Metkar, M., Pepin, C. S. & Moore, M. J. Tailor made: the art of therapeutic mRNA design. Nat. Rev. Drug Discov. 23, 67–83 (2024).
Google Scholar
Rohner, E., Yang, R., Foo, K. S., Goedel, A. & Chien, K. R. Unlocking the promise of mRNA therapeutics. Nat. Biotechnol. 40, 1586–1600 (2022).
Google Scholar
Baden, L. R. et al. Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine. N. Engl. J. Med. 384, 403–416 (2021).
Google Scholar
Longhurst, H. J. et al. CRISPR–Cas9 in vivo gene editing of KLKB1 for hereditary angioedema. N. Engl. J. Med. 390, 432–441 (2024).
Google Scholar
Gillmore, J. D. et al. CRISPR–Cas9 in vivo gene editing for transthyretin amyloidosis. N. Engl. J. Med. 385, 493–502 (2021).
Google Scholar
Kim, J., Eygeris, Y., Ryals, R. C., Jozić, A. & Sahay, G. Strategies for non-viral vectors targeting organs beyond the liver. Nat. Nanotechnol. 19, 428–447 (2024).
Google Scholar
Sahay, G., Alakhova, D. Y. & Kabanov, A. V. Endocytosis of nanomedicines. J. Control. Release 145, 182–195 (2010).
Google Scholar
Patel, S. et al. Brief update on endocytosis of nanomedicines. Adv. Drug Deliv. Rev. 144, 90–111 (2019).
Google Scholar
Cullis, P. R. & Hope, M. J. Lipid nanoparticle systems for enabling gene therapies. Mol. Ther. 25, 1467–1475 (2017).
Google Scholar
Chatterjee, S., Kon, E., Sharma, P. & Peer, D. Endosomal escape: a bottleneck for LNP-mediated therapeutics. Proc. Natl Acad. Sci. USA 121, e2307800120 (2024).
Google Scholar
Lindberg, M. et al. The gene transfection properties of a lipophosphoramidate derivative with two phytanyl chains. Biomaterials 33, 6240–6253 (2012).
Google Scholar
Bouraoui, A. et al. Cationic amphiphiles producing hexagonal aggregates: physico-chemical characterization and application to gene delivery. Org. Biomol. Chem. 18, 337–345 (2020).
Google Scholar
Berchel, M. et al. Lipophosphonate/lipophosphoramidates: a family of synthetic vectors efficient for gene delivery. Biochimie 94, 33–41 (2012).
Google Scholar
Akinc, A. et al. Targeted delivery of RNAi therapeutics with endogenous and exogenous ligand-based mechanisms. Mol. Ther. 18, 1357–1364 (2010).
Google Scholar
Sahay, G. et al. Efficiency of siRNA delivery by lipid nanoparticles is limited by endocytic recycling. Nat. Biotechnol. 31, 653–658 (2013).
Google Scholar
Munson, M. J. et al. A high-throughput Galectin-9 imaging assay for quantifying nanoparticle uptake, endosomal escape and functional RNA delivery. Commun. Biol. 4, 211 (2021).
Google Scholar
Herrera, M., Kim, J., Eygeris, Y., Jozic, A. & Sahay, G. Illuminating endosomal escape of polymorphic lipid nanoparticles that boost mRNA delivery. Biomater. Sci. 9, 4289–4300 (2021).
Google Scholar
Gilleron, J. et al. Image-based analysis of lipid nanoparticle–mediated siRNA delivery, intracellular trafficking and endosomal escape. Nat. Biotechnol. 31, 638–646 (2013).
Google Scholar
Paramasivam, P. et al. Endosomal escape of delivered mRNA from endosomal recycling tubules visualized at the nanoscale. J. Cell Biol. 221, e202110137 (2022).
Google Scholar
Laqtom, N. N. et al. CLN3 is required for the clearance of glycerophosphodiesters from lysosomes. Nature 609, 1005–1011 (2022).
Google Scholar
Fraix, A. et al. Cationic lipophosphoramidates with two disulfide motifs: synthesis, behaviour in reductive media and gene transfection activity. Org. Biomol. Chem. 11, 1650–1658 (2013).
