needed before the molecular mechanisms of mRNA decay and splicing regulation are added to the categories of biological dysfunctions implicated in leukodystrophies, neurodevelopmental and/or neurodegenerative diseases.
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Stegen M, Engler A, Ochsenfarth C, Manthey I, Peters J, Siffert W, Frey UH. Characterization of the G protein-coupled receptor kinase 6 promoter reveals a functional CREB binding site. PLoS One 2021; 16:e0247087. [PMID: 33600497 PMCID: PMC7891717 DOI: 10.1371/journal.pone.0247087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 02/01/2021] [Indexed: 11/21/2022] Open
Abstract
Background G protein-coupled receptor kinase 6 (GRK6) is part of the G protein-coupled receptor kinase family, whose members act as key regulators of seven-transmembrane receptor signalling. GRK6 seems to play a role in regulation of inflammatory processes, but mechanisms of transcriptional regulation of GRK6 expression in inflammatory cell lines have not been characterized. Protein kinase C (PKC) signalling is also involved in inflammatory regulation and an impact of PKC activation on GRK6 protein expression was described previously. Thus, the aim of this study was to 1) characterize the GRK6 promoter, and 2) investigate a potential influence of PKC on GRK6 expression. Methods Five deletion constructs of the GRK6 promoter were cloned. After transient transfection into a human T cell line, promoter activity was assessed using luciferase reporter gene assays. Putative transcription factor binding sites were identified, mutated, and binding was investigated using electrophoretic mobility shift assays (EMSA). Following stimulation with a PKC activator, GRK6 expression on mRNA and protein levels was assessed by reverse transcriptase qPCR and Western blots. Results Investigation of the GRK6 promoter revealed a putative cAMP responsive element (CRE), whose mutation led to decreased promoter activity (p = 0.0006). Functionality of the CRE binding protein (CREB) binding site was verified in EMSA blots. Stimulation with a PKC activator resulted in decreased GRK6 promoter activity (p = 0.0027), mRNA (p = 0.04) and protein expression. Conclusion We characterized the human GRK6 promoter and identified promoter activity to be influenced by a CREB binding site. PKC might be one determinant contributing to altered GRK6 expression.
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Affiliation(s)
- Maike Stegen
- Department of Anaesthesiology and Intensive Care Medicine, Essen University Hospital and University of Duisburg-Essen, Essen, Germany
- * E-mail:
| | - Andrea Engler
- Department of Anaesthesiology and Intensive Care Medicine, Essen University Hospital and University of Duisburg-Essen, Essen, Germany
| | - Crista Ochsenfarth
- Department of Anaesthesiology, Operative Intensive Care Medicine, Pain and Palliative Medicine, Marien Hospital Herne, Ruhr-University Bochum, Bochum, Germany
| | - Iris Manthey
- Institute of Pharmacogenetics, Essen University Hospital and University of Duisburg-Essen, Essen, Germany
| | - Jürgen Peters
- Department of Anaesthesiology and Intensive Care Medicine, Essen University Hospital and University of Duisburg-Essen, Essen, Germany
| | - Winfried Siffert
- Institute of Pharmacogenetics, Essen University Hospital and University of Duisburg-Essen, Essen, Germany
| | - Ulrich H. Frey
- Department of Anaesthesiology and Intensive Care Medicine, Essen University Hospital and University of Duisburg-Essen, Essen, Germany
- Department of Anaesthesiology, Operative Intensive Care Medicine, Pain and Palliative Medicine, Marien Hospital Herne, Ruhr-University Bochum, Bochum, Germany
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Jia XJ, Du Y, Jiang HJ, Li YZ, Xu YN, Si SY, Wang L, Hong B. Identification of Novel Compounds Enhancing SR-BI mRNA Stability through High-Throughput Screening. SLAS DISCOVERY 2019; 25:397-408. [PMID: 31858876 DOI: 10.1177/2472555219894543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Atherosclerosis is the pathological basis of most cardiovascular diseases. Reverse cholesterol transport (RCT) is a main mechanism of cholesterol homeostasis and involves the direct transport of high-density lipoprotein (HDL) cholesteryl ester by selective cholesterol uptake. Hepatic scavenger receptor class B member 1 (SR-BI) overexpression can effectively promote RCT and reduce atherosclerosis. SR-BI may be an important target for prevention or treatment of atherosclerotic disease. In our study, we inserted human SR-BI mRNA 3' untranslated region (3'UTR) downstream of the luciferase reporter gene, to establish a high-throughput screening model based on stably transfected HepG2 cells and to screen small-molecule compounds that can significantly enhance the mRNA stability of the SR-BI gene. Through multiple screenings of 25 755 compounds, the top five active compounds that have similar structures were obtained, with a positive rate of 0.19%. The five positive compounds could enhance the SR-BI expression and uptake of DiI-HDL in the hepatocyte HepG2. E238B-63 could also effectively extend the half-life of SR-BI mRNA and enhance the SR-BI mRNA and protein level and the uptake of DiI-HDL in hepatocytes in a time-dependent and dose-dependent manner. The structure-activity relationship analysis showed that the structure N-(3-hydroxy-2-pyridyl) carboxamide is possibly the key pharmacophore of the active compound, providing reference for acquiring candidate compounds with better activity. The positive small molecular compounds obtained in this study might become new drug candidates or lead compounds for the treatment of cardiovascular diseases and contribute to the further study of the posttranscriptional regulation mechanism of the SR-BI gene.
