1
|
Paremskaia AI, Kogan AA, Murashkina A, Naumova DA, Satish A, Abramov IS, Feoktistova SG, Mityaeva ON, Deviatkin AA, Volchkov PY. Codon-optimization in gene therapy: promises, prospects and challenges. Front Bioeng Biotechnol 2024; 12:1371596. [PMID: 38605988 PMCID: PMC11007035 DOI: 10.3389/fbioe.2024.1371596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Codon optimization has evolved to enhance protein expression efficiency by exploiting the genetic code's redundancy, allowing for multiple codon options for a single amino acid. Initially observed in E. coli, optimal codon usage correlates with high gene expression, which has propelled applications expanding from basic research to biopharmaceuticals and vaccine development. The method is especially valuable for adjusting immune responses in gene therapies and has the potenial to create tissue-specific therapies. However, challenges persist, such as the risk of unintended effects on protein function and the complexity of evaluating optimization effectiveness. Despite these issues, codon optimization is crucial in advancing gene therapeutics. This study provides a comprehensive review of the current metrics for codon-optimization, and its practical usage in research and clinical applications, in the context of gene therapy.
Collapse
Affiliation(s)
- Anastasiia Iu Paremskaia
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Anna A. Kogan
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Anastasiia Murashkina
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Daria A. Naumova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Anakha Satish
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Ivan S. Abramov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
- The MCSC named after A. S. Loginov, Moscow, Russia
| | - Sofya G. Feoktistova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Olga N. Mityaeva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Andrei A. Deviatkin
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Pavel Yu Volchkov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
- The MCSC named after A. S. Loginov, Moscow, Russia
| |
Collapse
|
2
|
Yu C, Kotsimbos T. Respiratory Infection and Inflammation in Cystic Fibrosis: A Dynamic Interplay among the Host, Microbes, and Environment for the Ages. Int J Mol Sci 2023; 24:ijms24044052. [PMID: 36835487 PMCID: PMC9966804 DOI: 10.3390/ijms24044052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The interplay between airway inflammation and infection is now recognized as a major factor in the pathobiology in cystic fibrosis (CF). A proinflammatory environment is seen throughout the CF airway resulting in classic marked and enduring neutrophilic infiltrations, irreversibly damaging the lung. Although this is seen to occur early, independent of infection, respiratory microbes arising at different timepoints in life and the world environment perpetuate this hyperinflammatory state. Several selective pressures have allowed for the CF gene to persist until today despite an early mortality. Comprehensive care systems, which have been a cornerstone of therapy for the past few decades, are now revolutionized by CF transmembrane conductance regulator (CTFR) modulators. The effects of these small-molecule agents cannot be overstated and can be seen as early as in utero. For an understanding of the future, this review looks into CF studies spanning the historical and present period.
Collapse
Affiliation(s)
- Christiaan Yu
- Department of Respiratory Medicine, Alfred Health, Melbourne, VIC 3004, Australia
- Correspondence: ; Tel.: +61-3-9076-20000
| | - Tom Kotsimbos
- Department of Respiratory Medicine, Alfred Health, Melbourne, VIC 3004, Australia
- Department of Medicine, Monash University, Alfred Campus, Melbourne, VIC 3004, Australia
| |
Collapse
|
3
|
Khabou B, Tabebi M, Siala-Sahnoun O, Mkaouar-Rebai E, Rebai A, Fakhfakh F. Potential dysfunctional effects of synonymous variants: Insights from an exhaustive in silico analysis of the ABCB4 gene. Ann Hum Genet 2018; 82:457-468. [PMID: 30079523 DOI: 10.1111/ahg.12276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/27/2018] [Accepted: 07/04/2018] [Indexed: 11/30/2022]
Abstract
The multiple drug resistance 3 (MDR3) protein is a canalicular phospholipid translocator involved in the bile secretion and encoded by the ABCB4 gene. Its deficiency is related to a large spectrum of liver diseases. Taking into account the increased evidence about the involvement of synonymous variants in inherited diseases, this study aims to explore the putative effects of silent genetic variants on the ABCB4 expression. We performed an exhaustive computational approach using ESE finder, RegRNA 2.0, MFOLD, SNPfold, and %MinMax software added to the measurement of the Relative Synonymous Codon Usage. This analysis included 216 synonymous variants distributed throughout the ABCB4 gene. Results have shown that 11 synonymous coding SNPs decrease the ESE activity, while 8 of them change the codon frequency. Besides, the c.24C>T variation, located 21 nucleotides downstream the start A (Adenine) U (Uracil) G (Glutamine) AUG causes an increase in the local stability. Moreover, the computational analysis of the 3'UTR region showed that six of the eight variants located in this region affected the Wild Type (WT) pattern of the miRNA targets sites and/or their proper display. The 26 sSNPs retained as putatively functional possessed a very low allele frequency, supporting their pathogenicity. In conclusion, the obtained results suggest that some synonymous SNPs in the ABCB4 gene, considered up to now as neutral, may be involved in the MDR3 deficiency.