Google Scholar
Atherton, F. R., Openshaw, H. T. & Todd, A. R. 174. Studies on phosphorylation. Part II. The reaction of dialkyl phosphites with polyhalogen compounds in presence of bases. A new method for the phosphorylation of amines. J. Chem. Soc. Resumed 1945, 660–663 (1945).
Corre, S. S. L., Berchel, M., Couthon-Gourvès, H., Haelters, J.-P. & Jaffrès, P.-A. Atherton–Todd reaction: mechanism, scope and applications. Beilstein J. Org. Chem. 10, 1166–1196 (2014).
Google Scholar
Pudovik, A. N. & Zametaeva, G. A. New synthesis of esters of phosphonic and thiophosphonic acids. XIII. Addition of diethyl thiophosphite to ketones and aldehydes. Izv. Akad. Nauk. SSSR Ser. Khim. 932–939 (1952).
Fields, E. K. The synthesis of esters of substituted amino phosphonic acids. J. Am. Chem. Soc. 74, 1528–1531 (1952).
Google Scholar
Corre, S. S. L. et al. Cationic lipophosphoramidates with two different lipid chains: synthesis and evaluation as gene carriers. Org. Biomol. Chem. 12, 1463–1474 (2014).
Google Scholar
Afonso, D. et al. Triggering bilayer to inverted-hexagonal nanostructure formation by thiol–ene click chemistry on cationic lipids: consequences on gene transfection. Soft Matter 12, 4516–4520 (2016).
Google Scholar
Sabnis, S. et al. A novel amino lipid series for mRNA delivery: improved endosomal escape and sustained pharmacology and safety in non-human primates. Mol. Ther. 26, 1509–1519 (2018).
Google Scholar
Sebastiani, F. et al. Apolipoprotein E binding drives structural and compositional rearrangement of mRNA-containing lipid nanoparticles. ACS Nano 15, 6709–6722 (2021).
Google Scholar
Ruberg, F. L., Grogan, M., Hanna, M., Kelly, J. W. & Maurer, M. S. Transthyretin amyloid cardiomyopathy: JACC state-of-the-art review. J. Am. Coll. Cardiol. 73, 2872–2891 (2019).
Google Scholar
Tozza, S. et al. The neuropathy in hereditary transthyretin amyloidosis: a narrative review. J. Peripher. Nerv. Syst. 26, 155–159 (2021).
Google Scholar
Musunuru, K. et al. In vivo CRISPR base editing of PCSK9 durably lowers cholesterol in primates. Nature 593, 429–434 (2021).
Google Scholar
Anzalone, A. V. et al. Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat. Biotechnol. 40, 731–740 (2022).
Google Scholar
Tomlinson, B., Patil, N. G., Fok, M. & Lam, C. W. K. Role of PCSK9 inhibitors in patients with familial hypercholesterolemia. Endocrinol. Metab. 36, 279–295 (2021).
Google Scholar
Bayona, A. et al. Loss-of-function mutation of PCSK9 as a protective factor in the clinical expression of familial hypercholesterolemia. Medicine 99, e21754 (2020).
Google Scholar
Abifadel, M. et al. Mutations in PCSK9 cause autosomal dominant hypercholesterolemia. Nat. Genet. 34, 154–156 (2003).
Google Scholar
Dahlman, J. E. et al. Barcoded nanoparticles for high throughput in vivo discovery of targeted therapeutics. Proc. Natl Acad. Sci. USA 114, 2060–2065 (2017).
Google Scholar
Lokugamage, M. P., Sago, C. D. & Dahlman, J. E. Testing thousands of nanoparticles in vivo using DNA barcodes. Curr. Opin. Biomed. Eng. 7, 1–8 (2018).
Google Scholar
Szklarczyk, D. et al. The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res. 51, D638–D646 (2022).
Google Scholar
Kanehisa, M., Furumichi, M., Sato, Y., Matsuura, Y. & Ishiguro-Watanabe, M. KEGG: biological systems database as a model of the real world. Nucleic Acids Res. 53, D672–D677 (2024).
Google Scholar
Tang, D. et al. SRplot: a free online platform for data visualization and graphing. PLoS ONE 18, e0294236 (2023).
Google Scholar
Kvainickas, A. et al. Cargo-selective SNX-BAR proteins mediate retromer trimer independent retrograde transport. J. Cell Biol. 216, 3677–3693 (2017).
