Transgene codon usage drives viral fitness and therapeutic efficacy in oncolytic adenoviruses

Núñez-Manchón, Estela; Farrera-Sal, Martí; Otero-Mateo, Marc; Castellano, Giancarlo; Moreno, Rafael; Medel, David Viladés; Alemany, Ramón; Villanueva, Eneko; Fillat, Cristina

doi:10.1093/narcan/zcab015

Cited by 3 publications

(3 citation statements)

References 29 publications

(35 reference statements)

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“…This contradicts the recommendation to use optimal host codons in transgenes to maximize gene expression. The study investigates the impact of transgene codon usage on viral fitness and finds that transgenes with higher GC3 content (optimal codon usage) have higher gene expression and viral replication, while those with lower GC3 content have lower expression and replication ( Núñez-Manchón et al, 2021 ). By tuning the codon usage of transgenes, it is possible to achieve better transgene expression without compromising viral replication, thus optimizing the therapeutic outcome.…”

Section: Codon Optimization For Gene Therapy Vectorsmentioning

confidence: 99%

Codon-optimization in gene therapy: promises, prospects and challenges

Paremskaia,

Kogan,

Murashkina

et al. 2024

Front. Bioeng. Biotechnol.

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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.

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Section: Codon Optimization For Gene Therapy Vectorsmentioning

confidence: 99%

Codon-optimization in gene therapy: promises, prospects and challenges

Paremskaia,

Kogan,

Murashkina

et al. 2024

Front. Bioeng. Biotechnol.

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“…The oligonucleotide sequences are available in Table S3. Annealed oligos were phosphorylated by T4 PNK (NEB) and inserted in the 3 UTR of the EGFP in the miRVec-EGFP plasmid overnight at 4 • C [16]. Plasmid constructions (miRVec-miR222-S and miRVec-Scramble) were tested by PCR using primer set miRVec_Val (Table S2), and positive colonies confirmed by Sanger Sequencing (Genewitz).…”

Section: Mirna Sponge Generationmentioning

confidence: 99%

Inhibition of miR-222 by Oncolytic Adenovirus-Encoded miRNA Sponges Promotes Viral Oncolysis and Elicits Antitumor Effects in Pancreatic Cancer Models

Raimondi

Gea‐Sorlí

Otero-Mateo

et al. 2021

Cancers

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Oncolytic adenoviruses (OA) are envisioned as a therapeutic option for patients with cancer, designed to preferentially replicate in cancer cells. However, the high number of genetic alterations in tumors can generate a context in which adenoviruses have difficulties replicating. Abnormal miRNAs expression is a trademark of pancreatic cancer, with several oncogenic miRNAs playing essential roles in cancer-associated pathways. The perturbed miRNome induces reprogramming of gene expression in host cells that can impact the complex interplay between cellular processes and viral replication. We have studied the effects of overexpressed miRNAs on oncolytic adenoviral activity and identified miRNAs modulators of adenoviral oncolysis in pancreatic cancer cells. Inhibition of the highly upregulated miR-222 sensitized cancer cells to oncolysis. To provide a therapeutic application to this insight, we engineered the oncolytic adenovirus AdNuPARmE1A with miR-222 binding sites, working as sponges to withdraw the miRNA from the cellular environment. AdNuPAR-E-miR222-S mediated-decrease of miR-222 expression in pancreatic cancer cells strongly improved the viral yield and enhanced the adenoviral cytotoxic effects. Antitumoral studies confirmed a high activity for AdNuPARmE1A-miR222-S in vivo, controlling tumor progression more effectively than the scrambled control virus in xenografts. We demonstrated that the increased antitumor potency of the novel oncolytic virus resulted from the combinatory effects of miR-222 oncomiR inhibition and the restoration of miR-222 target genes activity enhancing viral fitness.

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“…This in part motivates our focus on codon composition (as opposed to, for example general 5' stability) as transgene design algorithms commonly employ codon-level metrics to determine which synonymous site to employ within the transgene, sometimes in a gene position specific manner (e.g. [65][66][67]). Second, while CAI provides a useful surrogate for expression level of a gene in some species [8,36], understanding IO scores could augment such a metric providing a better proxy of protein abundance, potentially applicable also in species in which there is no evidence for translational selection [36] and no (hard to obtain) protein level measures.…”

Section: Introductionmentioning

confidence: 99%

Genes for highly abundant proteins in Escherichia coli avoid 5’ codons that promote ribosomal initiation

Lewin,

Daniels,

Hurst

2023

PLoS Comput Biol

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In many species highly expressed genes (HEGs) over-employ the synonymous codons that match the more abundant iso-acceptor tRNAs. Bacterial transgene codon randomization experiments report, however, that enrichment with such “translationally optimal” codons has little to no effect on the resultant protein level. By contrast, consistent with the view that ribosomal initiation is rate limiting, synonymous codon usage following the 5’ ATG greatly influences protein levels, at least in part by modifying RNA stability. For the design of bacterial transgenes, for simple codon based in silico inference of protein levels and for understanding selection on synonymous mutations, it would be valuable to computationally determine initiation optimality (IO) scores for codons for any given species. One attractive approach is to characterize the 5’ codon enrichment of HEGs compared with the most lowly expressed genes, just as translational optimality scores of codons have been similarly defined employing the full gene body. Here we determine the viability of this approach employing a unique opportunity: for Escherichia coli there is both the most extensive protein abundance data for native genes and a unique large-scale transgene codon randomization experiment enabling objective definition of the 5’ codons that cause, rather than just correlate with, high protein abundance (that we equate with initiation optimality, broadly defined). Surprisingly, the 5’ ends of native genes that specify highly abundant proteins avoid such initiation optimal codons. We find that this is probably owing to conflicting selection pressures particular to native HEGs, including selection favouring low initiation rates, this potentially enabling high efficiency of ribosomal usage and low noise. While the classical HEG enrichment approach does not work, rendering simple prediction of native protein abundance from 5’ codon content futile, we report evidence that initiation optimality scores derived from the transgene experiment may hold relevance for in silico transgene design for a broad spectrum of bacteria.

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Transgene codon usage drives viral fitness and therapeutic efficacy in oncolytic adenoviruses

Cited by 3 publications

References 29 publications

Codon-optimization in gene therapy: promises, prospects and challenges

Codon-optimization in gene therapy: promises, prospects and challenges

Inhibition of miR-222 by Oncolytic Adenovirus-Encoded miRNA Sponges Promotes Viral Oncolysis and Elicits Antitumor Effects in Pancreatic Cancer Models

Genes for highly abundant proteins in Escherichia coli avoid 5’ codons that promote ribosomal initiation

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