Engineered RNA Devices for In Vivo Targeted Therapeutics via Advanced Delivery Systems

Wei Luo , Xia Liu , Ying Han , Yijing Duan , Chuao Yu , Na Kong , Tian Xie

Aggregate ›› 2025, Vol. 6 ›› Issue (11) : e70191

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Aggregate ›› 2025, Vol. 6 ›› Issue (11) :e70191 DOI: 10.1002/agt2.70191
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Engineered RNA Devices for In Vivo Targeted Therapeutics via Advanced Delivery Systems
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Abstract

Engineered RNA devices can identify disease-specific markers and precisely regulate gene expression, which is of great significance to the development of precision medicine. Some studies are shifting the focus from systemic drug delivery to precise gene regulation. A series of targeted delivery technologies has achieved enrichment of RNA drugs in specific tissues/organs. However, the limited cellular selectivity of RNA remains a major obstacle to progress in this field. The cellular precise regulation still requires much improvement. In recent years, advances in synthetic biology have facilitated the development of various RNA devices capable of specifically recognizing intracellular transcripts, proteins, and microRNAs. Nevertheless, the application of these tools remains largely restricted to in vitro cell detection and cell fate manipulation, due to insufficient cross-disciplinary collaboration. Therefore, given the advantages of advanced delivery technologies, combined with the RNA devices that enable precise regulation of gene expression at the cellular level, now is an opportune moment to integrate these RNA devices with state-of-the-art delivery platforms. Such integration promises to enhance the efficacy of engineered RNA devices for precise in vivo targeted therapeutics. In this review, we highlight examples of the advances and current limitations of RNA devices, including toehold switches, microRNAs, and ADAR (adenosine deaminase acting on RNA) sensors for precision disease treatment via advanced delivery systems. These considerations are essential to develop strategies for the targeted therapeutic exploitation of RNA device-based and delivery systems as a powerful programmable biological platform. Furthermore, we will assess the current maturity of RNA device technology and identify emerging innovation areas expected to drive significant future progress.

Keywords

RNA devices / precise expression / in vivo / delivery platform / target theragnostic

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Wei Luo, Xia Liu, Ying Han, Yijing Duan, Chuao Yu, Na Kong, Tian Xie. Engineered RNA Devices for In Vivo Targeted Therapeutics via Advanced Delivery Systems. Aggregate, 2025, 6(11): e70191 DOI:10.1002/agt2.70191

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References

[1]

J. C. Denny and F. S. Collins, “Precision Medicine in 2030—Seven Ways to Transform Healthcare,” Cell 184 (2021): 1415–1419.

[2]

X. P. Yang, C. Yang, S. Zhang, et al., “Precision Treatment in Advanced Hepatocellular Carcinoma,” Cancer Cell 42 (2024): 180–197.

[3]

N. Mamidi, F. F. De Silva, and A. O. Mahmoudsalehi, “Advanced Disease Therapeutics Using Engineered Living Drug Delivery Systems,” Nanoscale 17 (2025): 7673–7696.

[4]

C. Liu, Q. Q. Shi, X. G. Huang, et al., “mRNA-Based Cancer Therapeutics,” Nature Reviews Cancer 23 (2023): 526–543.

[5]

Y. R. Zhu, L. Y. Zhu, X. Wang, et al., “RNA-Based Therapeutics: An Overview and Prospectus,” Cell Death & Disease 13 (2022): 644.

[6]

B. W. Li, I. O. Raji, A. G. R. Gordon, et al., “Accelerating Ionizable Lipid Discovery for mRNA Delivery Using Machine Learning and Combinatorial Chemistry,” Nature Materials 23 (2024): 1002–1008.

[7]

S. N. Bhatia and J. E. Dahlman, “RNA Delivery Systems,” Proceedings National Academy of Science USA 121 (2024): e2315789121.

[8]

Z. Y. Yi, L. Qu, H. X. Tang, et al., “Engineered Circular ADAR-Recruiting RNAs Increase the Efficiency and Fidelity of RNA Editing in Vitro and in Vivo,” Nature Biotechnology 40 (2022): 946–955.

[9]

A. Raguram, S. Banskota, and D. R. Liu, “Therapeutic in Vivo Delivery of Gene Editing Agents,” Cell 185 (2022): 2806–2827.

[10]

Y. M. Zhang, Y. S. Shi, M. M. Khan, et al., “Ocular RNA Nanomedicine: Engineered Delivery Nanoplatforms in Treating Eye Diseases,” Trends in Biotechnology 42 (2024): 1439–1452.

[11]

E. Rohner, R. Yang, K. S. Foo, et al., “Unlocking the Promise of mRNA Therapeutics,” Nature Biotechnology 40 (2022): 1586–1600.

[12]

R. van der Meel, P. A. Wender, O. M. Merkel, et al., “Next-Generation Materials for Nucleic Acid Delivery,” Nature Reviews Materials 10 (2025): 490–499.

[13]

J. R. Androsavich, “Frameworks for Transformational Breakthroughs in RNA-Based Medicines,” Nature Reviews Drug Discovery 23 (2024): 421–444.

[14]

Y. Fei, X. L. Yu, P. Y. Liu, et al., “Simplified Lipid Nanoparticles for Tissue- and Cell-Targeted mRNA Delivery Facilitate Precision Tumor Therapy in a Lung Metastasis Mouse Model,” Advanced Materials 36 (2024): e2409812.

[15]

Q. Cheng, T. Wei, L. Farbiak, et al., “Selective Organ Targeting (SORT) Nanoparticles for Tissue-specific mRNA Delivery and CRISPR-Cas Gene Editing,” Nature Nanotechnology 15 (2020): 313–320.