Google Scholar
Tavares, L. A. et al. AP-1γ2 is an adaptor protein 1 variant required for endosome-to-Golgi trafficking of the mannose-6-P receptor (CI-MPR) and ATP7B copper transporter. J. Biol. Chem. 300, 105700 (2024).
Google Scholar
Kiral, F. R., Kohrs, F. E., Jin, E. J. & Hiesinger, P. R. Rab GTPases and membrane trafficking in neurodegeneration. Curr. Biol. 28, R471–R486 (2018).
Google Scholar
Roy, S. G., Stevens, M. W., So, L. & Edinger, A. L. Reciprocal effects of rab7 deletion in activated and neglected T cells. Autophagy 9, 1009–1023 (2013).
Google Scholar
Liu, K. et al. Negative regulation of phosphatidylinositol 3-phosphate levels in early-to-late endosome conversion. J. Cell Biol. 212, 181–198 (2016).
Google Scholar
Liu, K. et al. WDR91 is a Rab7 effector required for neuronal development. J. Cell Biol. 216, 3307–3321 (2017).
Google Scholar
Cui, T., Li, B. & Li, W. NTLA-2001: opening a new era for gene therapy. Life Med. 1, 49–51 (2022).
Google Scholar
Wittrup, A. et al. Visualizing lipid-formulated siRNA release from endosomes and target gene knockdown. Nat. Biotechnol. 33, 870–876 (2015).
Google Scholar
Omo-Lamai, S. et al. Limiting endosomal damage sensing reduces inflammation triggered by lipid nanoparticle endosomal escape. Nat. Nanotechnol. 20, 1285–1297 (2025).
Google Scholar
Patel, S. et al. Boosting intracellular delivery of lipid nanoparticle-encapsulated mRNA. Nano Lett. 17, 5711–5718 (2017).
Google Scholar
Kim, J. et al. Microfluidic platform enables shearless aerosolization of lipid nanoparticles for mRNA inhalation. ACS Nano 18, 11335–11348 (2024).
Google Scholar
Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, R25 (2010).
Google Scholar
Chen, P. J. et al. Enhanced prime editing systems by manipulating cellular determinants of editing outcomes. Cell 184, 5635–5652.e29 (2021).
Google Scholar
Kim, J., Jozic, A. & Sahay, G. Naturally derived membrane lipids impact nanoparticle-based messenger RNA delivery. Cell. Mol. Bioeng. 13, 463–474 (2020).
Google Scholar
Eygeris, Y. et al. Thiophene-based lipids for mRNA delivery to pulmonary and retinal tissues. Proc. Natl Acad. Sci. USA 121, e2307813120 (2024).
Google Scholar
Gautam, M. et al. Lipid nanoparticles with PEG-variant surface modifications mediate genome editing in the mouse retina. Nat. Commun. 14, 6468 (2023).
Abu-Remaileh, M. et al. Lysosomal metabolomics reveals V-ATPase- and mTOR-dependent regulation of amino acid efflux from lysosomes. Science 358, 807–813 (2017).
Google Scholar
Wilmarth, P. A., Riviere, M. A. & David, L. L. Techniques for accurate protein identification in shotgun proteomic studies of human, mouse, bovine, and chicken lenses. J. Ocul. Biol. Dis. Infor. 2, 223–234 (2009).
Google Scholar
Chambers, M. C. et al. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 30, 918–920 (2012).
Google Scholar
McDonald, W. H. et al. MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications. Rapid Commun. Mass Spectrom. 18, 2162–2168 (2004).
Google Scholar
Eng, J. K., Jahan, T. A. & Hoopmann, M. R. Comet: an open-source MS/MS sequence database search tool. Proteomics 13, 22–24 (2013).
Google Scholar
Keller, A., Nesvizhskii, A. I., Kolker, E. & Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383–5392 (2002).
Google Scholar
Elias, J. E. & Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207–214 (2007).
Google Scholar
Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).
Google Scholar
Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 (2000).
Perez-Riverol, Y. et al. The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Res. 50, D543–D552 (2022).
Jozic, A. LNP Barcode Script. Source code. GitHub https://github.com/antonyjozic/lnp_barcode_script (2025).