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Affiliation(s)
- Xiao-Jian Jia
- Shenzhen Kangning Hospital & Shenzhen Mental Health Center, Shenzhen University Health Science Center, Shenzhen, PR China.,NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Yu Du
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Hua-Jun Jiang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Yong-Zhen Li
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Yan-Ni Xu
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Shu-Yi Si
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Li Wang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
| | - Bin Hong
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, PR China
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Lu BS, Yin YW, Zhang YP, Guo PY, Li W, Liu KL. Upregulation of NPL4 promotes bladder cancer cell proliferation by inhibiting DXO destabilization of cyclin D1 mRNA. Cancer Cell Int 2019; 19:149. [PMID: 31164795 PMCID: PMC6543671 DOI: 10.1186/s12935-019-0874-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/27/2019] [Indexed: 12/11/2022] Open
Abstract
Background NPL4 is an important cofactor of the valosin-containing protein (VCP)–NPL4–UFD1 complex. The VCP–NPL4–UFD1 has been considered as a ubiquitin proteasome system (UPS) regulator and response to protein degradation. While NPL4 plays important roles in various diseases, little is known about its functions in bladder cancer (BC). Methods MTT assays and colony forming test were performed to evaluate cell proliferation ability and Western blotting was used to detect protein expression. Cyclin D1 mRNA expression was detected using qRT-PCR, and coimmunoprecipitation (CoIP) was used to detect protein–protein interactions. Results NPL4 was upregulated in BC tissue and correlated with poor prognosis. Upregulation of NPL4 promoted cell proliferation while suppression of NPL4 reduced BC cell proliferation. Upregulation of NPL4 led to overexpression of cyclin D1 by enhancing its mRNA stability. Moreover, NPL4 was found to bind directly to DXO and induce its degradation. DXO was downregulated in BC tissue and regulated BC cell proliferation by destabilizing cyclin D1 mRNA. DXO-mediated NPL4 regulated BC cell proliferation by stabilizing cyclin D1 expression. Conclusions The NPL4/DXO/cyclin D1 axis exert crucial role in BC cell growth and is associated with prognosis and may represent a potential therapeutic target for BC.
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Affiliation(s)
- Bao-Sai Lu
- Department of Urology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang, 050000 Hebei People's Republic of China
| | - Yue-Wei Yin
- Department of Urology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang, 050000 Hebei People's Republic of China
| | - Yan-Ping Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang, 050000 Hebei People's Republic of China
| | - Ping-Ying Guo
- Department of Urology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang, 050000 Hebei People's Republic of China
| | - Wei Li
- Department of Urology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang, 050000 Hebei People's Republic of China
| | - Kai-Long Liu
- Department of Urology, The Second Hospital of Hebei Medical University, No. 215, Heping West Road, Shijiazhuang, 050000 Hebei People's Republic of China
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GAPDH as a model non-canonical AU-rich RNA binding protein. Semin Cell Dev Biol 2019; 86:162-173. [DOI: 10.1016/j.semcdb.2018.03.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/13/2018] [Accepted: 03/20/2018] [Indexed: 02/06/2023]
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Zucchelli S, Patrucco L, Persichetti F, Gustincich S, Cotella D. Engineering Translation in Mammalian Cell Factories to Increase Protein Yield: The Unexpected Use of Long Non-Coding SINEUP RNAs. Comput Struct Biotechnol J 2016; 14:404-410. [PMID: 27872686 PMCID: PMC5107644 DOI: 10.1016/j.csbj.2016.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/26/2022] Open
Abstract
Mammalian cells are an indispensable tool for the production of recombinant proteins in contexts where function depends on post-translational modifications. Among them, Chinese Hamster Ovary (CHO) cells are the primary factories for the production of therapeutic proteins, including monoclonal antibodies (MAbs). To improve expression and stability, several methodologies have been adopted, including methods based on media formulation, selective pressure and cell- or vector engineering. This review presents current approaches aimed at improving mammalian cell factories that are based on the enhancement of translation. Among well-established techniques (codon optimization and improvement of mRNA secondary structure), we describe SINEUPs, a family of antisense long non-coding RNAs that are able to increase translation of partially overlapping protein-coding mRNAs. By exploiting their modular structure, SINEUP molecules can be designed to target virtually any mRNA of interest, and thus to increase the production of secreted proteins. Thus, synthetic SINEUPs represent a new versatile tool to improve the production of secreted proteins in biomanufacturing processes.