[16]

Y. H. Sun, S. Chatterjee, X. Z. Lian, et al., “In Vivo Editing of Lung Stem Cells for Durable Gene Correction in Mice,” Science 384 (2024): 1196–1202.

[17]

J. G. Rurik, I. Tombácz, A. Yadegari, et al., “CAR T Cells Produced in Vivo to Treat Cardiac Injury,” Science 375 (2022): 91–96.

[18]

L. Breda, T. E. Papp, M. P. Triebwasser, et al., “In Vivo Hematopoietic Stem Cell Modification by mRNA Delivery,” Science 381 (2023): 436–443.

[19]

B. W. Li, R. S. Manan, S. Q. Liang, et al., “Combinatorial Design of Nanoparticles for Pulmonary mRNA Delivery and Genome Editing,” Nature Biotechnology 41 (2023): 1410–1415.

[20]

S. Liu, Q. Cheng, T. Wei, et al., “Membrane-destabilizing Ionizable Phospholipids for Organ-Selective mRNA Delivery and CRISPR-Cas Gene Editing,” Nature Materials 20 (2021): 701–710.

[21]

B. A. Pfeifer, M. Beitelshees, A. Hill, et al., “Harnessing Synthetic Biology for Advancing RNA Therapeutics and Vaccine Design,” NPJ Systems Biology and Applications 9 (2023): 60.

[22]

K. Qin, F. Liu, C. Zhang, et al., “Systems and Synthetic Biology for Plant Natural Product Pathway Elucidation,” Cell Reports 24 (2025): 115715.

[23]

A. Gupta, G. Park, S. Y. Park, et al., “Dsembler—DNA Assembly Designer: A Tool for Facilitating Assembly of Oligomers,” Journal of Microbiology and Biotechnology 35 (2025): e2412046.

[24]

P. B. Dykstra, M. Kaplan, and C. D. Smolke, “Engineering Synthetic RNA Devices for Cell Control,” Nature Reviews Genetics 23 (2022): 215–228.

[25]

T. Adachi and Y. Nakamura, “Aptamers: A Review of Their Chemical Properties and Modifications for Therapeutic Application,” Molecules 24 (2019): 4229.

[26]

J. Kim and E. Franco, “RNA Nanotechnology in Synthetic Biology,” Current Opinion in Biotechnology 63 (2020): 135–141.

[27]

P. R. Chen, L. Y. Wang, P. P. Qin, et al., “An RNA-Based Catalytic Hairpin Assembly Circuit Coupled With CRISPR-Cas12a for One-Step Detection of microRNAs,” Biosensors & Bioelectronics 207 (2022): 114152.

[28]

R. Kent and N. Dixon, “Contemporary Tools for Regulating Gene Expression in Bacteria,” Trends in Biotechnology 38 (2020): 316–333.

[29]

S. Choi, G. Lee, and J. Kim, “Cellular Computational Logic Using Toehold Switches,” International Journal of Molecular Sciences 23 (2022): 4265.

[30]

E. M. Zhao, A. S. Mao, H. de Puig, et al., “RNA-Responsive Elements for Eukaryotic Translational Control,” Nature Biotechnology 40 (2022): 539–545.

[31]

W. Kulsoom Ali and F. Wang, “Advancement in Synthetic Gene Circuits Engineering: An Alternative Strategy for microRNA Imaging and Disease Theranostics,” Biotechnology Advances 79 (2025): 108518.

[32]

H. Saito, T. Kobayashi, T. Hara, et al., “Synthetic Translational Regulation by an L7Ae-kink-Turn RNP Switch,” Nature Chemical Biology 6 (2010): 71–78.

[33]

M. Spöring, R. Boneberg, and J. S. Hartig, “Aptamer-Mediated Control of Polyadenylation for Gene Expression Regulation in Mammalian Cells,” ACS Synthetic Biology 9 (2020): 3008.

[34]

Y. J. Qian, J. Y. Li, S. L. Zhao, et al., “Programmable RNA Sensing for Cell Monitoring and Manipulation,” Nature 610 (2022): 713–721.

[35]

Y. C. Liu, Y. H. Zhan, Z. C. Chen, et al., “Directing Cellular Information Flow via CRISPR Signal Conductors,” Nature Methods 13 (2016): 938–944.

[36]

A. A. Green, P. A. Silver, J. J. Collins, et al., “Toehold Switches: De-Novo-Designed Regulators of Gene Expression,” Cell 159 (2014): 925–939.

[37]

K. Pardee, A. A. Green, M. K. Takahashi, et al., “Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components,” Cell 165 (2016): 1255–1266.

[38]

A. A. Green, J. Kim, D. Ma, et al., “Complex Cellular Logic Computation Using Ribocomputing Devices,” Nature 548 (2017): 117–121.

[39]

A. A. Green, “Synthetic Bionanotechnology: Synthetic Biology Finds a Toehold in Nanotechnology,” Emerging Topics in Life Sciences 3 (2019): 507.

[40]

S. J. Kim, M. Leong, M. B. Amrofell, et al., “Modulating Responses of Toehold Switches by an Inhibitory Hairpin,” ACS Synthetic Biology 8 (2019): 601–605.

[41]

J. A. Valeri, K. M. Collins, P. Ramesh, et al., “Sequence-to-Function Deep Learning Frameworks for Engineered Riboregulators,” Nature Communications 11 (2020): 5058.

