1
|
Albers S, Allen EC, Bharti N, Davyt M, Joshi D, Perez-Garcia CG, Santos L, Mukthavaram R, Delgado-Toscano MA, Molina B, Kuakini K, Alayyoubi M, Park KJJ, Acharya G, Gonzalez JA, Sagi A, Birket SE, Tearney GJ, Rowe SM, Manfredi C, Hong JS, Tachikawa K, Karmali P, Matsuda D, Sorscher EJ, Chivukula P, Ignatova Z. Engineered tRNAs suppress nonsense mutations in cells and in vivo. Nature 2023; 618:842-848. [PMID: 37258671 PMCID: PMC10284701 DOI: 10.1038/s41586-023-06133-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 04/25/2023] [Indexed: 06/02/2023]
Abstract
Nonsense mutations are the underlying cause of approximately 11% of all inherited genetic diseases1. Nonsense mutations convert a sense codon that is decoded by tRNA into a premature termination codon (PTC), resulting in an abrupt termination of translation. One strategy to suppress nonsense mutations is to use natural tRNAs with altered anticodons to base-pair to the newly emerged PTC and promote translation2-7. However, tRNA-based gene therapy has not yielded an optimal combination of clinical efficacy and safety and there is presently no treatment for individuals with nonsense mutations. Here we introduce a strategy based on altering native tRNAs into efficient suppressor tRNAs (sup-tRNAs) by individually fine-tuning their sequence to the physico-chemical properties of the amino acid that they carry. Intravenous and intratracheal lipid nanoparticle (LNP) administration of sup-tRNA in mice restored the production of functional proteins with nonsense mutations. LNP-sup-tRNA formulations caused no discernible readthrough at endogenous native stop codons, as determined by ribosome profiling. At clinically important PTCs in the cystic fibrosis transmembrane conductance regulator gene (CFTR), the sup-tRNAs re-established expression and function in cell systems and patient-derived nasal epithelia and restored airway volume homeostasis. These results provide a framework for the development of tRNA-based therapies with a high molecular safety profile and high efficacy in targeted PTC suppression.
Collapse
Affiliation(s)
- Suki Albers
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | - Nikhil Bharti
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Marcos Davyt
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | - Disha Joshi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | - Leonardo Santos
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany
| | | | | | | | | | | | | | | | | | - Amit Sagi
- Arcturus Therapeutics, San Diego, CA, USA
| | - Susan E Birket
- Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Guillermo J Tearney
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard-MIT Health Sciences and Technology, MA, Cambridge, USA
| | - Steven M Rowe
- Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Candela Manfredi
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Jeong S Hong
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | | | | | | | - Eric J Sorscher
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA.
- Children's Healthcare of Atlanta, Atlanta, GA, USA.
| | | | - Zoya Ignatova
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
| |
Collapse
|
2
|
de Alwis R, Gan ES, Chen S, Leong YS, Tan HC, Zhang SL, Yau C, Low JGH, Kalimuddin S, Matsuda D, Allen EC, Hartman P, Park KJJ, Alayyoubi M, Bhaskaran H, Dukanovic A, Bao Y, Clemente B, Vega J, Roberts S, Gonzalez JA, Sablad M, Yelin R, Taylor W, Tachikawa K, Parker S, Karmali P, Davis J, Sullivan BM, Sullivan SM, Hughes SG, Chivukula P, Ooi EE. A single dose of self-transcribing and replicating RNA-based SARS-CoV-2 vaccine produces protective adaptive immunity in mice. Mol Ther 2021; 29:1970-1983. [PMID: 33823303 PMCID: PMC8019652 DOI: 10.1016/j.ymthe.2021.04.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/18/2022] Open
Abstract
A self-transcribing and replicating RNA (STARR)-based vaccine (LUNAR-COV19) has been developed to prevent SARS-CoV-2 infection. The vaccine encodes an alphavirus-based replicon and the SARS-CoV-2 full-length spike glycoprotein. Translation of the replicon produces a replicase complex that amplifies and prolongs SARS-CoV-2 spike glycoprotein expression. A single prime vaccination in mice led to robust antibody responses, with neutralizing antibody titers increasing up to day 60. Activation of cell-mediated immunity produced a strong viral antigen-specific CD8+ T lymphocyte response. Assaying for intracellular cytokine staining for interferon (IFN)γ and interleukin-4 (IL-4)-positive CD4+ T helper (Th) lymphocytes as well as anti-spike glycoprotein immunoglobulin G (IgG)2a/IgG1 ratios supported a strong Th1-dominant immune response. Finally, single LUNAR-COV19 vaccination at both 2 μg and 10 μg doses completely protected human ACE2 transgenic mice from both mortality and even measurable infection following wild-type SARS-CoV-2 challenge. Our findings collectively suggest the potential of LUNAR-COV19 as a single-dose vaccine.