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Affiliation(s)
- Silvia Zucchelli
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy; Area of Neuroscience, SISSA, Trieste, Italy
| | - Laura Patrucco
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | | | - Stefano Gustincich
- Area of Neuroscience, SISSA, Trieste, Italy; Department of Neuroscience and Brain Technologies, Italian Institute of Technology (IIT), Genova, Italy
| | - Diego Cotella
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
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Yanuaryska RD, Miyoshi K, Adiningrat A, Horiguchi T, Tanimura A, Hagita H, Noma T. Sp6 regulation of Rock1 promoter activity in dental epithelial cells. THE JOURNAL OF MEDICAL INVESTIGATION 2016; 61:306-17. [PMID: 25264049 DOI: 10.2152/jmi.61.306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Sp6 is a transcription factor of the SP/KLF family and an indispensable regulator of the morphological dynamics of ameloblast differentiation during tooth development. However, the underlying molecular mechanisms remain unclear. We have previously identified one of the Sp6 downstream genes, Rock1, which is involved in ameloblast polarization. In this study, we investigated the transcriptional regulatory mechanisms of Rock1 by Sp6. First, we identified the transcription start sites (TSS) and cloned the 5'-flanking region of Rock1. Serial deletion analyses identified a critical region for Rock1 promoter activity within the 249-bp upstream region of TSS, and chromatin immunoprecipitation assays revealed Sp6-binding to this region. Subsequent transient transfection experiments showed that Rock1 promoter activity is enhanced by Sp6, but reduced by Sp1. Treatment of dental epithelial cells with the GC-selective DNA binding inhibitor, mithramycin A, affected Rock1 promoter activity in loss of enhancement by Sp6, but not repression by Sp1. Further site-directed mutagenesis indicated that the region from -206 to -150 contains responsive elements for Sp6. Taken together, we conclude that Sp6 positively regulates Rock1 transcription by direct binding to the Rock1 promoter region from -206 to -150, which functionally distinct from Sp1.
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Affiliation(s)
- Ryna Dwi Yanuaryska
- Department of Molecular Biology, Institute of Health Biosciences, the University of Tokushima Graduate School
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10
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Li N, Li Y, Zheng C, Huang J, Zhang S. Genome-wide comparative analysis of the codon usage patterns in plants. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0417-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Anji A, Kumari M. Guardian of Genetic Messenger-RNA-Binding Proteins. Biomolecules 2016; 6:4. [PMID: 26751491 PMCID: PMC4808798 DOI: 10.3390/biom6010004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/02/2015] [Accepted: 12/04/2015] [Indexed: 12/18/2022] Open
Abstract
RNA in cells is always associated with RNA-binding proteins that regulate all aspects of RNA metabolism including RNA splicing, export from the nucleus, RNA localization, mRNA turn-over as well as translation. Given their diverse functions, cells express a variety of RNA-binding proteins, which play important roles in the pathologies of a number of diseases. In this review we focus on the effect of alcohol on different RNA-binding proteins and their possible contribution to alcohol-related disorders, and discuss the role of these proteins in the development of neurological diseases and cancer. We further discuss the conventional methods and newer techniques that are employed to identify RNA-binding proteins.