Collapse
Affiliation(s)
- Boudour Khabou
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences, University of Sfax, Tunisia
| | - Mouna Tabebi
- Department of clinical and experimental medicine, Faculty of health sciences, Linköping University, Sweden
| | - Olfa Siala-Sahnoun
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences, University of Sfax, Tunisia
| | - Emna Mkaouar-Rebai
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences, University of Sfax, Tunisia
| | - Ahmed Rebai
- Molecular and Cellular Screening Process Laboratory, Centre of Biotechnology of Sfax, Sfax, Tunisia
| | - Faiza Fakhfakh
- Laboratory of Molecular and Functional Genetics, Faculty of Sciences, University of Sfax, Tunisia
| |
Collapse
|
4
|
Timing during translation matters: synonymous mutations in human pathologies influence protein folding and function. Biochem Soc Trans 2018; 46:937-944. [PMID: 30065107 DOI: 10.1042/bst20170422] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/18/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022]
Abstract
Ribosomes translate mRNAs with non-uniform speed. Translation velocity patterns are a conserved feature of mRNA and have evolved to fine-tune protein folding, expression and function. Synonymous single-nucleotide polymorphisms (sSNPs) that alter programmed translational speed affect expression and function of the encoded protein. Synergistic advances in next-generation sequencing have led to the identification of sSNPs associated with disease penetrance. Here, we draw on studies with disease-related proteins to enhance our understanding of mechanistic contributions of sSNPs to functional alterations of the encoded protein. We emphasize the importance of identification of sSNPs along with disease-causing mutations to understand genotype-phenotype relationships.
Collapse
|
5
|
Su JJ, Shang XY, Wan QY, Su JG. SNP-based susceptibility-resistance association and mRNA expression regulation analyses of tlr7 to grass carp Ctenopharyngodon idella reovirus. JOURNAL OF FISH BIOLOGY 2018; 92:1505-1525. [PMID: 29644700 DOI: 10.1111/jfb.13607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 02/24/2018] [Indexed: 05/10/2023]
Abstract
Eleven single nucleotide polymorphisms (SNP) in Ctenopharyngodon idella toll-like receptor 7 (citlr7) gene, containing two in the 5'-flanking region, three within the single intron and six distributed in the coding sequence (CDS), were identified. A case-control study of 73 susceptible individuals and 67 resistant individuals was conducted to test the SNPs-based susceptibility-resistance association and mRNA expression of citlr7 to grass carp reovirus (GCRV), showing that both 820 A/G and 1726 A/G were significantly correlative sites in genotype (P < 0·05). Multifactor dimensionality reduction (MDR) analysis suggested the exertion of antiviral effects of 820 A/G might rely on SNPs interactions of citlr7 and C. idella toll-like receptor 8 (citlr8). Combining the mortality rate and citlr7 mRNA expression, it was suggested that 1726 GG-genotyped individuals might be more resistant than 1726 A/G genotyped individuals, indicating the selection on synonymous mutations in 1726 A/G might be susceptibility-resistance-type specific. In addition, haplotype analysis uncovered no significantly correlative haplotypes in citlr7. These findings may provide an in-depth insight for the further functional research of citlr7. The potential genetic markers identified may contribute to the molecular and transgenic breeding of C. idella.
