1
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Giudice GC, Sonpavde GP. Vaccine approaches to treat urothelial cancer. Hum Vaccin Immunother 2024; 20:2379086. [PMID: 39043175 PMCID: PMC11268260 DOI: 10.1080/21645515.2024.2379086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/08/2024] [Indexed: 07/25/2024] Open
Abstract
Bladder cancer (BC) accounts for about 4% of all malignancies. Non-muscle-invasive BC, 75% of cases, is treated with transurethral resection and adjuvant intravesical instillation, while muscle-invasive BC warrants cisplatin-based perioperative chemotherapy. Although immune-checkpoint inhibitors, antibody drug conjugates and targeted agents have provided dramatic advances, metastatic BC remains a generally incurable disease and clinical trials continue to vigorously evaluate novel molecules. Cancer vaccines aim at activating the patient's immune system against tumor cells. Several means of delivering neoantigens have been developed, including peptides, antigen-presenting cells, virus, or nucleic acids. Various improvements are constantly being explored, such as adjuvants use and combination strategies. Nucleic acids-based vaccines are increasingly gaining attention in recent years, with promising results in other malignancies. However, despite the recent advantages, numerous obstacles persist. This review is aimed at describing the different types of cancer vaccines, their evaluations in UC patients and the more recent innovations in this field.
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Affiliation(s)
- Giulia Claire Giudice
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Guru P. Sonpavde
- AdventHealth Cancer Institute, University of Central Florida, Orlando, FL, USA
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2
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Weiss B, Dikstein R. Unraveling the landscapes and regulation of scanning, leaky scanning, and 48S initiation complex conformations. Cell Rep 2024; 43:114126. [PMID: 38630588 DOI: 10.1016/j.celrep.2024.114126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 01/19/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Scanning and initiation are critical steps in translation. Here, we utilized translation complex profiling (TCP-seq) to investigate 48S organization and eIF4G1-eIF1 inhibition impact. We provide global views of scanning and leaky scanning, uncovering a central role of eIF4G1-eIF1 in their regulation. We confirm AUG context importance, with non-leaky genes featuring a Kozak context and cytosine at positions -1 and +5. Capturing 48S complexes associated with eIF1, eIF4G1, eIF3, and eIF2 through selective TCP-seq revealed that the eIF3-scanning ribosome is highly vulnerable to eIF4G1-eIF1 inhibition, and eIF1 tends to dissociate upon AUG recognition. Initiation-site footprint analysis revealed a class spanning -12 to +18/19 from the AUG, representing the entire 48S and enriched with eIF2, eIF1, and eIF4G1, indicative of early initiation. Another eIF3-dependent class extends up to +26 and exhibits reduced eIF2 and eIF4G1 association, suggesting a late/alternative initiation complex. Our analysis provides an overview of scanning, initiation, and evidence for conformational rearrangements in vivo.
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Affiliation(s)
- Benjamin Weiss
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Rivka Dikstein
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
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3
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Gaudry MJ, Khudyakov J, Pirard L, Debier C, Crocker D, Crichton PG, Jastroch M. Terrestrial Birth and Body Size Tune UCP1 Functionality in Seals. Mol Biol Evol 2024; 41:msae075. [PMID: 38606905 PMCID: PMC11050727 DOI: 10.1093/molbev/msae075] [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: 10/04/2023] [Revised: 03/18/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
The molecular evolution of the mammalian heater protein UCP1 is a powerful biomarker to understand thermoregulatory strategies during species radiation into extreme climates, such as aquatic life with high thermal conductivity. While fully aquatic mammals lost UCP1, most semiaquatic seals display intact UCP1 genes, apart from large elephant seals. Here, we show that UCP1 thermogenic activity of the small-bodied harbor seal is equally potent compared to terrestrial orthologs, emphasizing its importance for neonatal survival on land. In contrast, elephant seal UCP1 does not display thermogenic activity, not even when translating a repaired or a recently highlighted truncated version. Thus, the thermogenic benefits for neonatal survival during terrestrial birth in semiaquatic pinnipeds maintained evolutionary selection pressure on UCP1 function and were only outweighed by extreme body sizes among elephant seals, fully eliminating UCP1-dependent thermogenesis.
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Affiliation(s)
- Michael J Gaudry
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Jane Khudyakov
- Department of Biological Sciences, University of the Pacific, Stockton, CA, USA
| | - Laura Pirard
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Cathy Debier
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Daniel Crocker
- Department of Biology, Sonoma State University, Rohnert Park, CA, USA
| | - Paul G Crichton
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, UK
| | - Martin Jastroch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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Hernández G, García A, Weingarten-Gabbay S, Mishra R, Hussain T, Amiri M, Moreno-Hagelsieb G, Montiel-Dávalos A, Lasko P, Sonenberg N. Functional analysis of the AUG initiator codon context reveals novel conserved sequences that disfavor mRNA translation in eukaryotes. Nucleic Acids Res 2024; 52:1064-1079. [PMID: 38038264 PMCID: PMC10853783 DOI: 10.1093/nar/gkad1152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
mRNA translation is a fundamental process for life. Selection of the translation initiation site (TIS) is crucial, as it establishes the correct open reading frame for mRNA decoding. Studies in vertebrate mRNAs discovered that a purine at -3 and a G at +4 (where A of the AUG initiator codon is numbered + 1), promote TIS recognition. However, the TIS context in other eukaryotes has been poorly experimentally analyzed. We analyzed in vitro the influence of the -3, -2, -1 and + 4 positions of the TIS context in rabbit, Drosophila, wheat, and yeast. We observed that -3A conferred the best translational efficiency across these species. However, we found variability at the + 4 position for optimal translation. In addition, the Kozak motif that was defined from mammalian cells was only weakly predictive for wheat and essentially non-predictive for yeast. We discovered eight conserved sequences that significantly disfavored translation. Due to the big differences in translational efficiency observed among weak TIS context sequences, we define a novel category that we termed 'barren AUG context sequences (BACS)', which represent sequences disfavoring translation. Analysis of mRNA-ribosomal complexes structures provided insights into the function of BACS. The gene ontology of the BACS-containing mRNAs is presented.
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Affiliation(s)
- Greco Hernández
- mRNA and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City 14080, Mexico
| | - Alejandra García
- mRNA and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City 14080, Mexico
| | - Shira Weingarten-Gabbay
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Rishi Kumar Mishra
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru-560012, India
| | - Tanweer Hussain
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru-560012, India
| | - Mehdi Amiri
- Department of Biochemistry and Goodman Cancer Institute. McGill University., Montreal, QC H3A 1A3, Canada
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University. 75 University Ave. W, Waterloo, ON N2L 3C5, Canada
| | - Angélica Montiel-Dávalos
- mRNA and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (INCan), Mexico City 14080, Mexico
| | - Paul Lasko
- Department of Biology, McGill University. Montreal, QC H3G 0B1, Canada
| | - Nahum Sonenberg
- Department of Biochemistry and Goodman Cancer Institute. McGill University., Montreal, QC H3A 1A3, Canada
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Porto E, Loula P, Strand S, Hankeln T. Molecular analysis of the human cytoglobin mRNA isoforms. J Inorg Biochem 2024; 251:112422. [PMID: 38016326 DOI: 10.1016/j.jinorgbio.2023.112422] [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: 04/28/2023] [Revised: 09/26/2023] [Accepted: 10/29/2023] [Indexed: 11/30/2023]
Abstract
Multiple functions have been proposed for the ubiquitously expressed vertebrate globin cytoglobin (Cygb), including nitric oxide (NO) metabolism, lipid peroxidation/signalling, superoxide dismutase activity, reactive oxygen/nitrogen species (RONS) scavenging, regulation of blood pressure, antifibrosis, and both tumour suppressor and oncogenic effects. Since alternative splicing can expand the biological roles of a gene, we investigated whether this mechanism contributes to the functional diversity of Cygb. By mining of cDNA data and molecular analysis, we identified five alternative mRNA isoforms for the human CYGB gene (V-1 to V-5). Comprehensive RNA-seq analyses of public datasets from human tissues and cells confirmed that the canonical CYGB V-1 isoform is the primary CYGB transcript in the majority of analysed datasets. Interestingly, we revealed that isoform V-3 represented the predominant CYGB variant in hepatoblastoma (HB) cell lines and in the majority of analysed normal and HB liver tissues. CYGB V-3 mRNA is transcribed from an alternate upstream promoter and hypothetically encodes a N-terminally truncated CYGB protein, which is not recognized by some antibodies used in published studies. Little to no transcriptional evidence was found for the other CYGB isoforms. Comparative transcriptomics and flow cytometry on CYGB+/+ and gene-edited CYGB-/- HepG2 HB cells did not unveil a knockout phenotype and, thus, a potential function for CYGB V-3. Our study reveals that the CYGB gene is transcriptionally more complex than previously described as it expresses alternative mRNA isoforms of unknown function. Additional experimental data are needed to clarify the biological meaning of those alternative CYGB transcripts.
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Affiliation(s)
- Elena Porto
- Institute of Organismic and Molecular Evolution, Molecular Genetics & Genome Analysis Group, Johannes Gutenberg University Mainz, J. J. Becher-Weg 30A, D-55128 Mainz, Germany
| | - Paraskevi Loula
- Institute of Organismic and Molecular Evolution, Molecular Genetics & Genome Analysis Group, Johannes Gutenberg University Mainz, J. J. Becher-Weg 30A, D-55128 Mainz, Germany
| | - Susanne Strand
- Department of Internal Medicine I, Molecular Hepatology, University Medical Center, Johannes Gutenberg University Mainz, Obere Zahlbacher Strasse 63, 55131 Mainz, Germany
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics & Genome Analysis Group, Johannes Gutenberg University Mainz, J. J. Becher-Weg 30A, D-55128 Mainz, Germany.
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Etherington RD, Bailey M, Boyer JB, Armbruster L, Cao X, Coates JC, Meinnel T, Wirtz M, Giglione C, Gibbs DJ. Nt-acetylation-independent turnover of SQUALENE EPOXIDASE 1 by Arabidopsis DOA10-like E3 ligases. PLANT PHYSIOLOGY 2023; 193:2086-2104. [PMID: 37427787 PMCID: PMC10602611 DOI: 10.1093/plphys/kiad406] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
The acetylation-dependent (Ac/)N-degron pathway degrades proteins through recognition of their acetylated N-termini (Nt) by E3 ligases called Ac/N-recognins. To date, specific Ac/N-recognins have not been defined in plants. Here we used molecular, genetic, and multiomics approaches to characterize potential roles for Arabidopsis (Arabidopsis thaliana) DEGRADATION OF ALPHA2 10 (DOA10)-like E3 ligases in the Nt-acetylation-(NTA)-dependent turnover of proteins at global- and protein-specific scales. Arabidopsis has two endoplasmic reticulum (ER)-localized DOA10-like proteins. AtDOA10A, but not the Brassicaceae-specific AtDOA10B, can compensate for loss of yeast (Saccharomyces cerevisiae) ScDOA10 function. Transcriptome and Nt-acetylome profiling of an Atdoa10a/b RNAi mutant revealed no obvious differences in the global NTA profile compared to wild type, suggesting that AtDOA10s do not regulate the bulk turnover of NTA substrates. Using protein steady-state and cycloheximide-chase degradation assays in yeast and Arabidopsis, we showed that turnover of ER-localized SQUALENE EPOXIDASE 1 (AtSQE1), a critical sterol biosynthesis enzyme, is mediated by AtDOA10s. Degradation of AtSQE1 in planta did not depend on NTA, but Nt-acetyltransferases indirectly impacted its turnover in yeast, indicating kingdom-specific differences in NTA and cellular proteostasis. Our work suggests that, in contrast to yeast and mammals, targeting of Nt-acetylated proteins is not a major function of DOA10-like E3 ligases in Arabidopsis and provides further insight into plant ERAD and the conservation of regulatory mechanisms controlling sterol biosynthesis in eukaryotes.