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Affiliation(s)
- Antje Anji
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - Meena Kumari
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
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Sidarovich V, Adami V, Quattrone A. High-throughput screening for chemical modulators of post-transcriptionally regulated genes. J Vis Exp 2015:52568. [PMID: 25867708 PMCID: PMC4401173 DOI: 10.3791/52568] [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] [Indexed: 10/31/2022] Open
Abstract
Both transcriptional and post-transcriptional regulation have a profound impact on genes expression. However, commonly adopted cell-based screening assays focus on transcriptional regulation, being essentially aimed at the identification of promoter-targeting molecules. As a result, post-transcriptional mechanisms are largely uncovered by gene expression targeted drug development. Here we describe a cell-based assay aimed at investigating the role of the 3' untranslated region (3' UTR) in the modulation of the fate of its mRNA, and at identifying compounds able to modify it. The assay is based on the use of a luciferase reporter construct containing the 3' UTR of a gene of interest stably integrated into a disease-relevant cell line. The protocol is divided into two parts, with the initial focus on the primary screening aimed at the identification of molecules affecting luciferase activity after 24 hr of treatment. The second part of the protocol describes the counter-screening necessary to discriminate compounds modulating luciferase activity specifically through the 3' UTR. In addition to the detailed protocol and representative results, we provide important considerations about the assay development and the validation of the hit(s) on the endogenous target. The described cell-based reporter gene assay will allow scientists to identify molecules modulating protein levels via post-transcriptional mechanisms dependent on a 3' UTR.
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Affiliation(s)
- Viktoryia Sidarovich
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento;
| | - Valentina Adami
- High Throughput Screening Core Facility, Centre for Integrative Biology, University of Trento
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento
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Palumbo MC, Farina L, Paci P. Kinetics effects and modeling of mRNA turnover. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:327-36. [PMID: 25727049 DOI: 10.1002/wrna.1277] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 12/12/2014] [Accepted: 01/09/2015] [Indexed: 01/08/2023]
Abstract
Broader comprehension of gene expression regulatory mechanisms can be gained from a global analysis of how transcription and degradation are coordinated to orchestrate complex cell responses. The role of messenger RNA (mRNA) turnover modulation in gene expression levels has become increasingly recognized. From such perspective, in this review we briefly illustrate how a simple but effective mathematical model of mRNA turnover and some experimental findings, may together shed light on the molecular mechanisms underpinning the major role of mRNA decay rates in shaping the kinetics of gene activation and repression.
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Affiliation(s)
- Maria Concetta Palumbo
- Institute for Computing Applications "Mauro Picone", National Research Council, Rome, Italy
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Akdeli N, Riemann K, Westphal J, Hess J, Siffert W, Bachmann HS. A 3'UTR polymorphism modulates mRNA stability of the oncogene and drug target Polo-like Kinase 1. Mol Cancer 2014; 13:87. [PMID: 24767679 PMCID: PMC4020576 DOI: 10.1186/1476-4598-13-87] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 04/15/2014] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The Polo-like Kinase 1 (PLK1) protein regulates cell cycle progression and is overexpressed in many malignant tissues. Overexpression is associated with poor prognosis in several cancer entities, whereby expression of PLK1 shows high inter-individual variability. Although PLK1 is extensively studied, not much is known about the genetic variability of the PLK1 gene. The function of PLK1 and the expression of the corresponding gene could be influenced by genomic variations. Hence, we investigated the gene for functional polymorphisms. Such polymorphisms could be useful to investigate whether PLK1 alters the risk for and the course of cancer and they could have an impact on the response to PLK1 inhibitors. METHODS The coding region, the 5' and 3'UTRs and the regulatory regions of PLK1 were systematically sequenced. We determined the allele frequencies and genotype distributions of putatively functional SNPs in 120 Caucasians and analyzed the linkage and haplotype structure using Haploview. The functional analysis included electrophoretic mobility shift assay (EMSA) for detected variants of the silencer and promoter regions and reporter assays for a 3'UTR polymorphism. RESULTS Four putatively functional polymorphisms were detected and further analyzed, one in the silencer region (rs57973275), one in the core promoter region (rs16972787), one in intron 3 (rs40076) and one polymorphism in the 3'untranslated region (3'UTR) of PLK1 (rs27770). Alleles of rs27770 display different secondary mRNA structures and showed a distinct allele-dependent difference in mRNA stability with a significantly higher reporter activity of the A allele (p < 0.01). CONCLUSION The present study provides evidence that at least one genomic variant of PLK1 has functional properties and influences expression of PLK1. This suggests polymorphisms of the PLK1 gene as an interesting target for further studies that might affect cancer risk, tumor progression as well as the response to PLK1 inhibitors.