[42]

S. Wang, N. J. Emery, and A. P. Liu, “A Novel Synthetic Toehold Switch for microRNA Detection in Mammalian Cells,” ACS Synthetic Biology 8 (2019): 1079–1088.

[43]

S. S. Jia, H. Lv, Q. Li, et al., “DNA-Based Biocomputing Circuits and Their Biomedical Applications,” Nature Reviews Bioengineering 3 (2025): 535–548.

[44]

G. L. Butterfield, S. J. Reisman, N. Iglesias, et al., “Gene Regulation Technologies for Gene and Cell Therapy,” Molecular Therapy 33 (2025): 2104–2122.

[45]

Y. B. Chen, W. H. Xia, Z. W. Pan, et al., “Development of a Cell-Free, Toehold Switch-Based Biosensor for Rapid and Sensitive Zika Virus Detection,” Analytical Chemistry 97 (2025): 3486–3494.

[46]

T. Jet, G. Gines, Y. Rondelez, et al., “Advances in Multiplexed Techniques for the Detection and Quantification of microRNAs,” Chemical Society Reviews 50 (2021): 4141–4161.

[47]

K. Gupta and E. Krieg, “Y-switch: A Spring-loaded Synthetic Gene Switch for Robust DNA/RNA Signal Amplification and Detection,” Nucleic Acids Research 52 (2024): e80.

[48]

C. Hu, X. R. Shi, B. Guo, et al., “Toehold-Based CRISPR-dCas9 Transcriptional Activation Platform for Spatiotemporally Controllable Gene Therapy in Tumor and Diabetic Mouse Models,” ACS Nano 19 (2025): 12277–12287.

[49]

F. Wong, D. C. He, A. Krishnan, et al., “Deep Generative Design of RNA Aptamers Using Structural Predictions,” Nature Computational Science 4 (2024): 829–839.

[50]

N. Mamidi, M. Poellmann, K. Javius-Jones, et al., “Innovative Hydrogel-Based Delivery Systems for Immunotherapy: A Review of Pre-Clinical Progress,” Nano Research 17 (2024): 9031–9043.

[51]

N. Mamidi, F. F. De Silva, A. B. Vacas, et al., “Multifaceted Hydrogel Scaffolds: Bridging the Gap Between Biomedical Needs and Environmental Sustainability,” Advances Healthcare Materials 13 (2024): e2401195.

[52]

Y. Yang and Z. F. Wang, “IRES-mediated Cap-Independent Translation, a Path Leading to Hidden Proteome,” Journal of Molecular Cell Biology 11 (2019): 911–919.

[53]

M. Shaposhnikov, J. Thakar, and B. C. Berk, “Value of Bioinformatics Models for Predicting Translational Control of Angiogenesis,” Circulation Research 136 (2025): 1147–1165.

[54]

I. S. Abaeva, C. Young, R. Warsaba, et al., “The Structure and Mechanism of Action of a Distinct Class of Dicistrovirus Intergenic Region IRESs,” Nucleic Acids Research 51 (2023): 9294–9313.

[55]

C. E. Hodgman and M. C. Jewett, “Characterizing IGR IRES-Mediated Translation Initiation for Use in Yeast Cell-Free Protein Synthesis,” Nature Biotechnology 31 (2014): 499.

[56]

H. Ning, G. Liu, L. Li, et al., “Rational Design of microRNA-Responsive Switch for Programmable Translational Control in Mammalian Cells,” Nature Communications 14 (2023): 7193.

[57]

F. Rastfeld, M. Hoffmann, S. Krüger, et al., “Selectively Expressed RNA Molecules as a Versatile Tool for Functionalized Cell Targeting,” Nature Communications 16 (2025): 420.

[58]

Z. Y. Feng, X. B. Zhang, J. Zhou, et al., “An in Vitro-transcribed Circular RNA Targets the Mitochondrial Inner Membrane Cardiolipin to Ablate EIF4G2+/PTBP1+ Pan-Adenocarcinoma,” Nature Cancer 5 (2024): 30–46.

[59]

W. C. Pan, Y. H. Lin, H. M. Iao, et al., “In Situ Magnetoelectric Generation of miRNA Sponges and Wireless Electric Stimulus by Conductive Granular Scaffolds for Nerve Regeneration,” Advanced Materials 37 (2025): e2500650.

[60]

A. T. Riley, J. M. Robson, A. Ulanova, et al., “Generative and Predictive Neural Networks for the Design of Functional RNA Molecules,” Nature Communications 16 (2025): 4155.

[61]

Y. Ma, Y. Q. Mao, S. R. Luo, et al., “Development and Characterization of a miRNA-responsive Circular RNA Expression System With Cell Type Specificity,” Molecular Therapy Nucleic Acids 36 (2025): 102450.

[62]

N. Quade, D. Boehringer, M. Leibundgut, et al., “Cryo-EM Structure of Hepatitis C Virus IRES Bound to the Human Ribosome at 3.9-Å Resolution,” Nature Communications 6 (2015): 7646.

[63]

Y. X. Zhou, J. C. Wu, S. H. Yao, et al., “DeepCIP: A Multimodal Deep Learning Method for the Prediction of Internal Ribosome Entry Sites of circRNAs,” Computers in Biology and Medicine 164 (2023): 107288.

[64]

P. Khare, S. X. Edgecomb, C. M. Hamadani, et al., “Lipid Nanoparticle-Mediated Drug Delivery to the Brain,” Advanced Drug Delivery Reviews 197 (2023): 114861.

[65]

C. Wang, S. Y. Wang, Y. E. Xue, et al., “Intravenous Administration of Blood-Brain Barrier-Crossing Conjugates Facilitates Biomacromolecule Transport Into Central Nervous System,” Nature Biotechnology (2024), https://doi.org/10.1038/s41587-024-02487-7.