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Affiliation(s)
- Ross D Etherington
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
| | - Mark Bailey
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
| | - Jean-Baptiste Boyer
- CEA, CNRS, Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Laura Armbruster
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Xulyu Cao
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
| | - Thierry Meinnel
- CEA, CNRS, Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, 69120, Germany
| | - Carmela Giglione
- CEA, CNRS, Université Paris-Saclay, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, 91198, France
| | - Daniel J Gibbs
- School of Biosciences, University of Birmingham, Edgbaston, West Midlands, B15 2TT, UK
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7
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Suhorukova AV, Sobolev DS, Milovskaya IG, Fadeev VS, Goldenkova-Pavlova IV, Tyurin AA. A Molecular Orchestration of Plant Translation under Abiotic Stress. Cells 2023; 12:2445. [PMID: 37887289 PMCID: PMC10605726 DOI: 10.3390/cells12202445] [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: 07/20/2023] [Revised: 09/12/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
The complexities of translational strategies make this stage of implementing genetic information one of the most challenging to comprehend and, simultaneously, perhaps the most engaging. It is evident that this diverse range of strategies results not only from a long evolutionary history, but is also of paramount importance for refining gene expression and metabolic modulation. This notion is particularly accurate for organisms that predominantly exhibit biochemical and physiological reactions with a lack of behavioural ones. Plants are a group of organisms that exhibit such features. Addressing unfavourable environmental conditions plays a pivotal role in plant physiology. This is particularly evident with the changing conditions of global warming and the irrevocable loss or depletion of natural ecosystems. In conceptual terms, the plant response to abiotic stress comprises a set of elaborate and intricate strategies. This is influenced by a range of abiotic factors that cause stressful conditions, and molecular genetic mechanisms that fine-tune metabolic pathways allowing the plant organism to overcome non-standard and non-optimal conditions. This review aims to focus on the current state of the art in the field of translational regulation in plants under abiotic stress conditions. Different regulatory elements and patterns are being assessed chronologically. We deem it important to focus on significant high-performance techniques for studying the genetic information dynamics during the translation phase.
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8
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Khalid K, Poh CL. The development of DNA vaccines against SARS-CoV-2. Adv Med Sci 2023; 68:213-226. [PMID: 37364379 PMCID: PMC10290423 DOI: 10.1016/j.advms.2023.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/07/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
BACKGROUND The COVID-19 pandemic exerted significant impacts on public health and global economy. Research efforts to develop vaccines at warp speed against SARS-CoV-2 led to novel mRNA, viral vectored, and inactivated vaccines being administered. The current COVID-19 vaccines incorporate the full S protein of the SARS-CoV-2 Wuhan strain but rapidly emerging variants of concern (VOCs) have led to significant reductions in protective efficacies. There is an urgent need to develop next-generation vaccines which could effectively prevent COVID-19. METHODS PubMed and Google Scholar were systematically reviewed for peer-reviewed papers up to January 2023. RESULTS A promising solution to the problem of emerging variants is a DNA vaccine platform since it can be easily modified. Besides expressing whole protein antigens, DNA vaccines can also be constructed to include specific nucleotide genes encoding highly conserved and immunogenic epitopes from the S protein as well as from other structural/non-structural proteins to develop effective vaccines against VOCs. DNA vaccines are associated with low transfection efficiencies which could be enhanced by chemical, genetic, and molecular adjuvants as well as delivery systems. CONCLUSIONS The DNA vaccine platform offers a promising solution to the design of effective vaccines. The challenge of limited immunogenicity in humans might be solved through the use of genetic modifications such as the addition of nuclear localization signal (NLS) peptide gene, strong promoters, MARs, introns, TLR agonists, CD40L, and the development of appropriate delivery systems utilizing nanoparticles to increase uptake by APCs in enhancing the induction of potent immune responses.
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Affiliation(s)
- Kanwal Khalid
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Bandar Sunway, Malaysia.
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9
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Russell PJ, Slivka JA, Boyle EP, Burghes AHM, Kearse MG. Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay. RNA (NEW YORK, N.Y.) 2023; 29:735-744. [PMID: 36878710 PMCID: PMC10187673 DOI: 10.1261/rna.079525.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/14/2023] [Indexed: 05/18/2023]
Abstract
It is estimated that nearly 50% of mammalian transcripts contain at least one upstream open reading frame (uORF), which are typically one to two orders of magnitude smaller than the downstream main ORF. Most uORFs are thought to be inhibitory as they sequester the scanning ribosome, but in some cases allow for translation reinitiation. However, termination in the 5' UTR at the end of uORFs resembles premature termination that is normally sensed by the nonsense-mediated mRNA decay (NMD) pathway. Translation reinitiation has been proposed as a method for mRNAs to prevent NMD. Here, we test how uORF length influences translation reinitiation and mRNA stability in HeLa cells. Using custom 5' UTRs and uORF sequences, we show that reinitiation can occur on heterologous mRNA sequences, favors small uORFs, and is supported when initiation occurs with more initiation factors. After determining reporter mRNA half-lives in HeLa cells and mining available mRNA half-life data sets for cumulative predicted uORF length, we conclude that translation reinitiation after uORFs is not a robust method for mRNAs to prevent NMD. Together, these data suggest that the decision of whether NMD ensues after translating uORFs occurs before reinitiation in mammalian cells.
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Affiliation(s)
- Paul J Russell
- Cellular, Molecular, and Biochemical Sciences Program, The Ohio State University, Columbus, Ohio 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jacob A Slivka
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Computer Science and Engineering, The Ohio State University, Columbus, Ohio 43210, USA
| | - Elaina P Boyle
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Arthur H M Burghes
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Michael G Kearse
- Cellular, Molecular, and Biochemical Sciences Program, The Ohio State University, Columbus, Ohio 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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10
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Kovaříková V, Špirková A, Šefčíková Z, Pisko J, Kalatová L, Koppel J, Fabian D, Čikoš Š. Gamma-aminobutyric acid (GABA) can affect physiological processes in preimplantation embryos via GABA A and GABA B receptors. Reprod Med Biol 2023; 22:e12528. [PMID: 37476368 PMCID: PMC10354355 DOI: 10.1002/rmb2.12528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/08/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023] Open
Abstract
Purpose Several widely used substances (e.g., some therapeutics or food supplements) can act on gamma-aminobutyric acid (GABA) receptors, and we investigated whether the activation of these receptors could affect the preimplantation embryo. Methods Transcripts of all GABA receptor subunits and selected proteins were examined using quantitative RT-PCR and immunohistochemistry. To analyze the effects of receptor activation, in vitro culture of mouse preimplantation embryos with natural and synthetic GABA receptor ligands was used. Results We detected nine GABA receptor transcripts in mouse blastocysts and 14 GABA receptor transcripts in ovulated oocytes. The results of this study indicate that ionotropic GABAA receptors can be formed from α5, β3, and γ3 (or δ, π) subunits, GABAA-ρ receptors can be formed from ρ2 subunits and metabotropic GABA receptors can be formed from GABAB1b and GABAB2 subunits in mouse blastocysts. Supplementing the culture medium with GABA at concentrations of 2-10 mM or with specific GABAA and GABAB receptor agonists (at concentrations of 10-100 μM) significantly increased the proportion of dead cells in blastocysts. The GABA-induced effects were prevented by pretreatment of embryos with GABAA and GABAB receptor antagonists. Conclusion The results of this study indicate that GABA and synthetic GABA receptor ligands can negatively affect preimplantation embryos via GABAA and GABAB receptors.
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Affiliation(s)
- Veronika Kovaříková
- Institute of Animal PhysiologyCentre of Biosciences of the Slovak Academy of SciencesKošiceSlovakia
| | - Alexandra Špirková
- Institute of Animal PhysiologyCentre of Biosciences of the Slovak Academy of SciencesKošiceSlovakia
| | - Zuzana Šefčíková
- Institute of Animal PhysiologyCentre of Biosciences of the Slovak Academy of SciencesKošiceSlovakia
| | - Jozef Pisko
- Institute of Animal PhysiologyCentre of Biosciences of the Slovak Academy of SciencesKošiceSlovakia
| | - Laura Kalatová
- Institute of Animal PhysiologyCentre of Biosciences of the Slovak Academy of SciencesKošiceSlovakia
| | - Juraj Koppel
- Institute of Animal PhysiologyCentre of Biosciences of the Slovak Academy of SciencesKošiceSlovakia
| | - Dušan Fabian
- Institute of Animal PhysiologyCentre of Biosciences of the Slovak Academy of SciencesKošiceSlovakia
| | - Štefan Čikoš
- Institute of Animal PhysiologyCentre of Biosciences of the Slovak Academy of SciencesKošiceSlovakia
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11
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Blocking AMPK β1 myristoylation enhances AMPK activity and protects mice from high-fat diet-induced obesity and hepatic steatosis. Cell Rep 2022; 41:111862. [PMID: 36543129 DOI: 10.1016/j.celrep.2022.111862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 10/07/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
AMP-activated protein kinase (AMPK) is a master regulator of cellular energy homeostasis and a therapeutic target for metabolic diseases. Co/post-translational N-myristoylation of glycine-2 (Gly2) of the AMPK β subunit has been suggested to regulate the distribution of the kinase between the cytosol and membranes through a "myristoyl switch" mechanism. However, the relevance of AMPK myristoylation for metabolic signaling in cells and in vivo is unclear. Here, we generated knockin mice with a Gly2-to-alanine point mutation of AMPKβ1 (β1-G2A). We demonstrate that non-myristoylated AMPKβ1 has reduced stability but is associated with increased kinase activity and phosphorylation of the Thr172 activation site in the AMPK α subunit. Using proximity ligation assays, we show that loss of β1 myristoylation impedes colocalization of the phosphatase PPM1A/B with AMPK in cells. Mice carrying the β1-G2A mutation have improved metabolic health with reduced adiposity, hepatic lipid accumulation, and insulin resistance under conditions of high-fat diet-induced obesity.