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Affiliation(s)
- Neval Akdeli
- Institute of Pharmacogenetics, University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Kathrin Riemann
- Institute of Pharmacogenetics, University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Jana Westphal
- Institute of Pharmacogenetics, University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Jochen Hess
- Institute of Pharmacogenetics, University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
- Department of Urology, University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Winfried Siffert
- Institute of Pharmacogenetics, University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
| | - Hagen S Bachmann
- Institute of Pharmacogenetics, University Hospital Essen, Hufelandstr. 55, 45147 Essen, Germany
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15
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Vindry C, Vo Ngoc L, Kruys V, Gueydan C. RNA-binding protein-mediated post-transcriptional controls of gene expression: integration of molecular mechanisms at the 3' end of mRNAs? Biochem Pharmacol 2014; 89:431-40. [PMID: 24735612 DOI: 10.1016/j.bcp.2014.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/02/2014] [Accepted: 04/03/2014] [Indexed: 01/17/2023]
Abstract
Initially identified as an occasional and peculiar mode of gene regulation in eukaryotes, RNA-binding protein-mediated post-transcriptional control of gene expression has emerged, over the last two decades, as a major contributor in the control of gene expression. A large variety of RNA-binding proteins (RBPs) allows the recognition of very diverse messenger RNA sequences and participates in the regulation of basically all cellular processes. Nevertheless, the rapid outcome of post-transcriptional regulations on the level of gene expression has favored the expansion of this type of regulation in cellular processes prone to rapid and frequent modulations such as the control of the inflammatory response. At the molecular level, the 3'untranslated region (3'UTR) of mRNA is a favored site of RBP recruitment. RBPs binding to these regions control gene expression through two major modes of regulation, namely mRNA decay and modulation of translational activity. Recent progresses suggest that these two mechanisms are often interdependent and might result one from the other. Therefore, different RBPs binding distinct RNA subsets could share similar modes of action at the molecular level. RBPs are frequent targets of post-translational modifications, thereby disclosing numerous possibilities for pharmacological interventions. However, redundancies of the transduction pathways controlling these modifications have limited the perspectives to define RBPs as new therapeutic targets. Through the analysis of several examples of RBPs binding to 3'untranslated region of mRNA, we present here recent progress and perspectives regarding this rapidly evolving field of molecular biology.
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Affiliation(s)
- Caroline Vindry
- Laboratoire de Biologie moléculaire du gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 12 rue des Profs. Jeener et Brachet, Gosselies 6041, Belgium
| | - Long Vo Ngoc
- Laboratoire de Biologie moléculaire du gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 12 rue des Profs. Jeener et Brachet, Gosselies 6041, Belgium
| | - Véronique Kruys
- Laboratoire de Biologie moléculaire du gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 12 rue des Profs. Jeener et Brachet, Gosselies 6041, Belgium
| | - Cyril Gueydan
- Laboratoire de Biologie moléculaire du gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles, 12 rue des Profs. Jeener et Brachet, Gosselies 6041, Belgium.
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Lazar J, O'Meara CC, Sarkis AB, Prisco SZ, Xu H, Fox CS, Chen MH, Broeckel U, Arnett DK, Moreno C, Provoost AP, Jacob HJ. SORCS1 contributes to the development of renal disease in rats and humans. Physiol Genomics 2013; 45:720-8. [PMID: 23780848 PMCID: PMC3742914 DOI: 10.1152/physiolgenomics.00089.2013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 06/14/2013] [Indexed: 12/14/2022] Open
Abstract
Many lines of evidence demonstrate that genetic variability contributes to chronic kidney disease susceptibility in humans as well as rodent models. Little progress has been made in discovering causal kidney disease genes in humans mainly due to genetic complexity. Here, we use a minimal congenic mapping strategy in the FHH (fawn hooded hypertensive) rat to identify Sorcs1 as a novel renal disease candidate gene. We investigated the hypothesis that genetic variation in Sorcs1 influences renal disease susceptibility in both rat and human. Sorcs1 is expressed in the kidney, and knocking out this gene in a rat strain with a sensitized genome background produced increased proteinuria. In vitro knockdown of Sorcs1 in proximal tubule cells impaired protein trafficking, suggesting a mechanism for the observed proteinuria in the FHH rat. Since Sorcs1 influences renal function in the rat, we went on to test this gene in humans. We identified associations between single nucleotide polymorphisms in SORCS1 and renal function in large cohorts of European and African ancestry. The experimental data from the rat combined with association results from different ethnic groups indicates a role for SORCS1 in maintaining proper renal function.