[66]

C. Wang, Y. E. Xue, T. Markovic, et al., “Blood-Brain-Barrier-Crossing Lipid Nanoparticles for mRNA Delivery to the Central Nervous System,” Nature Materials 24 (2025): 1653–1663.

[67]

X. F. Bian, Q. Guo, L. F. Yau, et al., “Berberine-inspired Ionizable Lipid for Self-Structure Stabilization and Brain Targeting Delivery of Nucleic Acid Therapeutics,” Nature Communications 16 (2025): 2368.

[68]

L. F. R. Gebert and I. J. MacRae, “Regulation of microRNA Function in Animals,” Nature Reviews Molecular Cell Biology 20 (2019): 21–37.

[69]

R. F. Shang, S. Lee, G. Senavirathne, et al., “microRNAs in Action: Biogenesis, Function and Regulation,” Nature Reviews Genetics 24 (2023): 816–833.

[70]

K. Saliminejad, H. R. K. Khorshid, S. S. Fard, et al., “An Overview of microRNAs: Biology, Functions, Therapeutics, and Analysis Methods,” Journal of Cellular Physiology 234 (2019): 5451–5465.

[71]

K. Masaki, Y. Fujita, and H. Saito, “microRNA-Responsive ON-OFF Hybrid mRNA Switch for Precise Protein Expression Control,” Molecular Therapy Nucleic Acids 36 (2025): 102609.

[72]

I. Abe, H. Ohno, M. Mochizuki, et al., “Split RNA Switch Orchestrates Pre- and Post-Translational Control to Enable Cell Type-Specific Gene Expression,” Nature Communications 16 (2025): 5362.

[73]

L. Wang, W. L. Xu, S. Zhang, et al., “Sensing and Guiding Cell-State Transitions by Using Genetically Encoded Endoribonuclease-Mediated microRNA Sensors,” Nature Biomedical Engineering 8 (2024): 1730–1743.

[74]

Y. X. Hu, C. Y. Li, Q. Y. Lu, et al., “Multiplex miRNA Reporting Platform for Real-Time Profiling of Living Cells,” Cellular and Chemical Biology 31 (2024): 150–162.e7.

[75]

Z. H. Liang, K. X. Tan, C. Y. Li, et al., “Self-Feedback Loop-Containing Synthetic mRNA Switches for Controlled microRNA Sensing,” Bioorganic Chemistry 144 (2024): 107081.

[76]

S. Kameda, H. Ohno, and H. Saito, “Synthetic Circular RNA Switches and Circuits That Control Protein Expression in Mammalian Cells,” Nucleic Acids Research 51 (2023): e24.

[77]

L. Prochazka, Y. S. Michaels, C. Lau, et al., “Synthetic Gene Circuits for Cell State Detection and Protein Tuning in Human Pluripotent Stem Cells,” Molecular Systems Biology 18 (2022): e10886.

[78]

Y. Tsujisaka, T. Hatani, C. Okubo, et al., “Purification of Human iPSC-Derived Cells at Large Scale Using microRNA Switch and Magnetic-Activated Cell Sorting,” Stem Cell Reports 17 (2022): 1772–1785.

[79]

Y. Fujita, M. Hirosawa, K. Hayashi, et al., “A Versatile and Robust Cell Purification System With an RNA-Only Circuit Composed of microRNA-Responsive ON and OFF Switches,” Science Advances 8 (2022): eabj1793.

[80]

M. Sano, K. Morishita, S. Oikawa, et al., “Live-cell Imaging of microRNA Expression With Post-Transcriptional Feedback Control,” Molecular Therapy Nucleic Acids 26 (2021): 547–556.

[81]

C. J. C. Parr, S. Wada, K. Kotake, et al., “N1-Methylpseudouridine Substitution Enhances the Performance of Synthetic mRNA Switches in Cells,” Nucleic Acids Research 48 (2020): e35.

[82]

H. Nakanishi and H. Saito, “Caliciviral Protein-based Artificial Translational Activator for Mammalian Gene Circuits With RNA-only Delivery,” Nature Communications 11 (2020): 1297.

[83]

K. Endo, K. Hayashi, and H. Saito, “Numerical Operations in Living Cells by Programmable RNA Devices,” Science Advances 5 (2019): eaax0835.

[84]

M. Hirosawa, Y. Fujita, and H. Saito, “Cell-type-specific CRISPR Activation With microRNA-Responsive acrlla4 Switch,” ACS Synthetic Biology 8 (2019): 1575–1582.

[85]

S. Matsuura, H. Ono, S. Kawasaki, et al., “Synthetic RNA-Based Logic Computation in Mammalian Cells,” Nature Communications 9 (2018): 4847.

[86]

M. Hirosawa, Y. Fujita, C. J. C. Parr, et al., “Cell-Type-Specific Genome Editing With a microRNA-Responsive CRISPR-Cas9 Switch,” Nucleic Acids Research 45 (2017): e118.

[87]

K. Miki, K. Endo, S. Takahashi, et al., “Efficient Detection and Purification of Cell Populations Using Synthetic microRNA Switches,” Cell Stem Cell 16 (2015): 699–711.

[88]

C. X. Zhang, B. L. Zhang, C. Tang, et al., “A Ratiometric Gene-Switch System for miRNA Sensing and Gene Regulation,” Small Methods 8 (2024): e2301266.