Collapse
MESH Headings
- Alphavirus/genetics
- Alphavirus/immunology
- Angiotensin-Converting Enzyme 2/genetics
- Angiotensin-Converting Enzyme 2/immunology
- Animals
- Antibodies, Neutralizing/biosynthesis
- Antibodies, Viral/biosynthesis
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/virology
- COVID-19/immunology
- COVID-19/pathology
- COVID-19/prevention & control
- COVID-19/virology
- COVID-19 Vaccines/administration & dosage
- COVID-19 Vaccines/biosynthesis
- COVID-19 Vaccines/genetics
- COVID-19 Vaccines/immunology
- Female
- Gene Expression
- Humans
- Immunity, Cellular/drug effects
- Immunity, Humoral/drug effects
- Interferon-gamma/genetics
- Interferon-gamma/immunology
- Interleukin-4/genetics
- Interleukin-4/immunology
- Mice
- Mice, Transgenic
- Replicon/immunology
- SARS-CoV-2/drug effects
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Th1 Cells/drug effects
- Th1 Cells/immunology
- Th1 Cells/virology
- Transgenes
- Treatment Outcome
- Vaccination/methods
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/biosynthesis
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- mRNA Vaccines
Collapse
Affiliation(s)
- Ruklanthi de Alwis
- Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Center, Singapore, Singapore; Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Esther S Gan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Shiwei Chen
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Yan Shan Leong
- Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Center, Singapore, Singapore
| | - Hwee Cheng Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Summer L Zhang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Clement Yau
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Jenny G H Low
- Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Center, Singapore, Singapore; Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore; Department of Infectious Disease, Singapore General Hospital, Singapore, Singapore
| | - Shirin Kalimuddin
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore; Department of Infectious Disease, Singapore General Hospital, Singapore, Singapore
| | - Daiki Matsuda
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Elizabeth C Allen
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Paula Hartman
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | | | - Maher Alayyoubi
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Hari Bhaskaran
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Adrian Dukanovic
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Yanjie Bao
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Brenda Clemente
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Jerel Vega
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Scott Roberts
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Jose A Gonzalez
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Marciano Sablad
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Rodrigo Yelin
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Wendy Taylor
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Kiyoshi Tachikawa
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Suezanne Parker
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Priya Karmali
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Jared Davis
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Brian M Sullivan
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Sean M Sullivan
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA.
| | - Steve G Hughes
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Pad Chivukula
- Arcturus Therapeutics, Inc., 10628 Science Center Drive, San Diego, CA 92121, USA
| | - Eng Eong Ooi
- Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Center, Singapore, Singapore; Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| |
Collapse
|
3
|
Wu Y, Park KJJ, Deighan C, Amaya P, Miller B, Pan Q, Zborowski M, Lustberg M, Chalmers J. Multiparameter Evaluation of the Heterogeneity of Circulating Tumor Cells Using Integrated RNA In Situ Hybridization and Immunocytochemical Analysis. Front Oncol 2016; 6:234. [PMID: 27878106 PMCID: PMC5099140 DOI: 10.3389/fonc.2016.00234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/18/2016] [Indexed: 12/25/2022] Open
Abstract
Circulating tumor cells (CTCs) are routinely identified as cytokeratin (CK)-positive, epithelial cell adhesion molecule (EpCAM)-positive, and CD45-negative and are enriched based on EpCAM. However, there are a number of methodological challenges regarding both isolation and characterization of these rare CTCs including downregulation or absence of EpCAM in a variety of solid tumors leading to the omission of subpopulations of CTCs, difficulties in analyzing RNA and protein targets in CTCs due to the rarity of these cells, and low levels of targets and technological limitations of visualizing the targets of interest on each individual cell. Building on our previous CTC research on CD45-based negative magnetic separation and four-color fluorescent immunocytochemical (ICC) staining, RNA in situ hybridization (ISH) was applied to fluorescently target mRNA sequences corresponding to tumor-related genes at the single CTC level. Multiple categories of markers are targeted including CK, human epidermal growth factor receptor family markers, Hedgehog pathway markers, human papillomavirus markers, and protein arginine methyltransferase 5. In addition, an integrated method of RNA ISH and fluorescent ICC staining was developed to visualize CTCs on both mRNA and protein levels. The robustness of the integrated co-ICC and RNA ISH staining was demonstrated by a series of tests on representative tumor markers of different categories. The integrated staining can incorporate the advantages of both RNA ISH and fluorescent ICC staining and provide more intense signals and more specific bindings. With this integrated staining methodology, distinct staining patterns were applied in this report to facilitate the searching and characterization of rare subgroups of CTCs. These results support the existence of diverse groups of CTCs at both protein and mRNA transcript levels and provide an analytical tool for the research on CTCs of rare subgroups.