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Affiliation(s)
- Jozef Lazar
- Department of Dermatology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Abstract
mRNA has become an important alternative to DNA as a tool for cell reprogramming. To be expressed, exogenous DNA must be transmitted through the cell cytoplasm and placed into the nucleus. In contrast, exogenous mRNA simply has to be delivered into the cytoplasm. This can result in a highly uniform transfection of the whole population of cells, an advantage that has not been observed with DNA transfer. The use of mRNA, instead of DNA, in medical applications increases protocol safety by abolishing the risk of transgene insertion into host genomes. In this chapter, we review the aspects of mRNA structure and function that are important for its "transgenic" behavior, such as the composition of mRNA molecules and complexes with RNA binding proteins, localization of mRNA in cytoplasmic compartments, translation, and the duration of mRNA expression. In immunotherapy, mRNA is employed in reprogramming of antigen presenting cells (vaccination) and cytolytic lymphocytes. Other applications include generation of induced pluripotent stem (iPS) cells, and genome engineering with modularly assembled nucleases. The most investigated applications of mRNA technology are also reviewed here.
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Cacace F, Paci P, Cusimano V, Germani A, Farina L. Stochastic modeling of expression kinetics identifies messenger half-lives and reveals sequential waves of co-ordinated transcription and decay. PLoS Comput Biol 2012; 8:e1002772. [PMID: 23144606 PMCID: PMC3493476 DOI: 10.1371/journal.pcbi.1002772] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Accepted: 09/23/2012] [Indexed: 11/19/2022] Open
Abstract
The transcriptome in a cell is finely regulated by a large number of molecular mechanisms able to control the balance between mRNA production and degradation. Recent experimental findings have evidenced that fine and specific regulation of degradation is needed for proper orchestration of a global cell response to environmental conditions. We developed a computational technique based on stochastic modeling, to infer condition-specific individual mRNA half-lives directly from gene expression time-courses. Predictions from our method were validated by experimentally measured mRNA decay rates during the intraerythrocytic developmental cycle of Plasmodium falciparum. We then applied our methodology to publicly available data on the reproductive and metabolic cycle of budding yeast. Strikingly, our analysis revealed, in all cases, the presence of periodic changes in decay rates of sequentially induced genes and co-ordination strategies between transcription and degradation, thus suggesting a general principle for the proper coordination of transcription and degradation machinery in response to internal and/or external stimuli.
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Affiliation(s)
| | - Paola Paci
- Università Campus Biomedico, Rome, Italy
- CNR-Institute of Systems Analysis and Computer Science (IASI), BioMathLab, Rome, Italy
- * E-mail:
| | | | - Alfredo Germani
- Dipartimento di Ingegneria e Scienze dell'Informazione e Matematica (DISIM), Università de L'Aquila, L'Aquila, Italy
| | - Lorenzo Farina
- Dipartimento di Informatica e Sistemistica, Sapienza Università di Roma, Rome, Italy
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Catalán Ú, Fernández-Castillejo S, Anglès N, Morelló JR, Yebras M, Solà R. Inhibition of the transcription factor c-Jun by the MAPK family, and not the NF-κB pathway, suggests that peanut extract has anti-inflammatory properties. Mol Immunol 2012; 52:125-32. [PMID: 22673210 DOI: 10.1016/j.molimm.2012.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 05/08/2012] [Accepted: 05/09/2012] [Indexed: 12/15/2022]
Abstract
BACKGROUND Tumor necrosis factor-α (TNF-α) is involved in inflammatory responses in atherosclerosis. We propose an in vitro cellular assay to evaluate the anti-inflammatory mechanisms of potential modifiers such as food extracts. In the current model we assessed an anti-inflammatory effect of polyphenol-rich peanut extract in lipopolysaccharide (LPS)-induced THP-1 monocytes. METHODS THP-1 monocytes were incubated with peanut extract (5, 25, 50 and 100 μg/mL) consisting of 39% flavonols, 37% flavanols and 24% phenolic acid (or BAY 11-7082 (5 μM) as experiment control) for 1 h and then stimulated with LPS (500 ng/mL) for 4 h. Cytotoxicity was measured as lactate dehydrogenase (LDH) activity release. NF-κB and MAPK family were determined by TransAm kit while TNF-α mRNA levels and its mRNA stability by RT-PCR. Intra- and extracellular TNF-α protein was measured by ELISA, and TNF-α converting enzyme (TACE) activity by a fluorimetric assay. RESULTS Peanut extract inhibited the maximal LPS-induced extracellular TNF-α protein secretion by 18%, 29% and 47% at 25, 50 and 100 μg/mL, respectively (P<0.05). LPS stimulation revealed that 85% of TNF-α was released extracellularly while 15% remained intracellular. Peanut extract did not modify NF-κB but, instead, reduced c-Jun transcription factor activity (P<0.05), decreased TNF-α mRNA (albeit non-significantly) and had no effect on mRNA stability and TACE activity. CONCLUSION Polyphenol-rich peanut extract reduces extracellular TNF-α protein by inhibiting c-Jun transcription factor from MAPK family, suggesting an anti-inflammatory effect. The proposed THP-1 monocyte model could be used to assess food extract impact (site and size effects) on the inflammation pathway.