Collapse
Affiliation(s)
- J J Su
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - X Y Shang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Q Y Wan
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China
| | - J G Su
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
- Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China
| |
Collapse
|
6
|
Athey J, Alexaki A, Osipova E, Rostovtsev A, Santana-Quintero LV, Katneni U, Simonyan V, Kimchi-Sarfaty C. A new and updated resource for codon usage tables. BMC Bioinformatics 2017; 18:391. [PMID: 28865429 PMCID: PMC5581930 DOI: 10.1186/s12859-017-1793-7] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/15/2017] [Indexed: 01/24/2023] Open
Abstract
Background Due to the degeneracy of the genetic code, most amino acids can be encoded by multiple synonymous codons. Synonymous codons naturally occur with different frequencies in different organisms. The choice of codons may affect protein expression, structure, and function. Recombinant gene technologies commonly take advantage of the former effect by implementing a technique termed codon optimization, in which codons are replaced with synonymous ones in order to increase protein expression. This technique relies on the accurate knowledge of codon usage frequencies. Accurately quantifying codon usage bias for different organisms is useful not only for codon optimization, but also for evolutionary and translation studies: phylogenetic relations of organisms, and host-pathogen co-evolution relationships, may be explored through their codon usage similarities. Furthermore, codon usage has been shown to affect protein structure and function through interfering with translation kinetics, and cotranslational protein folding. Results Despite the obvious need for accurate codon usage tables, currently available resources are either limited in scope, encompassing only organisms from specific domains of life, or greatly outdated. Taking advantage of the exponential growth of GenBank and the creation of NCBI’s RefSeq database, we have developed a new database, the High-performance Integrated Virtual Environment-Codon Usage Tables (HIVE-CUTs), to present and analyse codon usage tables for every organism with publicly available sequencing data. Compared to existing databases, this new database is more comprehensive, addresses concerns that limited the accuracy of earlier databases, and provides several new functionalities, such as the ability to view and compare codon usage between individual organisms and across taxonomical clades, through graphical representation or through commonly used indices. In addition, it is being routinely updated to keep up with the continuous flow of new data in GenBank and RefSeq. Conclusion Given the impact of codon usage bias on recombinant gene technologies, this database will facilitate effective development and review of recombinant drug products and will be instrumental in a wide area of biological research. The database is available at hive.biochemistry.gwu.edu/review/codon. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1793-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- John Athey
- Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, USA
| | - Aikaterini Alexaki
- Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, USA
| | - Ekaterina Osipova
- High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, USA
| | - Alexandre Rostovtsev
- High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, USA
| | - Luis V Santana-Quintero
- High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, USA
| | - Upendra Katneni
- Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, USA
| | - Vahan Simonyan
- High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, USA
| | - Chava Kimchi-Sarfaty
- Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, USA.
| |
Collapse
|
7
|
Bosch L, Bosch B, De Boeck K, Nawrot T, Meyts I, Vanneste D, Le Bourlegat CA, Croda J, da Silva Filho LVRF. Cystic fibrosis carriership and tuberculosis: hints toward an evolutionary selective advantage based on data from the Brazilian territory. BMC Infect Dis 2017; 17:340. [PMID: 28499359 PMCID: PMC5429554 DOI: 10.1186/s12879-017-2448-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/07/2017] [Indexed: 12/21/2022] Open
Abstract
Background The reason why Cystic Fibrosis (CF) is the most common fatal genetic disease among Caucasians has been incompletely studied. We aimed at deepening the hypothesis that CF carriers have a relative protection against Mycobacterium tuberculosis (Mtb) infection. Methods Applying spatial epidemiology, we studied the link between CF carriership rate and tuberculosis (TB) incidence in Brazil. We corrected for 5 potential environmental and 2 immunological confounders in this relation: monthly income, sanitary provisions, literacy rates, racial composition and population density along with AIDS incidence rates and diabetes mellitus type 2. Smoking data were incomplete and not available for analysis. Results A significant, negative correlation between CF carriership rate and TB incidence, independent of any of the seven confounders was found. Conclusion We provide exploratory support for the hypothesis that carrying a single CFTR mutation arms against Mtb infections.