[89]

W. J. Shu, K. Lee, Z. Ma, et al., “A Dual-regulation Inducible Switch System for microRNA Detection and Cell Type-Specific Gene Activation,” Theranostics 13 (2023): 2552–2561.

[90]

C. X. Zhang, X. R. Shi, and C. Tang, “Engineering Synthetic CopT/A-Based Genetic Biosensors for miRNA Imaging and Functional Gene Regulation,” Analytical Chemistry 95 (2023): 6748–6756.

[91]

Y. Yuan, B. Liu, P. Xie, et al., “Model-guided Quantitative Analysis of microRNA-Mediated Regulation on Competing Endogenous RNAs Using a Synthetic Gene Circuit,” Proceedings National Academy of Science USA 112 (2015): 3158–3163.

[92]

L. Wei, S. L. Li, P. C. Zhang, et al., “Characterizing microRNA-Mediated Modulation of Gene Expression Noise and Its Effect on Synthetic Gene Circuits,” Cell Reports 36 (2021): 109573.

[93]

T. Quarton, K. Ehrhardt, J. Lee, et al., “Mapping the Operational Landscape of microRNAs in Synthetic Gene Circuits,” NPJ Systems Biology and Applications 4 (2018): 6.

[94]

Y. Fei, X. L. Yu, P. Y. Liu, et al., “Simplified Lipid Nanoparticles for Tissue- and Cell-Targeted mRNA Delivery Facilitate Precision Tumor Therapy in a Lung Metastasis Mouse Model,” Advanced Materials 36 (2024): e2409812.

[95]

R. Jain, J. P. Frederick, E. Y. Huang, et al., “MicroRNAs Enable mRNA Therapeutics to Selectively Program Cancer Cells to Self-Destruct,” Nucleic Acid Therapeutics 28 (2018): 285–296.

[96]

X. R. Shi, C. Hu, B. Guo, et al., “A Toehold Switch Biosensor for Versatile miRNA Imaging and Therapeutic Application in Living Cells and Acute Liver Injury Mouse Models,” ACS Sensors 10 (2025): 4454–4466.

[97]

A. Garcia-Guerra, C. Sathyaprakash, O. G. de Jong, et al., “Tissue-Specific Modulation of CRISPR Activity by miRNA-Sensing Guide RNAs,” Nucleic Acids Research 53 (2025): gkaf016.

[98]

K. Masako, Y. Fujita, and H. Saito, “MicroRNA-Responsive ON-OFF Hybrid mRNA Switch for Precise Protein Expression Control,” Molecular Therapy Nucleic Acids 36 (2025): 102609.

[99]

O. Andries, S. Mc Cafferty, S. C. De Smedt, et al., “N1-Methylpseudouridine-Incorporated mRNA Outperforms Pseudouridine-Incorporated mRNA by Providing Enhanced Protein Expression and Reduced Immunogenicity in Mammalian Cell Lines and Mice,” Journal of Control Release 217 (2015): 337–344.

[100]

C. Coulouarn, V. M. Factor, J. B. Andersen, et al., “Loss of miR-122 Expression in Liver Cancer Correlates With Suppression of the Hepatic Phenotype and Gain of Metastatic Properties,” Oncogene 28 (2009): 3526–3536.

[101]

N. Ludwig, P. Leidinger, K. Becker, et al., “Distribution of miRNA Expression Across Human Tissues,” Nucleic Acids Research 44 (2016): 3865–3877.

[102]

H. Zhang, H. Liu, Y. Hu, et al., “Deep Generative Models Design mRNA Sequences With Enhanced Translational Capacity and Stability,” Science (2025), https://doi.org/10.1126/science.adr8470.

[103]

M. L. Pardi, J. Q. Wu, S. Kawasaki, et al., “Synthetic RNA-Based Post-Transcriptional Expression Control Methods and Genetic Circuits,” Advanced Drug Delivery Reviews 184 (2022): 114196.

[104]

G. Pérez-Ropero, R. Dolcemascolo, A. Pérez-Ràfols, et al., “Regulatory Effects of RNA-Protein Interactions Revealed by Reporter Assays of Bacteria Grown on Solid Media,” Biosensors (Basel) 8 (2025): 175.

[105]

J. Nowacki, M. Malenica, S. Schmeing, et al., “A Translational Repression Reporter Assay for the Analysis of RNA-Binding Protein Consensus Sites,” RNA Biology 20 (2023): 85–94.

[106]

S. Kawasaki, Y. Fujita, T. Nagaike, et al., “Synthetic mRNA Devices That Detect Endogenous Proteins and Distinguish Mammalian Cells,” Nucleic Acids Research 45 (2017): e117.

[107]

J. Yang and S. G. Ding, “Engineering L7Ae for RNA-only Delivery Kill Switch Targeting CMS2 Type Colorectal Cancer Cells,” ACS Synthetic Biology 10 (2021): 1095–1105.

[108]

J. Yang and S. G. Ding, “Chimeric RNA-Binding Protein-Based Killing Switch Targeting Hepatocellular Carcinoma Cells,” Molecular Therapy Nucleic Acids 25 (2021): 683–695.

[109]

T. Rothgangl, A. Tálas, E. I. Ioannidi, et al., “Treatment of a Metabolic Liver Disease in Mice With a Transient Prime Editing Approach,” Nature Biomedical Engineering 9 (2025): 1705–1718.

[110]

R. J. Jackson, C. U. Hellen, and T. V. Pestova, “The Mechanism of Eukaryotic Translation Initiation and Principles of Its Regulation,” Nature Reviews Molecular Cell Biology 11 (2010): 113–127.