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Affiliation(s)
- Úrsula Catalán
- Unitat de Recerca en Lípids i Arteriosclerosi, CIBERDEM, Hospital Universitari Sant Joan, IISPV, Universitat Rovira i Virgili, Reus, Tarragona, Spain
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Palanisamy V, Jakymiw A, Van Tubergen EA, D'Silva NJ, Kirkwood KL. Control of cytokine mRNA expression by RNA-binding proteins and microRNAs. J Dent Res 2012; 91:651-8. [PMID: 22302144 DOI: 10.1177/0022034512437372] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cytokines are critical mediators of inflammation and host defenses. Regulation of cytokines can occur at various stages of gene expression, including transcription, mRNA export, and post- transcriptional and translational levels. Among these modes of regulation, post-transcriptional regulation has been shown to play a vital role in controlling the expression of cytokines by modulating mRNA stability. The stability of cytokine mRNAs, including TNFα, IL-6, and IL-8, has been reported to be altered by the presence of AU-rich elements (AREs) located in the 3'-untranslated regions (3'UTRs) of the mRNAs. Numerous RNA-binding proteins and microRNAs bind to these 3'UTRs to regulate the stability and/or translation of the mRNAs. Thus, this paper describes the cooperative function between RNA-binding proteins and miRNAs and how they regulate AU-rich elements containing cytokine mRNA stability/degradation and translation. These mRNA control mechanisms can potentially influence inflammation as it relates to oral biology, including periodontal diseases and oral pharyngeal cancer progression.
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Affiliation(s)
- V Palanisamy
- Department of Craniofacial Biology, Medical University of South Carolina, Charleston, SC, USA
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Trowitzsch S, Klumpp M, Thoma R, Carralot JP, Berger I. Light it up: highly efficient multigene delivery in mammalian cells. Bioessays 2011; 33:946-55. [PMID: 22002169 DOI: 10.1002/bies.201100109] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Multigene delivery and expression systems are emerging as key technologies for many applications in contemporary biology. We have developed new methods for multigene delivery and expression in eukaryotic hosts for a variety of applications, including production of protein complexes for structural biology and drug development, provision of multicomponent protein biologics, and cell-based assays. We implemented tandem recombineering to facilitate rapid generation of multicomponent gene expression constructs for efficient transformation of mammalian cells, resulting in homogenous cell populations. Analysis of multiple parameters in living cells may require co-expression of fluorescently tagged sensors simultaneously in a single cell, at defined and ideally controlled ratios. Our method enables such applications by overcoming currently limiting challenges. Here, we review recent multigene delivery and expression strategies and their exploitation in mammalian cells. We discuss applications in drug discovery assays, interaction studies, and biologics production, which may benefit in the future from our novel approach.