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12
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The Somatic Mutation Landscape of UDP-Glycosyltransferase ( UGT) Genes in Human Cancers. Cancers (Basel) 2022; 14:cancers14225708. [PMID: 36428799 PMCID: PMC9688768 DOI: 10.3390/cancers14225708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
The human UDP-glycosyltransferase (UGTs) superfamily has a critical role in the metabolism of anticancer drugs and numerous pro/anti-cancer molecules (e.g., steroids, lipids, fatty acids, bile acids and carcinogens). Recent studies have shown wide and abundant expression of UGT genes in human cancers. However, the extent to which UGT genes acquire somatic mutations within tumors remains to be systematically investigated. In the present study, our comprehensive analysis of the somatic mutation profiles of 10,069 tumors from 33 different TCGA cancer types identified 3427 somatic mutations in UGT genes. Overall, nearly 18% (1802/10,069) of the assessed tumors had mutations in UGT genes with huge variations in mutation frequency across different cancer types, ranging from over 25% in five cancers (COAD, LUAD, LUSC, SKCM and UCSC) to less than 5% in eight cancers (LAML, MESO, PCPG, PAAD, PRAD, TGCT, THYM and UVM). All 22 UGT genes showed somatic mutations in tumors, with UGT2B4, UGT3A1 and UGT3A2 showing the largest number of mutations (289, 307 and 255 mutations, respectively). Nearly 65% (2260/3427) of the mutations were missense, frame-shift and nonsense mutations that have been predicted to code for variant UGT proteins. Furthermore, about 10% (362/3427) of the mutations occurred in non-coding regions (5' UTR, 3' UTR and splice sites) that may be able to alter the efficiency of translation initiation, miRNA regulation or the splicing of UGT transcripts. In conclusion, our data show widespread somatic mutations of UGT genes in human cancers that may affect the capacity of cancer cells to metabolize anticancer drugs and endobiotics that control pro/anti-cancer signaling pathways. This highlights their potential utility as biomarkers for predicting therapeutic efficacy and clinical outcomes.
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Bowling A, Eastman A, Merlo C, Lin G, West N, Patel S, Cutting G, Sharma N. Downstream Alternate Start Site Allows N-Terminal Nonsense Variants to Escape NMD and Results in Functional Recovery by Readthrough and Modulator Combination. J Pers Med 2022; 12:jpm12091448. [PMID: 36143233 PMCID: PMC9504986 DOI: 10.3390/jpm12091448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Genetic variants that introduce premature termination codons (PTCs) have remained difficult to therapeutically target due to lack of protein product. Nonsense mediated mRNA decay (NMD) targets PTC-bearing transcripts to reduce the potentially damaging effects of truncated proteins. Readthrough compounds have been tested on PTC-generating variants in attempt to permit translation through a premature stop. However, readthrough compounds have not proved efficacious in a clinical setting due to lack of stable mRNA. Here, we investigate N-terminal variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which have been shown to escape NMD, potentially through a mechanism of alternative translation initiation at downstream AUG codons. We hypothesized that N-terminal variants in CFTR that evade NMD will produce stable transcript, allowing CFTR function to be restored by a combination of readthrough and protein modulator therapy. We investigate this using two cell line models expressing CFTR-expression minigenes (EMG; HEK293s and CFBEs) and primary human nasal epithelial (NE) cells, and we test readthrough compounds G418 and ELX-02 in combination with CFTR protein modulators. HEK293 cells expressing the variants E60X and L88X generate CFTR-specific core glycosylated products that are consistent with downstream translation initiation. Mutation of downstream methionines at codons 150 and 152 does not result in changes in CFTR protein processing in cells expressing L88X-CFTR-EMG. However, mutation of methionine at 265 results in loss of detectable CFTR protein in cells expressing E60X, L88X, and Y122X CFTR-EMGs, indicating that downstream translation initiation is occurring at the AUG codon at position M265. In HEK293 stable cells harboring L88X, treatment with readthrough compounds alone allows for formation of full-length, but misfolded CFTR protein. Upon addition of protein modulators in combination with readthrough, we observe formation of mature, complex-glycosylated CFTR. In CFBE and NE cells, addition of readthrough ELX-02 and modulator therapy results in substantial recovery of CFTR function. Our work indicates that N-terminal variants generate stable CFTR transcript due to translation initiation at a downstream AUG codon. Thus, individuals with CF bearing 5′ nonsense variants that evade NMD are ideal candidates for treatment with clinically safe readthrough compounds and modulator therapy.
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Affiliation(s)
- Alyssa Bowling
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alice Eastman
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christian Merlo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
| | - Gabrielle Lin
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Natalie West
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
| | - Shivani Patel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD 21205, USA
| | - Garry Cutting
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Neeraj Sharma
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Correspondence:
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14
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Machine learning predicts translation initiation sites in neurologic diseases with nucleotide repeat expansions. PLoS One 2022; 17:e0256411. [PMID: 35648796 PMCID: PMC9159584 DOI: 10.1371/journal.pone.0256411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
A number of neurologic diseases associated with expanded nucleotide repeats, including an inherited form of amyotrophic lateral sclerosis, have an unconventional form of translation called repeat-associated non-AUG (RAN) translation. It has been speculated that the repeat regions in the RNA fold into secondary structures in a length-dependent manner, promoting RAN translation. Repeat protein products are translated, accumulate, and may contribute to disease pathogenesis. Nucleotides that flank the repeat region, especially ones closest to the initiation site, are believed to enhance translation initiation. A machine learning model has been published to help identify ATG and near-cognate translation initiation sites; however, this model has diminished predictive power due to its extensive feature selection and limited training data. Here, we overcome this limitation and increase prediction accuracy by the following: a) capture the effect of nucleotides most critical for translation initiation via feature reduction, b) implement an alternative machine learning algorithm better suited for limited data, c) build comprehensive and balanced training data (via sampling without replacement) that includes previously unavailable sequences, and d) split ATG and near-cognate translation initiation codon data to train two separate models. We also design a supplementary scoring system to provide an additional prognostic assessment of model predictions. The resultant models have high performance, with ~85-88% accuracy, exceeding that of the previously published model by >18%. The models presented here are used to identify translation initiation sites in genes associated with a number of neurologic repeat expansion disorders. The results confirm a number of sites of translation initiation upstream of the expanded repeats that have been found experimentally, and predict sites that are not yet established.
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15
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Kedia N, Banerjee S, Mondal A. A Comprehensive Roadmap Towards the Generation of an Influenza B Reporter Assay Using a Single DNA Polymerase-Based Cloning of the Reporter RNA Construct. Front Microbiol 2022; 13:868367. [PMID: 35694292 PMCID: PMC9174941 DOI: 10.3389/fmicb.2022.868367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
The mini-genome reporter assay is a key tool for conducting RNA virus research. However, procedural complications and the lack of adequate literature pose a major challenge in developing these assay systems. Here, we present a novel, yet generic and simple, cloning strategy for the construction of an influenza B virus reporter RNA template and describe an extensive standardization of the reporter RNP/polymerase activity assay for monitoring viral RNA synthesis in an infection-free setting. Using this assay system, we showed for the first time the effect of viral protein NS1 and host protein kinase C delta (PKCD) on influenza B virus RNA synthesis. In addition, the assay system showed promising results in evaluating the efficacy of antiviral drugs targeting viral RNA synthesis and virus propagation. Together, this work offers a detailed protocol for the standardization of the influenza virus minigenome assay and an excellent tool for screening of host factors and antivirals in a fast, user-friendly, and high-throughput manner.
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16
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Xu L, Liu P, Dai Z, Fan F, Zhang X. Fine-tuning the expression of pathway gene in yeast using a regulatory library formed by fusing a synthetic minimal promoter with different Kozak variants. Microb Cell Fact 2021; 20:148. [PMID: 34320991 PMCID: PMC8317321 DOI: 10.1186/s12934-021-01641-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/21/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Tailoring gene expression to balance metabolic fluxes is critical for the overproduction of metabolites in yeast hosts, and its implementation requires coordinated regulation at both transcriptional and translational levels. Although synthetic minimal yeast promoters have shown many advantages compared to natural promoters, their transcriptional strength is still limited, which restricts their applications in pathway engineering. RESULTS In this work, we sought to expand the application scope of synthetic minimal yeast promoters by enhancing the corresponding translation levels using specific Kozak sequence variants. Firstly, we chose the reported UASF-E-C-Core1 minimal promoter as a library template and determined its Kozak motif (K0). Next, we randomly mutated the K0 to generate a chimeric promoter library, which was able to drive green fluorescent protein (GFP) expression with translational strengths spanning a 500-fold range. A total of 14 chimeric promoters showed at least two-fold differences in GFP expression strength compared to the K0 control. The best one named K528 even showed 8.5- and 3.3-fold increases in fluorescence intensity compared with UASF-E-C-Core1 and the strong native constitutive promoter PTDH3, respectively. Subsequently, we chose three representative strong chimeric promoters (K540, K536, and K528) from this library to regulate pathway gene expression. In conjunction with the tHMG1 gene for squalene production, the K528 variant produced the best squalene titer of 32.1 mg/L in shake flasks, which represents a more than 10-fold increase compared to the parental K0 control (3.1 mg/L). CONCLUSIONS All these results demonstrate that this chimeric promoter library developed in this study is an effective tool for pathway engineering in yeast.
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Affiliation(s)
- Liping Xu
- School of Life Science, University of Science and Technology of China, No. 96, JinZhai Road, Baohe District, Hefei, Anhui, 230026, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Pingping Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, People's Republic of China
| | - Zhubo Dai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, People's Republic of China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, People's Republic of China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,National Innovation Center for Synthetic Biotechnology, Tianjin, 300308, People's Republic of China.
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17
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Detailed Dissection and Critical Evaluation of the Pfizer/BioNTech and Moderna mRNA Vaccines. Vaccines (Basel) 2021; 9:vaccines9070734. [PMID: 34358150 PMCID: PMC8310186 DOI: 10.3390/vaccines9070734] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 01/19/2023] Open
Abstract
The design of Pfizer/BioNTech and Moderna mRNA vaccines involves many different types of optimizations. Proper optimization of vaccine mRNA can reduce dosage required for each injection leading to more efficient immunization programs. The mRNA components of the vaccine need to have a 5′-UTR to load ribosomes efficiently onto the mRNA for translation initiation, optimized codon usage for efficient translation elongation, and optimal stop codon for efficient translation termination. Both 5′-UTR and the downstream 3′-UTR should be optimized for mRNA stability. The replacement of uridine by N1-methylpseudourinine (Ψ) complicates some of these optimization processes because Ψ is more versatile in wobbling than U. Different optimizations can conflict with each other, and compromises would need to be made. I highlight the similarities and differences between Pfizer/BioNTech and Moderna mRNA vaccines and discuss the advantage and disadvantage of each to facilitate future vaccine improvement. In particular, I point out a few optimizations in the design of the two mRNA vaccines that have not been performed properly.
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18
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Li G, Eriani G, Wang ED, Zhou XL. Distinct pathogenic mechanisms of various RARS1 mutations in Pelizaeus-Merzbacher-like disease. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1645-1660. [PMID: 33515434 DOI: 10.1007/s11427-020-1838-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 10/13/2020] [Indexed: 12/12/2022]
Abstract
Mutations of the genes encoding aminoacyl-tRNA synthetases are highly associated with various central nervous system disorders. Recurrent mutations, including c.5A>G, p.D2G; c.1367C>T, p.S456L; c.1535G>A, p.R512Q and c.1846_1847del, p. Y616Lfs*6 of RARS1 gene, which encodes two forms of human cytoplasmic arginyl-tRNA synthetase (hArgRS), are linked to Pelizaeus-Merzbacher-like disease (PMLD) with unclear pathogenesis. Among these mutations, c.5A>G is the most extensively reported mutation, leading to a p.D2G mutation in the N-terminal extension of the long-form hArgRS. Here, we showed the detrimental effects of R512Q substitution and ΔC mutations on the structure and function of hArgRS, while the most frequent mutation c.5A>G, p.D2G acted in a different manner without impairing hArgRS activity. The nucleotide substitution c.5A>G reduced translation of hArgRS mRNA, and an upstream open reading frame contributed to the suppressed translation of the downstream main ORF. Taken together, our results elucidated distinct pathogenic mechanisms of various RARS1 mutations in PMLD.