[111]

L. A. Passmore and J. Coller, “Roles of mRNA Poly (A) Tails in Regulation of Eukaryotic Gene Expression,” Nature Reviews Molecular Cell Biology 23 (2022): 93–106.

[112]

B. Strobel, M. Spöring, H. Klein, et al., “High-throughput Identification of Synthetic Riboswitches by Barcode-Free Amplicon-Sequencing in Human Cells,” Nature Communications 11 (2020): 714.

[113]

D. Kaida, M. G. Berg, I. Younis, et al., “U1 snRNP Protects Pre-mRNAs From Premature Cleavage and Polyadenylation,” Nature 468 (2010): 664–668.

[114]

J. W. Shao, S. C. Li, X. Y. Qiu, et al., “Engineered Poly(A)-Surrogates for Translational Regulation and Therapeutic Biocomputation in Mammalian Cells,” Cell Research 34 (2024): 31–46.

[115]

L. Qu, Z. Y. Yi, S. Y. Zhu, et al., “Programmable RNA Editing by Recruiting Endogenous ADAR Using Engineered RNAs,” Nature Biotechnology 37 (2019): 1059–1069.

[116]

S. M. Byrne, S. M. Burleigh, R. Fragoza, et al., “An Engineered U7 Small Nuclear RNA Scaffold Greatly Increases ADAR-mediated Programmable RNA Base Editing,” Nature Communications 16 (2025): 4860.

[117]

J. J. Wang, W. J. Zhang, S. G. Li, et al., “RNA Editing-Mediated Correction of TP53 Nonsense Mutations via Lipid Nanoparticle-delivered Circular ADAR-recruiting RNAs,” Journal of the American Chemical Society 147 (2025): 18512–18523.

[118]

H. Y. Li, Y. H. Qiu, B. W. Song, et al., “Engineering a Photoactivatable A-to-I RNA Base Editor for Gene Therapy in Vivo,” Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02610-2.

[119]

G. Y. Li, G. Chen, G. H. Yuan, et al., “Specific and Efficient RNA A-to-I Editing Through Cleavage of an ADAR Inhibitor,” Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02591-2.

[120]

P. Reautschnig, C. Fruhner, N. Wahn, et al., “Precise in Vivo RNA Base Editing With a Wobble-Enhanced Circular CLUSTER Guide RNA,” Nature Biotechnology 43 (2025): 545–557.

[121]

Z. Y. Yi, Y. X. Zhao, Z. X. Yi, et al., “Utilizing AAV-Mediated LEAPER 2.0 for Programmable RNA Editing in Non-Human Primates and Nonsense Mutation Correction in Humanized Hurler syndrome Mice,” Genome Biology 24 (2023): 243.

[122]

J. R. Sinnamon, M. E. Jacobson, J. F. Yung, et al., “Targeted RNA Editing in Brainstem Alleviates respiratory Dysfunction in a Mouse Model of Rett Syndrome,” Proceedings National Academy of Science USA 119 (2022): e2206053119.

[123]

Q. Q. Xiao, Z. J. Xu, Y. Y. Xue, et al., “Rescue of Autosomal Dominant Hearing Loss by in Vivo Delivery of Mini dCas13X-Derived RNA Base Editor,” Science Translational Medicine 14 (2022): eabn0449.

[124]

P. Monian, C. Shivalila, G. L. Lu, et al., “Endogenous ADAR-Mediated RNA Editing in Non-Human Primates Using Stereopure Chemically Modified Oligonucleotides,” Nature Biotechnology 40 (2022): 1093–1102.

[125]

D. Katrekar, J. Yen, Y. C. Xiang, et al., “Efficient in Vitro and in Vivo RNA Editing via Recruitment of Endogenous ADARs Using Circular Guide RNAs,” Nature Biotechnology 40 (2022): 938–945.

[126]

P. Reautschnig, N. Wahn, J. Wettengel, et al., “CLUSTER Guide RNAs Enable Precise and Efficient RNA Editing With Endogenous ADAR Enzymes in Vivo,” Nature Biotechnology 40 (2022): 759–768.

[127]

T. Merkle, S. Merz, P. Reautschnig, et al., “Precise RNA Editing by Recruiting Endogenous ADARs With Antisense Oligonucleotides,” Nature Biotechnology 37 (2019): 133–138.

[128]

L. L. Xiao, B. Qin, X. Y. Zhang, et al., “Precision Control of Cell Type-Specific Behavior via RNA Sensing and Editing,” Small Methods 9 (2025): e2400952.

[129]

P. P. Qin, P. R. Chen, L. Tan, et al., “Programming ADAR-Recruiting Hairpin RNA Sensor to Detect Endogenous Molecules,” Nucleic Acids Research 53 (2025): gkae1146.

[130]

X. C. Teng, X. Zhao, Y. C. Dai, et al., “ClickRNA-PROTAC for Tumor-Selective Protein Degradation and Targeted Cancer Therapy,” Journal of the American Chemical Society 146 (2024): 27382–27391.

[131]

R. V. Gayet, K. Ilia, S. Razavi, et al., “Autocatalytic Base Editing for RNA-Responsive Translational Control,” Nature Communications 14 (2023): 1339.

[132]

E. A. Matthews, J. B. Russ, Y. J. Qian, et al., “RNA-Programmable Cell-Type Monitoring and Manipulation in the Human Cortex With CellREADR,” Cell Reports 44 (2025): 116037.

[133]

K. E. Kaseniit, N. Katz, N. S. Kolber, et al., “Modular, Programmable RNA Sensing Using ADAR Editing in Living Cells,” Nature Biotechnology 41 (2023): 482–487.

