Respiratory Syncytial Virus (RSV) optimizes the translational landscape during infection DOI Creative Commons
Kyra Kerkhofs, Nicholas R. Guydosh, Mark A. Bayfield

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 3, 2024

Viral infection often triggers eukaryotic initiator factor 2α (eIF2α) phosphorylation, leading to global 5'-cap-dependent translation inhibition. RSV encodes messenger RNAs (mRNAs) mimicking 5'-cap structures of host mRNAs and thus inhibition cap-dependent initiation would likely also reduce viral translation. We confirmed that limits widespread unexpectedly found the fraction ribosomes within polysomes increases during infection, indicating higher ribosome loading on infection. AU-rich transcripts are less efficiently translated under normal conditions become more efficient at recruiting ribosomes, similar transcripts. transcribed in cytoplasmic inclusion bodies, where binding protein M2-1 has been shown bind shuttle them into cytoplasm. further demonstrated is polysomes, might deliver for

Language: Английский

Enhancing RNA-lipid nanoparticle delivery: Organ- and cell-specificity and barcoding strategies DOI Creative Commons
Pu-Sheng Wei,

Nagasri Thota,

Gresham John

et al.

Journal of Controlled Release, Journal Year: 2024, Volume and Issue: 375, P. 366 - 388

Published: Sept. 18, 2024

Recent advancements in RNA therapeutics highlight the critical need for precision gene delivery systems that target specific organs and cells. Lipid nanoparticles (LNPs) have emerged as key vectors delivering mRNA siRNA, offering protection against enzymatic degradation, enabling targeted cellular uptake, facilitating cargo release into cytosol. This review discusses development optimization of organ- cell-specific LNPs, focusing on their design, mechanisms action, therapeutic applications. We explore innovations such DNA/RNA barcoding, which facilitates high-throughput screening precise adjustments formulations. address major challenges, including improving endosomal escape, minimizing off-target effects, enhancing efficiencies. Notable clinical trials recent FDA approvals illustrate practical applications future potential LNP-based therapies. Our findings suggest while considerable progress has been made, continued research is essential to resolve existing limitations bridge gap between pre-clinical evaluation safety efficacy therapeutics. highlights dynamic LNP research. It outlines a roadmap RNA-based medicine.

Language: Английский

Citations

14
The regulatory landscape of 5′ UTRs in translational control during zebrafish embryogenesis DOI Creative Commons
Madalena M. Reimão-Pinto, Sebastian M. Castillo-Hair, Georg Seelig

et al.

Developmental Cell, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

The 5' UTRs of mRNAs are critical for translation regulation during development, but their in vivo regulatory features poorly characterized. Here, we report the landscape early zebrafish embryogenesis using a massively parallel reporter assay 18,154 sequences coupled to polysome profiling. We found that UTR suffices confer temporal dynamics initiation and identified 86 motifs enriched with distinct ribosome recruitment capabilities. A quantitative deep learning model, Danio Optimus 5-Prime (DaniO5P), combined role length, site context, upstream AUGs, sequence on recruitment. DaniO5P predicts activities maternal zygotic isoforms indicates modulating length motif grammar contributes dynamics. This study provides first model UTR-based development lays foundation identifying underlying molecular effectors.

Language: Английский

Citations

1
Macroevolutionary divergence of gene expression driven by selection on protein abundance DOI
Alexander L. Cope, Joshua G. Schraiber, Matthew W. Pennell

et al.

Science, Journal Year: 2025, Volume and Issue: 387(6738), P. 1063 - 1068

Published: March 6, 2025

The regulation of messenger RNA (mRNA) and protein abundances is well-studied, but less known about the evolutionary processes shaping their relationship. To address this, we derived a new phylogenetic model applied it to multispecies mammalian data. Our analyses reveal (i) strong stabilizing selection on over macroevolutionary time, (ii) mutations affecting mRNA minimally impact abundances, (iii) evolve under align with (iv) adapt faster than owing greater mutational opportunity. These conclusions are supported by comparisons parameters independent functional genomic By decomposing selective influences mRNA-protein dynamics, our approach provides framework for discovering rules that drive divergence in gene expression.

Language: Английский

Citations

1
Hypoxia and inflammation induce synergistic transcriptome turnover in macrophages DOI Creative Commons
Edward M.C. Courvan, Roy Parker

Cell Reports, Journal Year: 2024, Volume and Issue: 43(7), P. 114452 - 114452

Published: July 1, 2024

Macrophages are effector immune cells that experience substantial changes to oxygenation when transiting through tissues, especially entering tumors or infected wounds. How hypoxia alters gene expression and macrophage function at the post-transcriptional level remains poorly understood. Here, we use TimeLapse-seq measure how inflammatory activation modifies hypoxic response in primary macrophages. Nucleoside recoding sequencing allows derivation of steady-state transcript levels, degradation rates, transcriptional synthesis rates from same dataset. We find produces distinct responses resting Hypoxia induces destabilization mRNA transcripts, though macrophages substantially increase compared Increased RNA turnover results upregulation ribosomal protein genes downregulation extracellular matrix components Pathways regulated by decay vitro differentially tumor-associated implying mixed stimuli could induce regulation solid tumors.

Language: Английский

Citations

8
Recent Advancements in mRNA Vaccines: From Target Selection to Delivery Systems DOI Creative Commons
Zhongyan Wu,

Weilu Sun,

Hailong Qi

et al.