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Affiliation(s)
- Guang Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, UPR9002 CNRS, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, 67084, Strasbourg, France
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
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19
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A novel rare c.-39C>T mutation in the PROS1 5'UTR causing PS deficiency by creating a new upstream translation initiation codon. Clin Sci (Lond) 2020; 134:1181-1190. [PMID: 32426810 DOI: 10.1042/cs20200403] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/13/2020] [Accepted: 05/19/2020] [Indexed: 01/18/2023]
Abstract
Autosomal dominant inherited Protein S deficiency (PSD) (MIM 612336) is a rare disorder caused by rare mutations, mainly located in the coding sequence of the structural PROS1 gene, and associated with an increased risk of venous thromboembolism. To identify the molecular defect underlying PSD observed in an extended French pedigree with seven PSD affected members in whom no candidate deleterious PROS1 mutation was detected by Sanger sequencing of PROS1 exons and their flanking intronic regions or via an multiplex ligation-dependent probe amplification (MLPA) approach, a whole genome sequencing strategy was adopted. This led to the identification of a never reported C to T substitution at c.-39 from the natural ATG codon of the PROS1 gene that completely segregates with PSD in the whole family. This substitution ACG→ATG creates a new start codon upstream of the main ATG. We experimentally demonstrated in HeLa cells that the variant generates a novel overlapping upstream open reading frame (uORF) and inhibits the translation of the wild-type PS. This work describes the first example of 5'UTR PROS1 mutation causing PSD through the creation of an uORF, a mutation that is not predicted to be deleterious by standard annotation softwares, and emphasizes the need for better exploration of such type of non-coding variations in clinical genomics.
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20
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Han S, Liang Y, Ma Q, Xu Y, Zhang Y, Du W, Wang C, Li Y. LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property. Brief Bioinform 2020; 20:2009-2027. [PMID: 30084867 PMCID: PMC6954391 DOI: 10.1093/bib/bby065] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 06/20/2018] [Indexed: 12/31/2022] Open
Abstract
Discovering new long non-coding RNAs (lncRNAs) has been a fundamental step in lncRNA-related research. Nowadays, many machine learning-based tools have been developed for lncRNA identification. However, many methods predict lncRNAs using sequence-derived features alone, which tend to display unstable performances on different species. Moreover, the majority of tools cannot be re-trained or tailored by users and neither can the features be customized or integrated to meet researchers’ requirements. In this study, features extracted from sequence-intrinsic composition, secondary structure and physicochemical property are comprehensively reviewed and evaluated. An integrated platform named LncFinder is also developed to enhance the performance and promote the research of lncRNA identification. LncFinder includes a novel lncRNA predictor using the heterologous features we designed. Experimental results show that our method outperforms several state-of-the-art tools on multiple species with more robust and satisfactory results. Researchers can additionally employ LncFinder to extract various classic features, build classifier with numerous machine learning algorithms and evaluate classifier performance effectively and efficiently. LncFinder can reveal the properties of lncRNA and mRNA from various perspectives and further inspire lncRNA–protein interaction prediction and lncRNA evolution analysis. It is anticipated that LncFinder can significantly facilitate lncRNA-related research, especially for the poorly explored species. LncFinder is released as R package (https://CRAN.R-project.org/package=LncFinder). A web server (http://bmbl.sdstate.edu/lncfinder/) is also developed to maximize its availability.
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Affiliation(s)
- Siyu Han
- College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Yanchun Liang
- College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China.,Zhuhai Laboratory of Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Zhuhai College of Jilin University, Zhuhai, China
| | - Qin Ma
- Bioinformatics and Mathematical Biosciences Lab, Department of Agronomy, Horticulture and Plant Science, South Dakot State University, Brookings, SD, USA.,Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA
| | - Yangyi Xu
- College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Yu Zhang
- College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Wei Du
- College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Cankun Wang
- Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA
| | - Ying Li
- College of Computer Science and Technology, Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
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21
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Modification of the second translation initiation site restricts the replication of foot-and-mouth disease virus in PK-15 cells. Appl Microbiol Biotechnol 2020; 104:8455-8466. [PMID: 32820373 PMCID: PMC7471169 DOI: 10.1007/s00253-020-10810-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/23/2020] [Accepted: 08/02/2020] [Indexed: 11/22/2022]
Abstract
Abstract The translation initiation of foot-and-mouth disease virus (FMDV) occurs at two alternative initiation sites (Lab AUG and Lb AUG). Usually, the Lb AUG is more favorably used to initiate protein synthesis than the Lab AUG. To explore the effect of Lb AUG on FMDV replication and obtain FMDV with restricted replication, this initiation codon was mutated to a variety of non-AUG codons (UGG, AUC, CUG, and AAA). Fortunately, the modifications did not prevent viral viability but influenced replication characteristics of some FMDV mutants in a cell-specific manner, as was shown by the similar replication in BHK-21 cells and delayed growth kinetics in PK-15 cells. This attenuated phenotype of FMDV mutants in PK-15 cells was found to be correlated with reduced abilities to cleave eIF4GI and suppress interference (IFN) expression. As leader (L) protein was reported to be responsible for eIF4GI cleavage and inhibition of IFN expression, the in vivo L protein synthesis was examined during the infection of FMDV mutants. Our results showed that not only the total yield of L proteins was severely influenced but also the individual yield of L protein was seen to be affected, which implied that both the relative usage of the two initiation sites and overall translation efficiency were changed by Lb AUG modifications. In addition, the in vitro translation activity was also negatively regulated by Lb AUG mutations. Collectively, these findings suggested that the restricted replications of Lb AUG-modified FMDVs were related to the delayed eIF4GI cleavage and decreased ability to block IFN expression but were mainly determined by the inefficient translation initiation. FMDVs precisely with modifications of Lb AUG initiation codon may represent safer seed viruses for vaccine production. Key points • The polyprotein translation of FMDV initiates at two alternative initiation sites (Lab AUG and Lb AUG). In order to explore the effect of Lb AUG on FMDV replication and obtain FMDV with restricted replication, the Lb initiation AUG was mutated to a variety of non-AUG codons (UGG, AUC, CUG, and AAA), and four FMDV mutants with Lb AUG modification were generated. • We found that partial FMDV mutants grew almost as well as WT virus in BHK-21 cells, a typical cell line used for FMD vaccine production, but displayed impaired replication in IFN-competent PK-15 cells. • The attenuation of mutant FMDVs in PK-15 cells was found to be correlated with delayed eIF4GI cleavage and decreased ability to block IFN expression. • We proved that the attenuated phenotype of Lb AUG-modified FMDVs was mainly determined by the inefficient translation initiation, as demonstrated by the decrease of total yield of L proteins and individual production of L protein. • We successfully generated genetically engineered FMDV with attenuated phenotype. The approach of precise engineering of FMDV with the modification of initiation codon provides a safe platform to produce inactivated antigen vaccines.
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22
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Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context. Genome Res 2020; 30:974-984. [PMID: 32669370 PMCID: PMC7397870 DOI: 10.1101/gr.257352.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 06/25/2020] [Indexed: 12/13/2022]
Abstract
Eukaryotic translation initiation involves preinitiation ribosomal complex 5′-to-3′ directional probing of mRNA for codons suitable for starting protein synthesis. The recognition of codons as starts depends on the codon identity and on its immediate nucleotide context known as Kozak context. When the context is weak (i.e., nonoptimal), leaky scanning takes place during which a fraction of ribosomes continues the mRNA probing. We explored the relationship between the context of AUG codons annotated as starts of protein-coding sequences and the next AUG codon occurrence. We found that AUG codons downstream from weak starts occur in the same frame more frequently than downstream from strong starts. We suggest that evolutionary selection on in-frame AUGs downstream from weak start codons is driven by the advantage of the reduction of wasteful out-of-frame product synthesis and also by the advantage of producing multiple proteoforms from certain mRNAs. We confirmed translation initiation downstream from weak start codons using ribosome profiling data. We also tested translation of alternative start codons in 10 specific human genes using reporter constructs. In all tested cases, initiation at downstream start codons was more productive than at the annotated ones. In most cases, optimization of Kozak context did not completely abolish downstream initiation, and in the specific example of CMPK1 mRNA, the optimized start remained unproductive. Collectively, our work reveals previously uncharacterized forces shaping the evolution of protein-coding genes and points to the plurality of translation initiation and the existence of sequence features influencing start codon selection, other than Kozak context.
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23
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Khitun A, Slavoff SA. Proteomic Detection and Validation of Translated Small Open Reading Frames. ACTA ACUST UNITED AC 2020; 11:e77. [PMID: 31750990 DOI: 10.1002/cpch.77] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small open reading frames (smORFs) encode previously unannotated polypeptides or short proteins that regulate translation in cis (eukaryotes) and/or are independently functional (prokaryotes and eukaryotes). Ongoing efforts for complete annotation and functional characterization of smORF-encoded proteins have yielded novel regulators and therapeutic targets. However, because they are excluded from protein databases, initiate at non-AUG start codons, and produce few unique tryptic peptides, unannotated small proteins cannot be detected with standard proteomic methods. Here,, we outline a procedure for mass spectrometry-based detection of translated smORFs in cultured human cells from protein extraction, digestion, and LC-MS/MS, to database preparation and data analysis. Following proteomic detection, translation from a unique smORF may be validated via siRNA-based silencing or overexpression and epitope tagging. This is necessary to unambiguously assign a peptide to a smORF within a specific transcript isoform or genomic locus. Provided that sufficient starting material is available, this workflow can be applied to any cell type/organism and adjusted to study specific (patho)physiological contexts including, but not limited to, development, stress, and disease. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Protein extraction, size selection, and trypsin digestion Alternate Protocol 1: In-solution C8 column size selection Support Protocol 1: Chloroform/methanol precipitation Support Protocol 2: Reduction, alkylation, and in-solution protease digestion Support Protocol 3: Peptide de-salting Basic Protocol 2: Two-dimensional LC-MS/MS with ERLIC fractionation Basic Protocol 3: Transcriptomic database construction Alternate Protocol 2: Transcriptomics database generation with gffread Basic Protocol 4: Non-annotated peptide identification from LC-MS/MS data Basic Protocol 5: Validation using isotopically labeled synthetic peptide standards and siRNA Basic Protocol 6: Transcript validation using transient overexpression.