Collapse
Affiliation(s)
- Lander Bosch
- Department of Geography, University of Cambridge, Downing Place, Cambridge, CB2 3EN, UK.,Fundação Oswaldo Cruz Mato Grosso do Sul, Rua Gabriel Abrão s/n, Jardim das Nações, Campo Grande, MS, 79081-746, Brazil
| | - Barbara Bosch
- St Giles Laboratory of Human Genetics of Infectious Disease, Rockefeller branch, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA. .,Department of Pediatrics, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium.
| | - Kris De Boeck
- Department of Pediatrics, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Tim Nawrot
- Centre for Environmental Sciences, Hasselt University, Martelarenlaan 42, 3500, Hasselt, Belgium.,Department of Public Health & Primary Care, Occupational & Environmental Medicine, KULeuven, Herestraat 49, 3000, Leuven, Belgium
| | - Isabelle Meyts
- Department of Pediatrics, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Dominique Vanneste
- Division of Geography, KULeuven, Celestijnenlaan 200E, 3001, Leuven, Belgium
| | - Cleonice Alexandre Le Bourlegat
- Mestrado e Doutorado em Desenvolvimento Local, Universidade Católica Dom Bosco, Av. Tamandaré 6000, Jardim Seminário, Campo Grande, MS, 70117-900, Brazil
| | - Julio Croda
- Fundação Oswaldo Cruz Mato Grosso do Sul, Rua Gabriel Abrão s/n, Jardim das Nações, Campo Grande, MS, 79081-746, Brazil.,Faculdade de Ciências da Saúde, Universidade Federal de Grande Dourados, Rodovia Dourados, Itahum km 12, Cidade Universitaria, Cx. Postal 533, Dourados, MS, 79804-970, Brazil
| | - Luiz Vicente Ribeiro Ferreira da Silva Filho
- Instituto da Criança, Hospital das Clínicas, University of São Paulo Medical School, Av. Dr. Enéas Carvalho de Aguiar 647, São Paulo, SP, 05403-000, Brazil.,Instituto de Ensino e Pesquisa, Hospital Israelita Albert Einstein, Av. Albert Einstein 627, Morumbi, São Paulo, SP, 05652-000, Brazil
| |
Collapse
|
8
|
Palagano E, Susani L, Menale C, Ramenghi U, Berger M, Uva P, Oppo M, Vezzoni P, Villa A, Sobacchi C. Synonymous Mutations Add a Layer of Complexity in the Diagnosis of Human Osteopetrosis. J Bone Miner Res 2017; 32:99-105. [PMID: 27468155 DOI: 10.1002/jbmr.2929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 11/08/2022]
Abstract
Autosomal recessive osteopetroses (AROs) are rare, genetically heterogeneous skeletal diseases with increased bone density that are often lethal if left untreated. A precise molecular classification is relevant for the patient's management, because in some subgroups hematopoietic stem cell transplantation (HSCT), which is the only curative therapy, is contraindicated. In two unrelated ARO patients, the molecular analysis revealed the presence of a synonymous variant in known ARO genes, namely in the TCIRG1 gene in one patient and in the CLCN7 in the other patient, predicted to impact on the splicing process. In the latter case, sequencing of the transcript confirmed the splicing defect, whereas in the former, for whom an RNA sample was not available, the defect was reconstructed in vitro by the minigene technology. These results strongly suggest that these synonymous changes were responsible for the disease in our patients. Our findings are novel with respect to ARO and add to the few reports in literature dealing with different diseases, underlining the importance of cDNA analysis for the correct assessment of exonic changes, even when exome sequencing is performed. In particular, we highlight the possibility that at least in some cases ARO is due to synonymous changes, erroneously considered clinically silent, in the genes already described in literature, and suggest carefully reevaluating the sequencing results of these genes when mutations are not found at a first analysis. In addition, with respect to the CLCN7 gene, we suggest that synonymous variants might also contribute to the large spectrum of severity typical of CLCN7-dependent osteopetrosis through more subtle, but not negligible, effects on protein availability and functionality. © 2016 American Society for Bone and Mineral Research.