Vaccines, Journal Year: 2024, Volume and Issue: 12(8), P. 873 - 873

Published: Aug. 1, 2024

mRNA vaccines are leading a medical revolution. technologies utilize the host's own cells as bio-factories to produce proteins that serve antigens. This revolutionary approach circumvents complicated processes involved in traditional vaccine production and empowers with ability respond emerging or mutated infectious diseases rapidly. Additionally, robust cellular immune response elicited by has shown significant promise cancer treatment. However, inherent instability of complexity tumor immunity have limited its broader application. Although emergence pseudouridine ionizable cationic lipid nanoparticles (LNPs) made clinical application possible, there remains substantial potential for further improvement immunogenicity delivered antigens preventive therapeutic effects technology. Here, we review latest advancements vaccines, including but not target selection delivery systems. offers multifaceted perspective on this rapidly evolving field.

Language: Английский

Citations

7
Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts DOI Creative Commons
Kotaro Tomuro, Mari Mito, Hirotaka Toh

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Aug. 26, 2024

Ribosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism protein synthesis. However, current method substantial issues: contamination by rRNAs and lack appropriate methods to measure numbers in transcripts. Here, we overcome these hurdles through development "Ribo-FilterOut", separation footprints from subunits ultrafiltration, "Ribo-Calibration", relies external spike-ins stoichiometrically defined mRNA-ribosome complexes. A combination approaches estimates number ribosomes transcript, translation initiation rate, overall events before its decay, all genome-wide manner. Moreover, our reveals allocation under heat shock stress, during aging, across cell types. Our strategy modified profiling measures kinetic stoichiometric parameters cellular transcriptome. faces issues with rRNA measurements authors develop Ribo-FilterOut Ribo-Calibration, can be used estimate various conditions.

Language: Английский

Citations

6
Sequencing technologies to measure translation in single cells DOI
Michael VanInsberghe, Alexander van Oudenaarden

Nature Reviews Molecular Cell Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 20, 2025

Language: Английский

Citations

0
mRNA Vaccines: Design Principles, Mechanisms, and Manufacturing—Insights From COVID‐19 as a Model for Combating Infectious Diseases DOI

Saeideh Khorshid Sokhangouy,

Mohammad Amin Behzadi, Samira Rezaei

et al.

Biotechnology Journal, Journal Year: 2025, Volume and Issue: 20(2)

Published: Feb. 1, 2025

The full approval of two SARS-CoV-2 mRNA vaccines, Comirnaty and Spikevax, has greatly accelerated the development numerous vaccine candidates targeting infectious diseases cancer. vaccines provide a rapid, safe, versatile manufacturing process while eliciting strong humoral cellular immune responses, making them particularly beneficial for addressing emerging pandemics. Recent advancements in modified nucleotides lipid nanoparticle delivery systems have further emphasized potential this platform. Despite these transformative opportunities, significant improvements are needed to enhance efficacy, stability, immunogenicity. This review outlines fundamentals design, process, administration strategies, along with various optimization approaches. It also offers comprehensive overview developed since onset COVID-19 pandemic, challenges posed by variants, current strategies address variants. Finally, we discuss broad-spectrum combined examine future prospects

Language: Английский

Citations

0
Deciphering the landscape of cis-acting sequences in natural yeast transcript leaders DOI Creative Commons
Christina Akirtava, Gemma E. May, C. Joel McManus

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(5)

Published: Feb. 27, 2025

Abstract Protein synthesis is a vital process that highly regulated at the initiation step of translation. Eukaryotic 5′ transcript leaders (TLs) contain variety cis-acting features influence translation and messenger RNA stability. However, relative influences these in natural TLs are poorly characterized. To address this, we used massively parallel reporter assays (MPRAs) to quantify levels, ribosome loading, protein levels from 11,027 yeast vivo systematically compared impacts their sequence on gene expression. We found expression over two orders magnitude. While leaky scanning model using Kozak contexts (−4 +1 around AUG start) upstream AUGs (uAUGs) explained half variance across TLs, addition other ∼80% variation. Our analyses detected key features, quantified effects vivo, roles motifs reported an vitro study recruitment. In addition, our work quantitated alternative transcription start site usage yeast. Thus, provides new quantitative insights into TL sequences regulating

Language: Английский

Citations

0
Current Analytical Strategies for mRNA-Based Therapeutics DOI Creative Commons
Julien Camperi, Kamalakar Chatla, Emily Freund

et al.

Molecules, Journal Year: 2025, Volume and Issue: 30(7), P. 1629 - 1629

Published: April 6, 2025

Recent advancements in mRNA technology, utilized vaccines, immunotherapies, protein replacement therapies, and genome editing, have emerged as promising increasingly viable treatments. The rapid, potent, transient properties of mRNA-encoded proteins make them attractive tools for the effective treatment a variety conditions, ranging from infectious diseases to cancer single-gene disorders. capability rapid large-scale production therapeutics fueled global response COVID-19 pandemic. For clinical implementation, it is crucial deeply characterize control important attributes such purity/integrity, identity, structural quality features, functionality. This implies use powerful advanced analytical techniques characterization mRNA. Improvements electrophoresis, chromatography, mass spectrometry, sequencing, functionality assessments significantly enhanced detail information available product process characterization, well routine stability release testing. Here, we review latest mRNA-based therapeutics, typically employed by biopharmaceutical industry eventual market release.

Language: Английский

Citations

0