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Affiliation(s)
- Alexandra Khitun
- Department of Chemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, Connecticut.,Chemical Biology Institute, Yale University, West Haven, Connecticut.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
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24
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Mazalovska M, Kouokam JC. Transiently Expressed Mistletoe Lectin II in Nicotiana benthamiana Demonstrates Anticancer Activity In Vitro. Molecules 2020; 25:E2562. [PMID: 32486427 PMCID: PMC7321061 DOI: 10.3390/molecules25112562] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/25/2020] [Accepted: 05/30/2020] [Indexed: 12/24/2022] Open
Abstract
Mistletoe (Viscum album) extracts have been used as alternative and complementary therapeutic preparations in multiple cancers for decades. Mistletoe lectins (ML-I, ML-II, and ML-III) are considered to be the main anticancer components of such preparations. In the present study, ML-II was transiently expressed in Nicotiana benthamiana using the pEAQ-HT expression system. Expression levels of up to 60 mg/kg of the infiltrated plant tissue were obtained, and a three-fold increase was achieved by adding the endoplasmic reticulum (ER) retention signal KDEL to the native ML-II sequence. The native protein containing His-tag and KDEL was purified by immobilized metal affinity chromatography (IMAC) and gel filtration. We found that the recombinant ML-II lectin was glycosylated and retained its carbohydrate-binding activity. In addition, we demonstrated that plant produced ML-II displayed anticancer activity in vitro, inhibiting non-small cell lung cancer H460 and A549 cells with EC50 values of 4 and 3.5 µg/mL, respectively. Annexin V-448A and PI double staining revealed that cell cytotoxicity occurred via apoptosis induction. These results indicate that ML-II transiently expressed in N. benthamiana plants is a promising candidate as an anticancer agent, although further optimization of production and purification methods is required to enable further in vitro testing, as well as in vivo assays.
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Affiliation(s)
- Milena Mazalovska
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, USA;
- Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - J. Calvin Kouokam
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, USA;
- Center for Predictive Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
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25
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Blanco N, Williams AJ, Tang D, Zhan D, Misaghi S, Kelley RF, Simmons LC. Tailoring translational strength using Kozak sequence variants improves bispecific antibody assembly and reduces product‐related impurities in CHO cells. Biotechnol Bioeng 2020; 117:1946-1960. [DOI: 10.1002/bit.27347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/06/2020] [Accepted: 03/29/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Noelia Blanco
- Departments of Cell CultureGenentech, Inc., 1 DNA Way South San Francisco California
| | - Ambrose J. Williams
- Departments of Purification DevelopmentGenentech, Inc., 1 DNA Way South San Francisco California
| | - Danming Tang
- Departments of Cell CultureGenentech, Inc., 1 DNA Way South San Francisco California
| | - Dejin Zhan
- Departments of Cell CultureGenentech, Inc., 1 DNA Way South San Francisco California
| | - Shahram Misaghi
- Departments of Cell CultureGenentech, Inc., 1 DNA Way South San Francisco California
| | - Robert F. Kelley
- Departments of Drug DeliveryGenentech, Inc., 1 DNA Way South San Francisco California
| | - Laura C. Simmons
- Departments of Cell CultureGenentech, Inc., 1 DNA Way South San Francisco California
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26
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Demongeot J, Seligmann H. Why Is AUG the Start Codon?: Theoretical Minimal RNA Rings: Maximizing Coded Information Biases 1st Codon for the Universal Initiation Codon AUG. Bioessays 2020; 42:e1900201. [PMID: 32227358 DOI: 10.1002/bies.201900201] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 02/09/2020] [Indexed: 01/04/2023]
Abstract
The rational design of theoretical minimal RNA rings predetermines AUG as the universal start codon. This design maximizes coded amino acid diversity over minimal sequence length, defining in silico theoretical minimal RNA rings, candidate ancestral genes. RNA rings code for 21 amino acids and a stop codon after three consecutive translation rounds, and form a degradation-delaying stem-loop hairpin. Twenty-five RNA rings match these constraints, ten start with the universal initiation codon AUG. No first codon bias exists among remaining RNA rings. RNA ring design predetermines AUG as initiation codon. This is the only explanation yet for AUG as start codon. RNA ring design determines additional RNA ring gene- and tRNA-like properties described previously, because it presumably mimics constraints on life's primordial RNAs.
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Affiliation(s)
- Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, Université Grenoble Alpes, La Tronche, F-38700, France
| | - Hervé Seligmann
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, Université Grenoble Alpes, La Tronche, F-38700, France.,The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, 91404, Israel
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27
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The Multifaceted Roles of the Tumor Susceptibility Gene 101 (TSG101) in Normal Development and Disease. Cancers (Basel) 2020; 12:cancers12020450. [PMID: 32075127 PMCID: PMC7073217 DOI: 10.3390/cancers12020450] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/13/2022] Open
Abstract
The multidomain protein encoded by the Tumor Susceptibility Gene 101 (TSG101) is ubiquitously expressed and is suggested to function in diverse intracellular processes. In this review, we provide a succinct overview of the main structural features of the protein and their suggested roles in molecular and cellular functions. We then summarize, in more detail, key findings from studies using genetically engineered animal models that demonstrate essential functions of TSG101 in cell proliferation and survival, normal tissue homeostasis, and tumorigenesis. Despite studies on cell lines that provide insight into the molecular underpinnings by which TSG101 might function as a negative growth regulator, a biologically significant role of TSG101 as a tumor suppressor has yet to be confirmed using genuine in vivo cancer models. More recent observations from several cancer research teams suggest that TSG101 might function as an oncoprotein. A potential role of post-translational mechanisms that control the expression of the TSG101 protein in cancer is being discussed. In the final section of the review, we summarize critical issues that need to be addressed to gain a better understanding of biologically significant roles of TSG101 in cancer.
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28
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Goodson-Gregg FJ, Rothbard B, Zhang A, Wright PW, Li H, Walker-Sperling VE, Carrington M, Anderson SK. Tuning of NK-Specific HLA-C Expression by Alternative mRNA Splicing. Front Immunol 2020; 10:3034. [PMID: 31998314 PMCID: PMC6966967 DOI: 10.3389/fimmu.2019.03034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/11/2019] [Indexed: 01/05/2023] Open
Abstract
A complex system regulating HLA-C expression in NK cells, driven by an NK-specific promoter that produces alternatively spliced variants of the 5'-UTR has been recently identified. Exon content of the NK-specific 5'-UTR varies strikingly across HLA-C alleles, with some exons being allele specific. In order to investigate the possibility that allelic variation in the 5'-UTR modulates HLA-C expression levels, cDNAs containing several distinct classes of 5'-UTR were compared. Subtle changes in 5'-UTR content had a significant effect on the expression of HLA-C * 03 and HLA-C * 12 cDNA clones, suggesting that alternative splicing can fine-tune the level of protein expression. The HLA-C * 06 allele was found to be highly expressed in relation to the other alleles studied. However, its increased expression was primarily associated with differences in the peptide-binding groove. Although the impact of allele-specific alternative splicing of NK-Pro transcripts on protein levels can be modest when compared with the effect of changes in peptide-loading, alternative splicing may represent an additional regulatory mechanism to fine-tune HLA-C levels within NK cells in distinct tissue environments or at different stages of maturation in order to achieve optimal levels of missing-self recognition.
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Affiliation(s)
- Frederick J Goodson-Gregg
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Brian Rothbard
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Amy Zhang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Paul W Wright
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Hongchuan Li
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Victoria E Walker-Sperling
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
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29
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Fesenko I, Kirov I, Kniazev A, Khazigaleeva R, Lazarev V, Kharlampieva D, Grafskaia E, Zgoda V, Butenko I, Arapidi G, Mamaeva A, Ivanov V, Govorun V. Distinct types of short open reading frames are translated in plant cells. Genome Res 2019; 29:1464-1477. [PMID: 31387879 PMCID: PMC6724668 DOI: 10.1101/gr.253302.119] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023]
Abstract
Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of 10 plant species examined. Mass spectrometry analysis of proteomic and peptidomic data sets suggested that tens of sORFs located on distinct parts of mRNAs and long noncoding RNAs (lncRNAs) are translated, including conserved sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Functional analysis of four lncRNA-encoded peptides showed that sORFs-encoded peptides are involved in regulation of growth and differentiation in moss. Knocking out lncRNA-encoded peptides resulted in a decrease of moss growth. In contrast, the overexpression of these peptides resulted in a diverse range of phenotypic effects. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.
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Affiliation(s)
- Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Ilya Kirov
- Laboratory of marker-assisted and genomic selection of plants, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russian Federation
| | - Andrey Kniazev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Regina Khazigaleeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vassili Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russian Federation
| | - Daria Kharlampieva
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Ekaterina Grafskaia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russian Federation
| | - Viktor Zgoda
- Laboratory of System Biology, Institute of Biomedical Chemistry, 119121 Moscow, Russian Federation
| | - Ivan Butenko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Georgy Arapidi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation.,Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
| | - Anna Mamaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vadim Ivanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation
| | - Vadim Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation
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30
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Hernández G, Osnaya VG, Pérez-Martínez X. Conservation and Variability of the AUG Initiation Codon Context in Eukaryotes. Trends Biochem Sci 2019; 44:1009-1021. [PMID: 31353284 DOI: 10.1016/j.tibs.2019.07.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 06/22/2019] [Accepted: 07/02/2019] [Indexed: 01/30/2023]
Abstract
Selection of the translation initiation site (TIS) is a crucial step during translation. In the 1980s Marylin Kozak performed key studies on vertebrate mRNAs to characterize the optimal TIS consensus sequence, the Kozak motif. Within this motif, conservation of nucleotides in crucial positions, namely a purine at -3 and a G at +4 (where the A of the AUG is numbered +1), is essential for TIS recognition. Ever since its characterization the Kozak motif has been regarded as the optimal sequence to initiate translation in all eukaryotes. We revisit here published in silico data on TIS consensus sequences, as well as experimental studies from diverse eukaryotic lineages, and propose that, while the -3A/G position is universally conserved, the remaining variability of the consensus sequences enables their classification as optimal, strong, and moderate TIS sequences.
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Affiliation(s)
- Greco Hernández
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (Instituto Nacional de Cancerología, INCan), 22 San Fernando Avenue, Tlalpan, 14080 Mexico City, Mexico.
| | - Vincent G Osnaya
- Translation and Cancer Laboratory, Unit of Biomedical Research on Cancer, National Institute of Cancer (Instituto Nacional de Cancerología, INCan), 22 San Fernando Avenue, Tlalpan, 14080 Mexico City, Mexico
| | - Xochitl Pérez-Martínez
- Department of Molecular Genetics, Cell Physiology Institute (Instituto de Fisiología Celular), Universidad Nacional Autónoma de México (UNAM), 04510 Mexico City, Mexico
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31
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Mogilenko DA, Shavva VS, Dizhe EB, Orlov SV. Characterization of Distal and Proximal Alternative Promoters of the Human ApoA-I Gene. Mol Biol 2019. [DOI: 10.1134/s0026893319030129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Liang XH, Shen W, Crooke ST. Specific Increase of Protein Levels by Enhancing Translation Using Antisense Oligonucleotides Targeting Upstream Open Frames. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 28639196 DOI: 10.1007/978-981-10-4310-9_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A number of diseases are caused by low levels of key proteins; therefore, increasing the amount of specific proteins in human bodies is of therapeutic interest. Protein expression is downregulated by some structural or sequence elements present in the 5' UTR of mRNAs, such as upstream open reading frames (uORF). Translation initiation from uORF(s) reduces translation from the downstream primary ORF encoding the main protein product in the same mRNA, leading to a less efficient protein expression. Therefore, it is possible to use antisense oligonucleotides (ASOs) to specifically inhibit translation of the uORF by base-pairing with the uAUG region of the mRNA, redirecting translation machinery to initiate from the primary AUG site. Here we review the recent findings that translation of specific mRNAs can be enhanced using ASOs targeting uORF regions. Appropriately designed and optimized ASOs are highly specific, and they act in a sequence- and position-dependent manner, with very minor off-target effects. Protein levels can be increased using this approach in different types of human and mouse cells, and, importantly, also in mice. Since uORFs are present in around half of human mRNAs, the uORF-targeting ASOs may thus have valuable potential as research tools and as therapeutics to increase the levels of proteins for a variety of genes.