Collapse
Affiliation(s)
- Eleonora Palagano
- Humanitas Clinical and Research Institute, Rozzano, Italy.,Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Lucia Susani
- Humanitas Clinical and Research Institute, Rozzano, Italy.,National Research Council-Institute of Genetics and Biomedical Research (CNR-IRGB), Milan Unit, Milan, Italy
| | - Ciro Menale
- Humanitas Clinical and Research Institute, Rozzano, Italy.,National Research Council-Institute of Genetics and Biomedical Research (CNR-IRGB), Milan Unit, Milan, Italy
| | - Ugo Ramenghi
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Massimo Berger
- Pediatric Onco-Hematology and Stem Cell Transplant Division, Regina Margherita Children Hospital, City of Health and Science, Turin, Italy
| | - Paolo Uva
- CRS4, Science and Technology Park Polaris, Pula, Italy
| | - Manuela Oppo
- CRS4, Science and Technology Park Polaris, Pula, Italy.,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Paolo Vezzoni
- Humanitas Clinical and Research Institute, Rozzano, Italy.,National Research Council-Institute of Genetics and Biomedical Research (CNR-IRGB), Milan Unit, Milan, Italy
| | - Anna Villa
- Humanitas Clinical and Research Institute, Rozzano, Italy.,National Research Council-Institute of Genetics and Biomedical Research (CNR-IRGB), Milan Unit, Milan, Italy
| | - Cristina Sobacchi
- Humanitas Clinical and Research Institute, Rozzano, Italy.,National Research Council-Institute of Genetics and Biomedical Research (CNR-IRGB), Milan Unit, Milan, Italy
| |
Collapse
|
9
|
Whisper mutations: cryptic messages within the genetic code. Oncogene 2015; 35:3753-9. [PMID: 26657150 DOI: 10.1038/onc.2015.454] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/28/2015] [Accepted: 10/28/2015] [Indexed: 01/17/2023]
Abstract
Recent years have seen a great expansion in our understandings of how silent mutations can drive a disease and that mRNAs are not only mere messengers between the genome and the encoded proteins but also encompass regulatory activities. This review focuses on how silent mutations within open reading frames can affect the functional properties of the encoded protein. We describe how mRNAs exert control of cell biological processes governed by the encoded proteins via translation kinetics, protein folding, mRNA stability, spatio-temporal protein expression and by direct interactions with cellular factors. These examples illustrate how additional levels of information lie within the coding sequences and that the degenerative genetic code is not redundant and have co-evolved with the encoded proteins. Hence, so called synonymous mutations are not always silent but 'whisper'.
Collapse
|
10
|
Bali V, Lazrak A, Guroji P, Fu L, Matalon S, Bebok Z. A synonymous codon change alters the drug sensitivity of ΔF508 cystic fibrosis transmembrane conductance regulator. FASEB J 2015; 30:201-13. [PMID: 26336913 DOI: 10.1096/fj.15-273714] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/31/2015] [Indexed: 11/11/2022]
Abstract
Synonymous mutations, such as I507-ATC→ATT, in deletion of Phe508 in cystic fibrosis transmembrane conductance regulator (ΔF508 CFTR), the most frequent disease-associated mutant of CFTR, may affect protein biogenesis, structure, and function and contribute to an altered disease phenotype. Small-molecule drugs are being developed to correct ΔF508 CFTR. To understand correction mechanisms and the consequences of synonymous mutations, we analyzed the effect of mechanistically distinct correctors, corrector 4a (C4) and lumacaftor (VX-809), on I507-ATT and I507-ATC ΔF508 CFTR biogenesis and function. C4 stabilized I507-ATT ΔF508 CFTR band B, but without considerable biochemical and functional correction. VX-809 biochemically corrected ∼10% of both of the variants, leading to stable, forskolin+3-isobutyl-1-methylxanthine (IBMX)-activated whole-cell currents in the presence of the corrector. Omitting VX-809 during whole-cell recordings led to a spontaneous decline of the currents, suggesting posttranslational stabilization by VX-809. Treatment of cells with the C4+VX-809 combination resulted in enhanced rescue and 2-fold higher forskolin+IBMX-activated currents of both I507-ATT and I507-ATC ΔF508 CFTR, compared with VX-809 treatment alone. The lack of an effect of C4 on I507-ATC ΔF508 CFTR, but its additive effect in combination with VX-809, implies that C4 acted on VX-809-modified I507-ATC ΔF508 CFTR. Our results suggest that binding of C4 and VX-809 to ΔF508 CFTR is conformation specific and provide evidence that synonymous mutations can alter the drug sensitivity of proteins.
Collapse
Affiliation(s)
- Vedrana Bali
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ahmed Lazrak
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Purushotham Guroji
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Lianwu Fu
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sadis Matalon
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Zsuzsanna Bebok
- *Department of Cell, Developmental, and Integrative Biology, Department of Anesthesiology and Perioperative Medicine, The Lung Injury and Repair Research Center, and The Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| |
Collapse
|