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Luo W, Yu QS, Salcedo I, Holloway HW, Lahiri DK, Brossi A, Tweedie D, Greig NH. Design, synthesis and biological assessment of novel N-substituted 3-(phthalimidin-2-yl)-2,6-dioxopiperidines and 3-substituted 2,6-dioxopiperidines for TNF-α inhibitory activity. Bioorg Med Chem 2011; 19:3965-72. [PMID: 21658960 PMCID: PMC5187979 DOI: 10.1016/j.bmc.2011.05.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2011] [Revised: 05/10/2011] [Accepted: 05/17/2011] [Indexed: 11/19/2022]
Abstract
Eight novel 2-(2,6-dioxopiperidin-3-yl)phthalimidine EM-12 dithiocarbamates 9 and 10, N-substituted 3-(phthalimidin-2-yl)-2,6-dioxopiperidines 11-14 and 3-substituted 2,6-dioxopiperidines 16 and 18 were synthesized as tumor necrosis factor-α (TNF-α) synthesis inhibitors. Synthesis involved utilization of a novel condensation approach, a one-pot reaction involving addition, iminium rearrangement and elimination, to generate the phthalimidine ring required for the creation of compounds 9-14. Agents were, thereafter, quantitatively assessed for their ability to suppress the synthesis on TNF-α in a lipopolysaccharide (LPS)-challenged mouse macrophage-like cellular screen, utilizing cultured RAW 264.7 cells. Whereas compounds 9, 14 and 16 exhibited potent TNF-α lowering activity, reducing TNF-α by up to 48% at 30 μM, compounds 12, 17 and 18 presented moderate TNF-α inhibitory action. The TNF-α lowering properties of these analogs proved more potent than that of revlimid (3) and thalidomide (1). In particular, N-dithiophthalimidomethyl-3-(phthalimidin-2-yl)-2,6-dioxopiperidine 14 not only possessed the greatest potency of the analogs to reduce TNF-α synthesis, but achieved this with minor cellular toxicity at 30 μM. The pharmacological focus of the presented compounds is towards the development of well-tolerated agents to ameliorate the neuroinflammation, that is, commonly associated with neurodegenerative disorders, epitomized by Alzheimer's disease and Parkinson's disease.
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Affiliation(s)
- Weiming Luo
- Drug Design & Development Section, Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Qian-sheng Yu
- Drug Design & Development Section, Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Isidro Salcedo
- Drug Design & Development Section, Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Harold W. Holloway
- Drug Design & Development Section, Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Debomoy K. Lahiri
- Department of Psychiatry, Institute of Psychiatric Research, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Arnold Brossi
- School of Pharmacy, University of North Carolina at Chapel Hill, North Carolina 27599, USA
| | - David Tweedie
- Drug Design & Development Section, Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Nigel H. Greig
- Drug Design & Development Section, Laboratory of Neurosciences, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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Yin K, Deng X, Mo ZC, Zhao GJ, Jiang J, Cui LB, Tan CZ, Wen GB, Fu Y, Tang CK. Tristetraprolin-dependent post-transcriptional regulation of inflammatory cytokine mRNA expression by apolipoprotein A-I: role of ATP-binding membrane cassette transporter A1 and signal transducer and activator of transcription 3. J Biol Chem 2011; 286:13834-45. [PMID: 21339300 DOI: 10.1074/jbc.m110.202275] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Atherosclerosis is an inflammatory disease characterized by the accumulation of macrophages in the arterial intima. The activated macrophages secreted more pro-inflammatory cytokines, such as tumor necrosis factor (TNF)-α, which promote the development of the disease. Apolipoprotein A-I (apoA-I), the major component of high density lipoprotein, is involved in reverse cholesterol transport of lipid metabolism. Recently, it has been found that apoA-I suppresses inflammation via repression of inflammatory cytokine expression; the mechanisms of the apoA-I-suppressive action, however, are not yet well characterized. In this study, we have for the first time found that apoA-I suppresses the expression of some inflammatory cytokines induced by lipopolysaccharide via a specific post-transcriptional regulation process, namely mRNA destabilization, in macrophages. Our further studies have also shown that AU-rich elements in the 3'-untranslated region of TNF-α mRNA are responsive to the apoA-I-mediated mRNA destabilization. The apoA-I-induced inflammatory cytokine mRNA destabilization was associated with increased expression of mRNA-destabilizing protein tristetraprolin through a JAK2/STAT3 signaling pathway-dependent manner. When blocking interaction of apoA-I with ATP-binding membrane cassette transporter A1 (ABCA1), a major receptor for apoA-I in macrophages, it would almost totally abolish the effect of apoA-I on tristetraprolin expression. These results present not only a novel mechanism for the apoA-I-mediated inflammation suppression in macrophages but also provide new insights for developing strategies for modulating vascular inflammation and atherosclerosis.
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Affiliation(s)
- Kai Yin
- Institute of Cardiovascular Research, Key Laboratory for Atherosclerology of Hunan Province, Life Science Research Center, University of South China, Hengyang, 421001, China
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