Collapse
Affiliation(s)
- Yongqi Wu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University , Columbus, OH , USA
| | - Kyoung-Joo Jenny Park
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University , Columbus, OH , USA
| | - Clayton Deighan
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University , Columbus, OH , USA
| | - Peter Amaya
- Department of Biomedical Engineering, The Ohio State University , Columbus, OH , USA
| | - Brandon Miller
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University , Columbus, OH , USA
| | - Quintin Pan
- Department of Otolaryngology-Head and Neck Surgery, The James Cancer Hospital and Solove Research Institute, Wexner Medical Center at The Ohio State University , Columbus, OH , USA
| | - Maciej Zborowski
- Department of Biomedical Engineering, Cleveland Clinic , Cleveland, OH , USA
| | - Maryam Lustberg
- Breast Medical Oncology, Department of Internal Medicine, James Cancer Hospital, Ohio State University Comprehensive Cancer Center , Columbus, OH , USA
| | - Jeffery Chalmers
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA; Analytical Cytometry Shared Resource, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| |
Collapse
|
4
|
Oliveira-Costa JP, de Carvalho AF, da Silveira DGG, Amaya P, Wu Y, Park KJJ, Gigliola MP, Lustberg M, Buim MEC, Ferreira EN, Kowalski LP, Chalmers JJ, Soares FA, Carraro DM, Ribeiro-Silva A. Gene expression patterns through oral squamous cell carcinoma development: PD-L1 expression in primary tumor and circulating tumor cells. Oncotarget 2016; 6:20902-20. [PMID: 26041877 PMCID: PMC4673238 DOI: 10.18632/oncotarget.3939] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/05/2015] [Indexed: 01/07/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common tumor of the oral cavity and has been associated with poor prognosis. Scarce prognostic markers are available for guiding treatment and/or sub-classifying patients. This study aims to identify biomarkers by searching for genes whose expression is increased or decreased during tumor progression (through T1 to T4 stages). Thirty-six samples from all tumor size stages (from T1 to T4) were analyzed using cDNA microarrays. Selected targets were analyzed by immunohistochemistry and in circulating tumor cells by immunofluorescence and Nanostring. Correlation was shown between PD-L1 and tumor size and lymph node metastasis, HOXB9 and tumor size, BLNK and perineural invasion, and between ZNF813 and perineural invasion. PD-L1 positivity was an independent prognostic factor in this cohort (p = 0.044, HH = 0.426). In CTCs from patients with locally advanced OSCC, we found a strong cytoplasmatic expression of PD-L1. PD-L1 is a ligand of PD-1 and is believed to limit T cell activity in inflammatory responses and limit autoimmune diseases. We demonstrated an important role for PD-L1 in primary tumors according to tumor size, and in disease specific survival. Therefore, we could further determine individuals with PD-L1+ CTCs, and possibly follow treatment using CTCs.
Collapse
Affiliation(s)
- Joao Paulo Oliveira-Costa
- Department of Pathology, Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Alex Fiorini de Carvalho
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center, Sao Paulo, Brazil
| | | | - Peter Amaya
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
| | - Yongqi Wu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
| | - Kyoung-Joo Jenny Park
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
| | - Mabel Pinilla Gigliola
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center, Sao Paulo, Brazil
| | - Maryam Lustberg
- Stefanie Spielman Comprehensive Breast Center, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | | | | | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C. Camargo Cancer Center, Sao Paulo, Brazil
| | - Jeffrey J Chalmers
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
| | | | - Dirce Maria Carraro
- Laboratory of Genomics and Molecular Biology, CIPE, A.C. Camargo Cancer Center, Sao Paulo, Brazil
| | - Alfredo Ribeiro-Silva
- Department of Pathology, Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, Brazil
| |
Collapse
|
5
|
|