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Affiliation(s)
- Xue-Hai Liang
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, USA.
| | - Wen Shen
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, USA
| | - Stanley T Crooke
- Department of Core Antisense Research, Ionis Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA, 92010, USA
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33
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Sumirtanurdin R, Thalib AY, Cantona K, Abdulah R. Effect of genetic polymorphisms on Alzheimer's disease treatment outcomes: an update. Clin Interv Aging 2019; 14:631-642. [PMID: 30992661 PMCID: PMC6445219 DOI: 10.2147/cia.s200109] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Genetic variations in individuals may cause differences in the response to cholinesterase inhibitor drugs used in the treatment of Alzheimer's disease (AD). Through this review, we aimed to understand the potential relationship between genetic polymorphisms and treatment response in AD. We conducted a systematic review of the studies published from 2006 to 2018 that assessed the relationship between genetic polymorphisms and the pharmacotherapeutic outcomes of patients with AD. Via several possible mechanisms, genetic polymorphisms of many genes, including ABCA1, ApoE3, CYP2D6, CHAT, CHRNA7, and ESR1, appear to have strong correlations with the treatment response of patients with AD. Indeed, these genetic polymorphisms, either in the form of single nucleotide polymorphisms or direct changes to one or more amino acids, have been shown to cause differences in the therapeutic response. In summary, our findings indicate that genetic polymorphisms should be considered in the management of AD to achieve both effective and efficient treatment outcomes in terms of cost and prognosis.
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Affiliation(s)
- Riyadi Sumirtanurdin
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Indonesia,
| | - Amirah Y Thalib
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Indonesia,
| | - Kelvin Cantona
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Indonesia,
| | - Rizky Abdulah
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Indonesia, .,Center of Excellence in Higher Education for Pharmaceutical Care Innovation, Universitas Padjadjaran, Jatinangor, Indonesia,
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34
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Norder H, Twagirumugabe T, Said J, Tian Y, Tang KW, Lindh M. High Frequency of Either Altered Pre-Core StartCodon or Weakened Kozak Sequence in the CorePromoter Region in Hepatitis B Virus A1 Strainsfrom Rwanda. Genes (Basel) 2019; 10:genes10030182. [PMID: 30813638 PMCID: PMC6471190 DOI: 10.3390/genes10030182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is endemic in Rwanda and is a major etiologic agent for chronic liver disease in the country. In a previous analysis of HBV strains from Rwanda, the S genes of most strains segregated into one single clade of subgenotype, A1. More than half (55%) of the anti-HBe positive individuals were viremic. In this study, 23 complete HBV genomes and the core promoter region (CP) from 18 additional strains were sequenced. Phylogenetic analysis of complete genomes confirmed that most Rwandan strain formed a single unique clade, within subgenotype A1. Strains from 17 of 22 (77%) anti-HBe positive HBV carriers had either mutated the precore start codon (9 strains with either CUG, ACG, UUG, or AAG) or mutations in the Kozak sequence preceding the pre-core start codon (8 strains). These mutually exclusive mutations were also identified in subgenotypes A1 (70/266; 26%), A2 (12/255; 5%), and A3 (26/49; 53%) sequences from the GenBank. The results showed that previous, rarely described HBV variants, expressing little or no HBeAg, are selected in anti-HBe positive subgenotype Al carriers from Rwanda and that mutations reducing HBeAg synthesis might be unique for a particular HBV clade, not just for a specific genotype or subgenotype.
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Affiliation(s)
- Heléne Norder
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, 405 30 Gothenburg, Sweden.
| | - Theogene Twagirumugabe
- School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.
| | - Joanna Said
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, 405 30 Gothenburg, Sweden.
| | - Yarong Tian
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, 405 30 Gothenburg, Sweden.
| | - Ka-Wei Tang
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, 405 30 Gothenburg, Sweden.
| | - Magnus Lindh
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, Gothenburg University, 405 30 Gothenburg, Sweden.
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35
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Lorenzo-Orts L, Witthoeft J, Deforges J, Martinez J, Loubéry S, Placzek A, Poirier Y, Hothorn LA, Jaillais Y, Hothorn M. Concerted expression of a cell cycle regulator and a metabolic enzyme from a bicistronic transcript in plants. NATURE PLANTS 2019; 5:184-193. [PMID: 30737513 DOI: 10.1038/s41477-019-0358-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/04/2019] [Indexed: 05/15/2023]
Abstract
Eukaryotic mRNAs frequently contain upstream open reading frames (uORFs), encoding small peptides that may control translation of the main ORF (mORF). Here, we report the characterization of a distinct bicistronic transcript in Arabidopsis. We analysed loss-of-function phenotypes of the inorganic polyphosphatase TRIPHOSPHATE TUNNEL METALLOENZYME 3 (AtTTM3), and found that catalytically inactive versions of the enzyme could fully complement embryo and growth-related phenotypes. We could rationalize these puzzling findings by characterizing a uORF in the AtTTM3 locus encoding CELL DIVISION CYCLE PROTEIN 26 (CDC26), an orthologue of the cell cycle regulator. We demonstrate that AtCDC26 is part of the plant anaphase promoting complex/cyclosome (APC/C), regulates accumulation of APC/C target proteins and controls cell division, growth and embryo development. AtCDC26 and AtTTM3 are translated from a single transcript conserved across the plant lineage. While there is no apparent biochemical connection between the two gene products, AtTTM3 coordinates AtCDC26 translation by recruiting the transcript into polysomes. Our work highlights that uORFs may encode functional proteins in plant genomes.
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Affiliation(s)
- Laura Lorenzo-Orts
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
| | - Janika Witthoeft
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Jules Deforges
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Jacobo Martinez
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Sylvain Loubéry
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Aleksandra Placzek
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Yves Poirier
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Ludwig A Hothorn
- Institute of Biostatistics, Leibniz University, Hannover, Germany
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France
| | - Michael Hothorn
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland.
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
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36
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Abrahams L, Hurst LD. Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts. Mol Biol Evol 2018; 34:3064-3080. [PMID: 28961919 PMCID: PMC5850271 DOI: 10.1093/molbev/msx223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Beyond selection for optimal protein functioning, coding sequences (CDSs) are under selection at the RNA and DNA levels. Here, we identify a possible signature of “dual-coding,” namely extensive adenine (A) enrichment at bacterial CDS fourth sites. In 99.07% of studied bacterial genomes, fourth site A use is greater than expected given genomic A-starting codon use. Arguing for nucleotide level selection, A-starting serine and arginine second codons are heavily utilized when compared with their non-A starting synonyms. Several models have the ability to explain some of this trend. In part, A-enrichment likely reduces 5′ mRNA stability, promoting translation initiation. However T/U, which may also reduce stability, is avoided. Further, +1 frameshifts on the initiating ATG encode a stop codon (TGA) provided A is the fourth residue, acting either as a frameshift “catch and destroy” or a frameshift stop and adjust mechanism and hence implicated in translation initiation. Consistent with both, genomes lacking TGA stop codons exhibit weaker fourth site A-enrichment. Sequences lacking a Shine–Dalgarno sequence and those without upstream leader genes, that may be more error prone during initiation, have greater utilization of A, again suggesting a role in initiation. The frameshift correction model is consistent with the notion that many genomic features are error-mitigation factors and provides the first evidence for site-specific out of frame stop codon selection. We conjecture that the NTG universal start codon may have evolved as a consequence of TGA being a stop codon and the ability of NTGA to rapidly terminate or adjust a ribosome.
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Affiliation(s)
- Liam Abrahams
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Laurence D Hurst
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
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37
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Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
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38
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Kwon H, Jang D, Choi M, Lee J, Jeong K, Pak Y. Alternative translation initiation of Caveolin-2 desensitizes insulin signaling through dephosphorylation of insulin receptor by PTP1B and causes insulin resistance. Biochim Biophys Acta Mol Basis Dis 2018; 1864:2169-2182. [PMID: 29604334 DOI: 10.1016/j.bbadis.2018.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/08/2018] [Accepted: 03/26/2018] [Indexed: 12/30/2022]
Abstract
Insulin resistance, defined as attenuated sensitivity responding to insulin, impairs insulin action. Direct causes and molecular mechanisms of insulin resistance have thus far remained elusive. Here we show that alternative translation initiation (ATI) of Caveolin-2 (Cav-2) regulates insulin sensitivity. Cav-2β isoform yielded by ATI desensitizes insulin receptor (IR) via dephosphorylation by protein-tyrosine phosphatase 1B (PTP1B), and subsequent endocytosis and lysosomal degradation of IR, causing insulin resistance. Blockage of Cav-2 ATI protects against insulin resistance by preventing Cav-2β-PTP1B-directed IR desensitization, thereby normalizing insulin sensitivity and glucose uptake. Our findings show that Cav-2β is a negative regulator of IR signaling, and identify a mechanism causing insulin resistance through control of insulin sensitivity via Cav-2 ATI.
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Affiliation(s)
- Hayeong Kwon
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Donghwan Jang
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Moonjeong Choi
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jaewoong Lee
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Kyuho Jeong
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Yunbae Pak
- Division of Life Science, Graduate School of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea.
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Acevedo JM, Hoermann B, Schlimbach T, Teleman AA. Changes in global translation elongation or initiation rates shape the proteome via the Kozak sequence. Sci Rep 2018; 8:4018. [PMID: 29507361 PMCID: PMC5838203 DOI: 10.1038/s41598-018-22330-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/21/2018] [Indexed: 11/23/2022] Open
Abstract
The sequence context surrounding the AUG start codon of an open reading frame - the ‘Kozak sequence’ - affects the probability with which a scanning ribosome will recognize the start codon and start translating there. A significant number of transcripts in animals such as Drosophila contain weak Kozak sequences. This is predicted to cause constitutively low translation of these transcripts. We study here the additional possibility that these mRNAs have weak Kozak sequences to allow for the regulation of their translation in response to stress or altered cellular signaling. We find that transcripts with weak Kozak sequences are less sensitive to drops in global elongation rates and more sensitive to drops in global initiation rates compared to transcripts with strong Kozak sequences. This provides a mechanism by which changes in these global translation parameters differentially affect different pools of mRNAs depending on their Kozak sequence, thereby shaping the proteome. Interestingly, mRNAs with weak Kozak sequences are enriched for genes involved in neurobiology, suggesting that they constitute a functional group that can be translationally co-regulated.
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Affiliation(s)
- Julieta M Acevedo
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,National Center for Tumor Diseases (NCT), partner site, Heidelberg, Germany
| | - Bernhard Hoermann
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Heidelberg University, 69120, Heidelberg, Germany
| | - Tilo Schlimbach
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. .,Heidelberg University, 69120, Heidelberg, Germany. .,National Center for Tumor Diseases (NCT), partner site, Heidelberg, Germany.
