Pseudouridine and <i>N</i>1-methylpseudouridine as potent nucleotide analogues for RNA therapy and vaccine development

Ho, Lyana L. Y.; Schiess, Gabriel H. A.; Miranda, Pâmella; Weber, Gerald; Astakhova, Kira

doi:10.1039/d4cb00022f

Cited by 3 publications

(2 citation statements)

References 65 publications

(162 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The safety profile of the vaccine mirrored that of traditional vaccines 86 , further building the case for the use of mRNA-based vaccines 84 . This is the first example of an FDA approved therapeutic of synthetic mRNA with modified nucleosides.…”

Section: Clinical Translation Of ψ Mrna: Therapeutics and Diagnosticsmentioning

confidence: 93%

See 1 more Smart Citation

Transcriptome-wide detection and characterization of pseudouridine mRNA modifications across diverse human cell lines

McCormick

View full text Add to dashboard Cite

Pseudouridine (Ψ) is among the most abundant RNA modification in the human transcriptome and plays crucial roles in modulating mRNA stability, enhancing translation efficiency, and optimizing mRNA structure. The accurate detection and characterization of Ψ on mRNA is hindered by several factors, including the low abundance of mRNA, tissue-specific and cell-to-cell heterogeneity, and technical limitations. Nanopore direct RNA sequencing (DRS) enables full-length transcript sequencing while preserving post-transcriptional modifications in their native context. This technology allows for transcriptome-wide, amplification-free characterization of modifications at single nucleotide resolution. Differential analysis across different cell types can enhance our understanding of how Ψ influences gene regulation. We previously developed Mod-p ID, leveraging the systematic U-to-C basecalling error caused by the presence of Ψ on a native RNA strand to detect and map relative Ψ occupancy across the human transcriptome by comparing to an unmodified transcriptome. This tool can answer fundamental questions regarding the prevalence, conservation, and cell type-specific expression of Ψ across diverse tissue types.In this dissertation, we 1) develop a universal negative control as a community resource to provide a foundation for transcriptome-wide detection and characterization of RNA modifications, and 2) apply this resource for a comprehensive Ψ analysis across diverse human cell types using Mod-p ID.We first generated and characterized a multicellular in vitro transcribed (IVT), unmodified transcriptome (pan-IVT) from six immortalized human cell lines derived from diverse tissue types to provide a comprehensive negative control for public use within the RNA modification field. IVT libraries consist of paired transcripts assembled from canonical nucleotides using poly-A selected RNA. We show that combining multiple cell lines increases transcriptome coverage, helping to enrich data sets used for RNA modification analysis.We then sequenced the native transcriptomes of six human cell lines using DRS and used the Mod-p ID algorithm to catalog the relative positional occupancy of Ψ in each cell line. We show that Ψ sites can be conserved across cell lines, suggesting the presence of Ψ is important for normal cellular function or is cell-type specific, indicating the Ψ may also be consequential for cell-specific function.The transcriptome-wide annotated datasets constructed in this dissertation provide scientists across the RNA modification field with a negative control to conduct their own RNA modification analysis with the pan-IVT and highlight biologically interesting Ψ sites for robust functionalization studies.

show abstract

Section: Clinical Translation Of ψ Mrna: Therapeutics and Diagnosticsmentioning

confidence: 93%

“…In addition, PUS enzymes have been proposed as diagnostic biomarkers for a number of oncological indications. 84 . m1Ψ modified mRNA enhanced stability and translational efficiency of the viral spike protein, leading to prolonged protein expression and robust immune response 85 .…”

Section: Clinical Translation Of ψ Mrna: Therapeutics and Diagnosticsmentioning

confidence: 99%

Transcriptome-wide detection and characterization of pseudouridine mRNA modifications across diverse human cell lines

McCormick

View full text Add to dashboard Cite

show abstract

Rationalizing the effects of RNA modifications on protein interactions

Vandelli,

Broglia,

Armaos

et al. 2024

Molecular Therapy - Nucleic Acids

View full text Add to dashboard Cite

Recent Advances and Prospects in RNA Drug Development

Tani

2024

IJMS

View full text Add to dashboard Cite

RNA therapeutics have undergone remarkable evolution since their inception in the late 1970s, revolutionizing medicine by offering new possibilities for treating previously intractable diseases. The field encompasses various modalities, including antisense oligonucleotides (ASOs), small interfering RNAs (siRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs), each with unique mechanisms and applications. The foundation was laid in 1978 with the discovery that synthetic oligonucleotides could inhibit viral replication, followed by pivotal developments such as RNA interference’s discovery in 1998. The COVID-19 pandemic marked a crucial turning point, demonstrating the potential of mRNA vaccines and accelerating interest in RNA-based approaches. However, significant challenges remain, including stability issues, delivery to target tissues, potential off-target effects, and immunogenicity concerns. Recent advancements in chemical modifications, delivery systems, and the integration of AI technologies are addressing these challenges. The field has seen notable successes, such as approved treatments for spinal muscular atrophy and hereditary transthyretin-mediated amyloidosis. Looking ahead, RNA therapeutics show promise for personalized medicine approaches, particularly in treating genetic disorders and cancer. The continued evolution of this field, driven by technological innovations and deeper understanding of RNA biology, suggests a transformative impact on future medical treatments. The purpose of this review is to provide a comprehensive overview of the evolution, current state, and prospects of RNA therapeutics.

show abstract

Pseudouridine and N1-methylpseudouridine as potent nucleotide analogues for RNA therapy and vaccine development

Abstract: N1-Methylpseudouridine, and its “parent” analogue pseudouridine, are potent nucleotide analogues for RNA therapy and vaccine development.

Cited by 3 publications

References 65 publications

Transcriptome-wide detection and characterization of pseudouridine mRNA modifications across diverse human cell lines

Transcriptome-wide detection and characterization of pseudouridine mRNA modifications across diverse human cell lines

Rationalizing the effects of RNA modifications on protein interactions

Recent Advances and Prospects in RNA Drug Development

Contact Info

Product

Resources

About