[134]

K. Y. Jiang, J. Koob, X. D. Chen, et al., “Programmable Eukaryotic Protein Synthesis With RNA Sensors by Harnessing ADAR,” Nature Biotechnology 41 (2023): 698–707.

[135]

E. Dolgin, “tRNA Therapeutics Burst Onto Startup Scene,” Nature Biotechnology 40 (2022): 283–286.

[136]

J. A. Doudna and E. Charpentier, “Genome Editing. The New Frontier of Genome Engineering With CRISPR-Cas9,” Science 346 (2014): 1258096.

[137]

B. Q. Lin, Y. An, L. Y. Meng, et al., “Control of CRISPR-Cas9 With Small Molecule-Activated Allosteric Aptamer Regulating sgRNAs,” Chemical Communications 55 (2019): 12223–12226.

[138]

K. M. Davis, V. Pattanayak, D. B. Thompson, et al., “Small Molecule-Triggered Cas9 Protein With Improved Genome-Editing Specificity,” Nature Chemical Biology 11 (2015): 316–318.

[139]

K. I. Liu, M. N. B. Ramli, C. W. A. Woo, et al., “A Chemical-Inducible CRISPR-Cas9 System for Rapid Control of Genome Editing,” Nature Chemical Biology 12 (2016): 980–987.

[140]

B. Zetsche, S. E. Volz, and F. Zhang, “A Split-Cas9 Architecture for Inducible Genome Editing and Transcription Modulation,” Nature Biotechnology 33 (2015): 139–142.

[141]

C. T. Wei, N. A. Popp, O. Peleg, et al., “A Chemically Controlled Cas9 Switch Enables Temporal Modulation of Diverse Effectors,” Nature Chemical Biology 19 (2023): 981–991.

[142]

S. Senturk, N. H. Shirole, D. G. Nowak, et al., “Rapid and Tunable Method to Temporally Control Gene Editing Based on Conditional Cas9 Stabilization,” Nature Communications 8 (2017): 14370.

[143]

B. Nabet, J. M. Roberts, D. L. Buckley, et al., “The dTAG System for Immediate and Target-Specific Protein Degradation,” Nature Chemical Biology 14 (2018): 431–441.

[144]

B. Maji, C. L. Moore, B. Zetsche, et al., “Multidimensional Chemical Control of CRISPR-Cas9,” Nature Chemical Biology 13 (2017): 9–11.

[145]

X. X. Zhou, X. Z. Zou, H. K. Chung, et al., “A Single-chain Photoswitchable CRISPR-Cas9 Architecture for Light-Inducible Gene Editing and Transcription,” ACS Chemical Biology 13 (2018): 443–448.

[146]

F. Richter, I. Fonfara, B. Bouazza, et al., “Engineering of Temperature- and Light-Switchable Cas9 Variants,” Nucleic Acids Research 44 (2016): 10003.

[147]

Y. Nihongaki, F. Kawano, T. Nakajima, et al., “Photoactivatable CRISPR-Cas9 for Optogenetic Genome Editing,” Nature Biotechnology 33 (2015): 755–760.

[148]

F. Kawano, H. Suzuki, A. Furuya, et al., “Engineered Pairs of Distinct Photoswitches for Optogenetic Control of Cellular Proteins,” Nature Communications 6 (2015): 6256.

[149]

L. Zhang, X. J. Zhang, L. Qiu, et al., “Near-Infrared Light Activatable Chemically Induced CRISPR System,” Light Science Applications 14 (2025): 229.

[150]

R. M. Liu, J. Yao, S. Y. Zhou, et al., “Spatiotemporal Control of RNA Metabolism and CRISPR-Cas Functions Using Engineered Photoswitchable RNA-Binding Proteins,” Nature Protocols 19 (2024): 374.

[151]

J. Carlson-Stevermer, R. Kelso, A. Kadina, et al., “CRISPR off Enables Spatio-Temporal Control of CRISPR Editing,” Nature Communications 11 (2020): 5041.

[152]

Q. R. Ferry, R. Lyutova, and T. A. Fulga, “Rational Design of Inducible CRISPR Guide RNAs for De Novo Assembly of Transcriptional Programs,” Nature Communications 8 (2017): 14633.

[153]

K. H. Siu and W. Chen, “Riboregulated Toehold-Gated gRNA for Programmable CRISPR-Cas9 Function,” Nature Chemical Biology 15 (2019): 217–220.

[154]

P. K. Jain, V. Ramanan, A. G. Schepers, et al., “Development of Light-Activated CRISPR Using Guide RNAs With Photocleavable Protectors,” Angewandte Chemie International Edition 55 (2016): 12440–12444.

[155]

Y. J. Sun, W. D. Chen, J. Liu, et al., “A Conformational Restriction Strategy for the Control of CRISPR/Cas Gene Editing With Photoactivatable Guide RNAs,” Angewandte Chemie International Edition 62 (2023): e202212413.

[156]

S. Peng, Z. Tan, S. Y. Chen, et al., “Integrating CRISPR-Cas12a With a DNA Circuit as a Generic Sensing Platform for Amplified Detection of microRNA,” Chemical Science 11 (2020): 7362–7368.

[157]

N. Bagheri, A. Chamorro, A. Idili, et al., “PAM-engineered Toehold Switches as Input-Responsive Activators of CRISPR-Cas12a for Sensing Applications,” Angewandte Chemie International Edition 63 (2024): e202319677.

[158]

S. Y. Chen, R. J. Wang, S. Peng, et al., “PAM-Less Conditional DNA Substrates Leverage Trans-Cleavage of CRISPR-Cas12a for Versatile Live-Cell Biosensing,” Chemical Science 13 (2022): 2011–2020.