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40
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41
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Lee KH, Oghamian S, Park JA, Kang L, Laird PW. The REMOTE-control system: a system for reversible and tunable control of endogenous gene expression in mice. Nucleic Acids Res 2017; 45:12256-12269. [PMID: 28981717 PMCID: PMC5716148 DOI: 10.1093/nar/gkx829] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/07/2017] [Indexed: 12/30/2022] Open
Abstract
We report here a robust, tunable, and reversible transcription control system for endogenous genes. The REMOTE-control system (Reversible Manipulation of Transcription at Endogenous loci) employs enhanced lac repression and tet activation systems. With this approach, we show in mouse embryonic stem cells that endogenous Dnmt1 gene transcription could be up- or downregulated in a tunable, inducible, and reversible manner across nearly two orders of magnitude. Transcriptional repression of Dnmt1 by REMOTE-control was potent enough to cause embryonic lethality in mice, reminiscent of a genetic knockout of Dnmt1 and could substantially suppress intestinal polyp formation when applied to an ApcMin model. Binding by the enhanced lac repressor was sufficiently tight to allow strong attenuation of transcriptional elongation, even at operators located many kilobases downstream of the transcription start site and to produce invariably tight repression of all of the strong viral/mammalian promoters tested. Our approach of targeting tet transcriptional activators to the endogenous Dnmt1 promoter resulted in robust upregulation of this highly expressed housekeeping gene. Our system provides exquisite control of the level, timing, and cell-type specificity of endogenous gene expression, and the potency and versatility of the system will enable high resolution in vivo functional analyses.
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Affiliation(s)
- Kwang-Ho Lee
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | | | - Jin-A Park
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Liang Kang
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
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42
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Hayashi N, Sasaki S, Takahashi H, Yamashita Y, Naito S, Onouchi H. Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest. Nucleic Acids Res 2017. [PMID: 28637336 PMCID: PMC5587730 DOI: 10.1093/nar/gkx528] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Specific sequences of certain nascent peptides cause programmed ribosomal arrest during mRNA translation to control gene expression. In eukaryotes, most known regulatory arrest peptides are encoded by upstream open reading frames (uORFs) present in the 5′-untranslated region of mRNAs. However, to date, a limited number of eukaryotic uORFs encoding arrest peptides have been reported. Here, we searched for arrest peptide-encoding uORFs among Arabidopsis thaliana uORFs with evolutionarily conserved peptide sequences. Analysis of in vitro translation products of 22 conserved uORFs identified three novel uORFs causing ribosomal arrest in a peptide sequence-dependent manner. Stop codon-scanning mutagenesis, in which the effect of changing the uORF stop codon position on the ribosomal arrest was examined, and toeprint analysis revealed that two of the three uORFs cause ribosomal arrest during translation elongation, whereas the other one causes ribosomal arrest during translation termination. Transient expression assays showed that the newly identified arrest-causing uORFs exerted a strong sequence-dependent repressive effect on the expression of the downstream reporter gene in A. thaliana protoplasts. These results suggest that the peptide sequences of the three uORFs identified in this study cause ribosomal arrest in the uORFs, thereby repressing the expression of proteins encoded by the main ORFs.
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Affiliation(s)
- Noriya Hayashi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Shun Sasaki
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Chiba 263-8522, Japan
| | - Yui Yamashita
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Satoshi Naito
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.,Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Hitoshi Onouchi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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43
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Svitkin YV, Cheng YM, Chakraborty T, Presnyak V, John M, Sonenberg N. N1-methyl-pseudouridine in mRNA enhances translation through eIF2α-dependent and independent mechanisms by increasing ribosome density. Nucleic Acids Res 2017; 45:6023-6036. [PMID: 28334758 PMCID: PMC5449617 DOI: 10.1093/nar/gkx135] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 02/20/2017] [Indexed: 12/21/2022] Open
Abstract
Certain chemical modifications confer increased stability and low immunogenicity to in vitro transcribed mRNAs, thereby facilitating expression of therapeutically important proteins. Here, we demonstrate that N1-methyl-pseudouridine (N1mΨ) outperforms several other nucleoside modifications and their combinations in terms of translation capacity. Through extensive analysis of various modified transcripts in cell-free translation systems, we deconvolute the different components of the effect on protein expression independent of mRNA stability mechanisms. We show that in addition to turning off the immune/eIF2α phosphorylation-dependent inhibition of translation, the incorporated N1mΨ nucleotides dramatically alter the dynamics of the translation process by increasing ribosome pausing and density on the mRNA. Our results indicate that the increased ribosome loading of modified mRNAs renders them more permissive for initiation by favoring either ribosome recycling on the same mRNA or de novo ribosome recruitment.
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Affiliation(s)
- Yuri V Svitkin
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada
| | | | | | | | | | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montréal, Québec H3A 1A3, Canada.,Rosalind and Morris Goodman Cancer Research Centre, Montréal, Québec H3A 1A3, Canada
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44
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von Bohlen AE, Böhm J, Pop R, Johnson DS, Tolmie J, Stücker R, Morris-Rosendahl D, Scherer G. A mutation creating an upstream initiation codon in the SOX9 5' UTR causes acampomelic campomelic dysplasia. Mol Genet Genomic Med 2017; 5:261-268. [PMID: 28546996 PMCID: PMC5441400 DOI: 10.1002/mgg3.282] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/10/2017] [Accepted: 02/10/2017] [Indexed: 11/23/2022] Open
Abstract
Background Campomelic dysplasia (CD) is a semilethal developmental disorder caused by mutations in and around SOX9. CD is characterized by multiple skeletal malformations including bending (campomelia) of long bones. Surviving patients frequently have the acampomelic form of CD (ACD). Methods This is a single case report on a patient with clinical and radiological features of ACD who has no mutation in the SOX9 protein‐coding sequence nor a translocation with breakpoint in the SOX9 regulatory domain. We include functional studies of the novel mutant protein in vitro and in cultured cells. Results The patient was found to have a de novo heterozygous mutation c.‐185G>A in the SOX9 5′UTR. The mutation creates an upstream translation start codon, uAUG, with a much better fit of its flanking sequence to the Kozak consensus than the wild‐type AUG. By in vitro transcription‐translation and transient transfection into COS‐7 cells, we show that the uAUG leads to translation of a short peptide from a reading frame that terminates just after the wild‐type AUG start codon. This results in reduced translation of the wild‐type protein, compatible with the milder phenotype of the patient. Conclusion Findings support the notion that more mildly affected, surviving CD/ACD patients carry mutant SOX9 alleles with residual expression of SOX9 wild‐type protein. Although rarely described in human genetic disease and for the first time here for CD, mutations creating upstream AUG codons may be more common than generally assumed.
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Affiliation(s)
- Anna E von Bohlen
- Institute of Human GeneticsUniversity of FreiburgFreiburgGermany.,Present address: Klinik für AnästhesiologieOperative Intensivmedizin und SchmerztherapieUniklinikum Gießen und MarburgGießenGermany
| | - Johann Böhm
- Institute of Human GeneticsUniversity of FreiburgFreiburgGermany.,Present address: Department of Translational Medicine and NeurogeneticsIGBMCIllkirchFrance
| | - Ramona Pop
- Institute of Human GeneticsUniversity of FreiburgFreiburgGermany.,Present address: Broad Institute of MIT and HarvardCambridgeMassachusetts02142USA.,Present address: Harvard Stem Cell InstituteCambridgeMassachusetts02138USA.,Present address: Department of Stem Cell and Regenerative BiologyHarvard UniversityCambridgeMassachusetts02138USA
| | - Diana S Johnson
- Institute of Medical GeneticsYorkhill NHS TrustGlasgowUK.,Present address: Clinical GeneticsSheffield Children's Hospital NHS Foundation TrustSheffieldUK
| | - John Tolmie
- Institute of Medical GeneticsYorkhill NHS TrustGlasgowUK
| | | | - Deborah Morris-Rosendahl
- Institute of Human GeneticsUniversity of FreiburgFreiburgGermany.,Present address: Clinical Genetics and GenomicsRoyal Brompton and Harefield NHS Foundation Trust and National Heart and Lung InstituteImperial College LondonLondonUK
| | - Gerd Scherer
- Institute of Human GeneticsUniversity of FreiburgFreiburgGermany
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45
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The Five Immune Forces Impacting DNA-Based Cancer Immunotherapeutic Strategy. Int J Mol Sci 2017; 18:ijms18030650. [PMID: 28304339 PMCID: PMC5372662 DOI: 10.3390/ijms18030650] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/06/2017] [Accepted: 03/13/2017] [Indexed: 12/26/2022] Open
Abstract
DNA-based vaccine strategy is increasingly realized as a viable cancer treatment approach. Strategies to enhance immunogenicity utilizing tumor associated antigens have been investigated in several pre-clinical and clinical studies. The promising outcomes of these studies have suggested that DNA-based vaccines induce potent T-cell effector responses and at the same time cause only minimal side-effects to cancer patients. However, the immune evasive tumor microenvironment is still an important hindrance to a long-term vaccine success. Several options are currently under various stages of study to overcome immune inhibitory effect in tumor microenvironment. Some of these approaches include, but are not limited to, identification of neoantigens, mutanome studies, designing fusion plasmids, vaccine adjuvant modifications, and co-treatment with immune-checkpoint inhibitors. In this review, we follow a Porter’s analysis analogy, otherwise commonly used in business models, to analyze various immune-forces that determine the potential success and sustainable positive outcomes following DNA vaccination using non-viral tumor associated antigens in treatment against cancer.
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46
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Šimčíková M, Prather KLJ, Prazeres DMF, Monteiro GA. Towards effective non-viral gene delivery vector. Biotechnol Genet Eng Rev 2017; 31:82-107. [PMID: 27160661 DOI: 10.1080/02648725.2016.1178011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Despite very good safety records, clinical trials using plasmid DNA failed due to low transfection efficiency and brief transgene expression. Although this failure is both due to poor plasmid design and to inefficient delivery methods, here we will focus on the former. The DNA elements like CpG motifs, selection markers, origins of replication, cryptic eukaryotic signals or nuclease-susceptible regions and inverted repeats showed detrimental effects on plasmids' performance as biopharmaceuticals. On the other hand, careful selection of promoter, polyadenylation signal, codon optimization and/or insertion of introns or nuclear-targeting sequences for therapeutic protein expression can enhance the clinical efficacy. Minimal vectors, which are devoid of the bacterial backbone and consist exclusively of the eukaryotic expression cassette, demonstrate better performance in terms of expression levels, bioavailability, transfection rates and increased therapeutic effects. Although the results are promising, minimal vectors have not taken over the conventional plasmids in clinical trials due to challenging manufacturing issues.