[159]

Y. Xiong, J. J. Zhang, Z. L. Yang, et al., “Functional DNA Regulated CRISPR-Cas12a Sensors for Point-of-Care Diagnostics of Non-Nucleic-Acid Targets,” Journal of the American Chemical Society 142 (2020): 207–213.

[160]

P. P. Qin, P. R. Chen, N. Deng, et al., “Switching the Activity of CRISPR/Cas12a Using an Allosteric Inhibitory Aptamer for Biosensing,” Analytical Chemistry 94 (2022): 15908–15914.

[161]

M. D. Liang, Z. L. Li, W. S. Wang, et al., “A CRISPR-Cas12a-Derived Biosensing Platform for the Highly Sensitive Detection of Diverse Small Molecules,” Nature Communications 10 (2019): 3672.

[162]

C. L. Jiao, S. Sharma, G. Dugar, et al., “Noncanonical crRNAs Derived From Host Transcripts Enable Multiplexable RNA Detection by Cas9,” Science 372 (2021): 941–948.

[163]

L. X. Cao, W. H. Chen, W. Y. Kang, et al., “Engineering Stimuli-Responsive CRISPR-Cas Systems for Versatile Biosensing,” Analytical and Bioanalytical Chemistry 417 (2025): 1699–1711.

[164]

J. Q. Zhang, Y. Z. Zhou, J. Qiao, et al., “Recent Advances in Spatiotemporal Control of the CRISPR/Cas9 System,” Colloids and Surfaces B, Biointerfaces 248 (2025): 114474.

[165]

M. Fontana, S. D. Solomon, J. Kachadourian, et al., “CRISPR-Cas9 Gene Editing With Nexiguran Ziclumeran for ATTR Cardiomyopathy,” New England Journal of Medicine 391 (2024): 2231–2241.

[166]

A. Raguram, S. Banskota, and D. R. Liu, “Therapeutic in Vivo Delivery of Gene Editing Agents,” Cell 185 (2022): 2806–2827.

[167]

R. van der Meel, P. A. Wender, O. M. Merkel, et al., “Next-generation Materials for Nucleic Acid Delivery,” Nature Reviews Materials 10 (2025): 490–499.

[168]

X. Li, J. Wang, W. Hu, et al., “Nanoparticle Technology for mRNA: Delivery Strategy, Clinical Application and Developmental Landscape,” Theranostics 14 (2024): 738–760.

[169]

S. Omo-Lamai, Y. Wang, M. N. Patel, et al., “Limiting Endosomal Damage Sensing Reduces Inflammation Triggered by Lipid Nanoparticle Endosomal Escape,” Nature Nanotechnology 20 (2025): 1285–1297.

[170]

R. Münter, E. Christensen, T. L. Andresen, et al., “Studying How Administration Route and Dose Regulates Antibody Generation Against LNPs for mRNA Delivery With Single-Particle Resolution,” Molecular Therapy Methods Clinical Development 11 (2023): 450.

[171]

L. J. Billing, L. Martin, T. Henser-Brownhill, et al., “Precision Targeting of Myeloid Cells via Peptide Dendrimer-Lipid Nanocarriers: A Novel Platform for Potent Cancer Immunotherapies,” Advanced Science 19 (2025): e14417.

[172]

M. Vadovics, W. Zhao, E. F. Daley, et al., “Tailoring the Adjuvanticity of Lipid Nanoparticles by PEG Lipid Ratio and Phospholipid Modifications,” Nature Nanotechnology 20 (2025): 1312–1322.

[173]

J. H. Skerritt, C. Tucek-Szabo, B. Sutton, et al., “The Platform Technology Approach to mRNA Product Development and Regulation,” Vaccines 11 (2024): 528.

[174]

Y. Shi, M. Shi, Y. Wang, et al., “Progress and Prospects of mRNA-Based Drugs in Pre-Clinical and Clinical Applications,” Signal Transduction Target Therapy 9 (2024): 322.

[175]

A. Ogawa, S. Watanabe, I. Ozerova, et al., “Adenosine Kinase and ADAL Coordinate Detoxification of Modified Adenosines to Safeguard Metabolism,” Cell (2025), https://doi.org/10.1016/j.cell.2025.07.041.

[176]

B. A. Pfeifer, M. Beitelshees, A. Hill, et al., “Harnessing Synthetic Biology for Advancing RNA Therapeutics and Vaccine Design,” NPJ Systems Biology and Applications 9 (2023): 60.

[177]

H. Zhang, H. Liu, Y. Xu, et al., “Deep Generative Models Design mRNA Sequences With Enhanced Translational Capacity and Stability,” Science (2025), https://doi.org/10.1126/science.adr8470.

[178]

C. Q. Wu, R. Y. Wu, Q. L. Zhang, et al., “Harnessing Catalytic RNA Circuits for Construction of Artificial Signaling Pathways in Mammalian Cells,” Angewandte Chemie International Edition 63 (2024): e202319309.

[179]

F. Alonso-Valenteen, S. Mikhael, H. Wang, et al., “Systemic HER3 Ligand-Mimicking Nanobioparticles Enter the Brain and Reduce Intracranial Tumour Growth,” Nature Nanotechnology 20 (2025): 683–696.

[180]

A. Vaidya, S. Moore, S. Chatterjee, et al., “Expanding RNAi to Kidneys, Lungs, and Spleen via Selective ORgan Targeting (SORT) siRNA Lipid Nanoparticles,” Advanced Materials 36 (2024): e2313791.

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