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Affiliation(s)
- Michaela Šimčíková
- a MIT-Portugal Program.,b iBB-Institute for Bioengineering and Biosciences , Lisbon , Portugal
| | - Kristala L J Prather
- a MIT-Portugal Program.,c Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , MA , USA
| | - Duarte M F Prazeres
- a MIT-Portugal Program.,c Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , MA , USA.,d Department of Bioengineering , Instituto Superior Técnico , Lisbon , Portugal
| | - Gabriel A Monteiro
- a MIT-Portugal Program.,c Department of Chemical Engineering , Massachusetts Institute of Technology , Cambridge , MA , USA.,d Department of Bioengineering , Instituto Superior Técnico , Lisbon , Portugal
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47
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Desaulniers AT, Cederberg RA, Lents CA, White BR. Expression and Role of Gonadotropin-Releasing Hormone 2 and Its Receptor in Mammals. Front Endocrinol (Lausanne) 2017; 8:269. [PMID: 29312140 PMCID: PMC5732264 DOI: 10.3389/fendo.2017.00269] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 09/26/2017] [Indexed: 11/13/2022] Open
Abstract
Gonadotropin-releasing hormone 1 (GnRH1) and its receptor (GnRHR1) drive mammalian reproduction via regulation of the gonadotropins. Yet, a second form of GnRH (GnRH2) and its receptor (GnRHR2) also exist in mammals. GnRH2 has been completely conserved throughout 500 million years of evolution, signifying high selection pressure and a critical biological role. However, the GnRH2 gene is absent (e.g., rat) or inactivated (e.g., cow and sheep) in some species but retained in others (e.g., human, horse, and pig). Likewise, many species (e.g., human, chimpanzee, cow, and sheep) retain the GnRHR2 gene but lack the appropriate coding sequence to produce a full-length protein due to gene coding errors; although production of GnRHR2 in humans remains controversial. Certain mammals lack the GnRHR2 gene (e.g., mouse) or most exons entirely (e.g., rat). In contrast, old world monkeys, musk shrews, and pigs maintain the coding sequence required to produce a functional GnRHR2. Like GnRHR1, GnRHR2 is a 7-transmembrane, G protein-coupled receptor that interacts with Gαq/11 to mediate cell signaling. However, GnRHR2 retains a cytoplasmic tail and is only 40% homologous to GnRHR1. A role for GnRH2 and its receptor in mammals has been elusive, likely because common laboratory models lack both the ligand and receptor. Uniquely, both GnRH2 and GnRHR2 are ubiquitously expressed; transcript levels are abundant in peripheral tissues and scarcely found in regions of the brain associated with gonadotropin secretion, suggesting a divergent role from GnRH1/GnRHR1. Indeed, GnRH2 and its receptor are not physiological modulators of gonadotropin secretion in mammals. Instead, GnRH2 and GnRHR2 coordinate the interaction between nutritional status and sexual behavior in the female brain. Within peripheral tissues, GnRH2 and its receptor are novel regulators of reproductive organs. GnRH2 and GnRHR2 directly stimulate steroidogenesis within the porcine testis. In the female, GnRH2 and its receptor may help mediate placental function, implantation, and ovarian steroidogenesis. Furthermore, both the GnRH2 and GnRHR2 genes are expressed in human reproductive tumors and represent emerging targets for cancer treatment. Thus, GnRH2 and GnRHR2 have diverse functions in mammals which remain largely unexplored.
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Affiliation(s)
- Amy T. Desaulniers
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Rebecca A. Cederberg
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | | | - Brett R. White
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
- *Correspondence: Brett R. White,
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48
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Long Noncoding RNA Identification: Comparing Machine Learning Based Tools for Long Noncoding Transcripts Discrimination. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8496165. [PMID: 28042575 PMCID: PMC5153550 DOI: 10.1155/2016/8496165] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/05/2016] [Accepted: 10/13/2016] [Indexed: 12/27/2022]
Abstract
Long noncoding RNA (lncRNA) is a kind of noncoding RNA with length more than 200 nucleotides, which aroused interest of people in recent years. Lots of studies have confirmed that human genome contains many thousands of lncRNAs which exert great influence over some critical regulators of cellular process. With the advent of high-throughput sequencing technologies, a great quantity of sequences is waiting for exploitation. Thus, many programs are developed to distinguish differences between coding and long noncoding transcripts. Different programs are generally designed to be utilised under different circumstances and it is sensible and practical to select an appropriate method according to a certain situation. In this review, several popular methods and their advantages, disadvantages, and application scopes are summarised to assist people in employing a suitable method and obtaining a more reliable result.
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49
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Sultan LD, Mileshina D, Grewe F, Rolle K, Abudraham S, Głodowicz P, Niazi AK, Keren I, Shevtsov S, Klipcan L, Barciszewski J, Mower JP, Dietrich A, Ostersetzer-Biran O. The Reverse Transcriptase/RNA Maturase Protein MatR Is Required for the Splicing of Various Group II Introns in Brassicaceae Mitochondria. THE PLANT CELL 2016; 28:2805-2829. [PMID: 27760804 PMCID: PMC5155343 DOI: 10.1105/tpc.16.00398] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 09/26/2016] [Accepted: 10/19/2016] [Indexed: 05/18/2023]
Abstract
Group II introns are large catalytic RNAs that are ancestrally related to nuclear spliceosomal introns. Sequences corresponding to group II RNAs are found in many prokaryotes and are particularly prevalent within plants organellar genomes. Proteins encoded within the introns themselves (maturases) facilitate the splicing of their own host pre-RNAs. Mitochondrial introns in plants have diverged considerably in sequence and have lost their maturases. In angiosperms, only a single maturase has been retained in the mitochondrial DNA: the matR gene found within NADH dehydrogenase 1 (nad1) intron 4. Its conservation across land plants and RNA editing events, which restore conserved amino acids, indicates that matR encodes a functional protein. However, the biological role of MatR remains unclear. Here, we performed an in vivo investigation of the roles of MatR in Brassicaceae. Directed knockdown of matR expression via synthetically designed ribozymes altered the processing of various introns, including nad1 i4. Pull-down experiments further indicated that MatR is associated with nad1 i4 and several other intron-containing pre-mRNAs. MatR may thus represent an intermediate link in the gradual evolutionary transition from the intron-specific maturases in bacteria into their versatile spliceosomal descendants in the nucleus. The similarity between maturases and the core spliceosomal Prp8 protein further supports this intriguing theory.
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Affiliation(s)
- Laure D Sultan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Daria Mileshina
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 67084 Strasbourg, France
| | - Felix Grewe
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
| | - Katarzyna Rolle
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Sivan Abudraham
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Paweł Głodowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Adnan Khan Niazi
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 67084 Strasbourg, France
| | - Ido Keren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Sofia Shevtsov
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Liron Klipcan
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
| | - André Dietrich
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 67084 Strasbourg, France
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
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50
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Yang X, Sethi A, Yanek LR, Knapper C, Nordestgaard BG, Tybjærg-Hansen A, Becker DM, Mathias RA, Remaley AT, Becker LC. SCARB1 Gene Variants Are Associated With the Phenotype of Combined High High-Density Lipoprotein Cholesterol and High Lipoprotein (a). ACTA ACUST UNITED AC 2016; 9:408-418. [PMID: 27651445 DOI: 10.1161/circgenetics.116.001402] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/20/2016] [Indexed: 02/03/2023]
Abstract
BACKGROUND SR-B1 (scavenger receptor class B type 1), encoded by the gene SCARB1, is a lipoprotein receptor that binds both high-density lipoprotein (HDL) and low-density lipoprotein. We reported that SR-B1 is also a receptor for lipoprotein (a) (Lp(a)), mediating cellular uptake of Lp(a) in vitro and promoting clearance of Lp(a) in vivo. Although genetic variants in SCARB1 are associated with variations in HDL level, no SCARB1 variants affecting Lp(a) have been reported. METHODS AND RESULTS In an index subject with high levels of HDL cholesterol and Lp(a), SCARB1 was sequenced and demonstrated a missense mutation resulting in an S129L substitution in exon 3. To follow up, 2 cohorts (GeneSTAR, the family-based Genetic Study of Atherosclerosis Risk [n=543], and CCHS, the population-based Copenhagen City Heart Study [n=5835]) were screened for combined HDL cholesterol and Lp(a) elevations. Subjects with the extreme phenotype (HDL >80 mg/dL and Lp(a) >100 nmol/L in GeneSTAR, n=8, and >100 mg/dL in CCHS, n=9) underwent sequencing of SCARB1 exons; 15 of 18 from the combined population demonstrated genetic variants, including rare or uncommon missense or splice site mutations in 9 and homozygous synonymous variants in 6. Functional studies with 4 of the SCARB1 variants (c.386C>T, c.631-14T>G, c.4G>A, and c.631-53mC>T & c.726+55mCG>CA) showed decreased receptor function in vitro. CONCLUSIONS Human SCARB1 gene variants are associated with a new lipid phenotype, characterized by high levels of both HDL cholesterol and Lp(a). SCARB1 exonic variants often result in diminished function of translated SR-B1 via reduced binding/intracellular transport of Lp(a).
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Affiliation(s)
- Xiaoping Yang
- From the Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD (X.Y., L.R.Y., D.M.B., R.A.M., L.C.B.); Lipoprotein Metabolism Section, Pulmonary and Vascular Medicine Branch, NHLBI, National Institutes of Health, Bethesda, MD (A.S., C.K., A.T.R.); and Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H.)
| | - Amar Sethi
- From the Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD (X.Y., L.R.Y., D.M.B., R.A.M., L.C.B.); Lipoprotein Metabolism Section, Pulmonary and Vascular Medicine Branch, NHLBI, National Institutes of Health, Bethesda, MD (A.S., C.K., A.T.R.); and Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H.)
| | - Lisa R Yanek
- From the Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD (X.Y., L.R.Y., D.M.B., R.A.M., L.C.B.); Lipoprotein Metabolism Section, Pulmonary and Vascular Medicine Branch, NHLBI, National Institutes of Health, Bethesda, MD (A.S., C.K., A.T.R.); and Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H.)
| | - Cathy Knapper
- From the Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD (X.Y., L.R.Y., D.M.B., R.A.M., L.C.B.); Lipoprotein Metabolism Section, Pulmonary and Vascular Medicine Branch, NHLBI, National Institutes of Health, Bethesda, MD (A.S., C.K., A.T.R.); and Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H.)
| | - Børge G Nordestgaard
- From the Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD (X.Y., L.R.Y., D.M.B., R.A.M., L.C.B.); Lipoprotein Metabolism Section, Pulmonary and Vascular Medicine Branch, NHLBI, National Institutes of Health, Bethesda, MD (A.S., C.K., A.T.R.); and Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H.)
| | - Anne Tybjærg-Hansen
- From the Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD (X.Y., L.R.Y., D.M.B., R.A.M., L.C.B.); Lipoprotein Metabolism Section, Pulmonary and Vascular Medicine Branch, NHLBI, National Institutes of Health, Bethesda, MD (A.S., C.K., A.T.R.); and Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H.)
| | - Diane M Becker
- From the Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD (X.Y., L.R.Y., D.M.B., R.A.M., L.C.B.); Lipoprotein Metabolism Section, Pulmonary and Vascular Medicine Branch, NHLBI, National Institutes of Health, Bethesda, MD (A.S., C.K., A.T.R.); and Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H.)
| | - Rasika A Mathias
- From the Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD (X.Y., L.R.Y., D.M.B., R.A.M., L.C.B.); Lipoprotein Metabolism Section, Pulmonary and Vascular Medicine Branch, NHLBI, National Institutes of Health, Bethesda, MD (A.S., C.K., A.T.R.); and Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H.)
| | - Alan T Remaley
- From the Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD (X.Y., L.R.Y., D.M.B., R.A.M., L.C.B.); Lipoprotein Metabolism Section, Pulmonary and Vascular Medicine Branch, NHLBI, National Institutes of Health, Bethesda, MD (A.S., C.K., A.T.R.); and Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H.)
| | - Lewis C Becker
- From the Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD (X.Y., L.R.Y., D.M.B., R.A.M., L.C.B.); Lipoprotein Metabolism Section, Pulmonary and Vascular Medicine Branch, NHLBI, National Institutes of Health, Bethesda, MD (A.S., C.K., A.T.R.); and Copenhagen University Hospital, Faculty of Health Sciences, University of Copenhagen, Denmark (B.G.N., A.T.-H.).
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