Abstract
This chapter serves as a guide for researchers embarking on circular RNA-based translational studies. It provides a foundation for the successful encapsulation of circular RNA into lipid nanoparticles (LNPs) and facilitates progress in this emerging field. Crucial scientific methods and techniques involved in the formulation process, particle characterization, and downstream processing of circ-LNPs are covered. The production of in vitro transcribed circular RNA-containing LNPs based on a commercially available lipid mix is provided, in addition to the fundamentals for successful encapsulation based on lipid mixes composed of single components. Furthermore, the transfection and validation protocols for the identification of a functional and potentially therapeutic circRNA candidate for initial in vitro verification, before subsequent LNP studies, are explained.
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References
Ren S et al (2020) Circular RNAs: promising molecular biomarkers of human aging-related diseases via functioning as an miRNA sponge. Mol Ther Methods Clin Dev 18:215–229
Beermann J, Piccoli MT, Viereck J, Thum T (2016) Non-coding RNAs in development and disease: background, mechanisms, and therapeutic approaches. Physiol Rev 96:1297–1325
Kaczmarek JC, Kowalski PS, Anderson DG (2017) Advances in the delivery of RNA therapeutics: from concept to clinical reality. Genome Med 9:60
Neufeldt D, Cushman S, Bär C, Thum T (2023) Circular RNAs at the intersection of cancer and heart disease: potential therapeutic targets in cardio-oncology. Cardiovasc Res cvad013. https://doi.org/10.1093/cvr/cvad013
Santer L, Bar C, Thum T (2019) Circular RNAs: a novel class of functional RNA molecules with a therapeutic perspective. Mol Ther 27:1350–1363
Bar C, Chatterjee S, Thum T (2016) Long noncoding RNAs in cardiovascular pathology, diagnosis, and therapy. Circulation 134:1484–1499
Chen L-L, Yang L (2015) Regulation of circRNA biogenesis. RNA Biol 12:381–388
Yu C-Y, Kuo H-C (2019) The emerging roles and functions of circular RNAs and their generation. J Biomed Sci 26:29
Jeck WR, Sharpless NE (2014) Detecting and characterizing circular RNAs. Nat Biotechnol 32:453–461
Shan K et al (2017) Circular noncoding RNA HIPK3 mediates retinal vascular dysfunction in diabetes mellitus. Circulation 136:1629–1642
Zhong Z, Lv M, Chen J (2016) Screening differential circular RNA expression profiles reveals the regulatory role of circTCF25-miR-103a-3p/miR-107-CDK6 pathway in bladder carcinoma. Sci Rep 6:30919
Yu C-Y et al (2017) The circular RNA circBIRC6 participates in the molecular circuitry controlling human pluripotency. Nat Commun 8:1149
Tian F, Yu CT, Ye WD, Wang Q (2017) Cinnamaldehyde induces cell apoptosis mediated by a novel circular RNA hsa_circ_0043256 in non-small cell lung cancer. Biochem Biophys Res Commun 493:1260–1266
Holdt LM, Kohlmaier A, Teupser D (2018) Circular RNAs as therapeutic agents and targets. Front Physiol 9:1262
Chen X, Lu Y (2021) Circular RNA: biosynthesis in vitro. Front Bioeng Biotechnol 9:787881
Huang C-K, Kafert-Kasting S, Thum T (2020) Preclinical and clinical development of noncoding RNA therapeutics for cardiovascular disease. Circ Res 126:663–678
Hunkler HJ, Groß S, Thum T, Bär C (2022) Non-coding RNAs: key regulators of reprogramming, pluripotency, and cardiac cell specification with therapeutic perspective for heart regeneration. Cardiovasc Res 118:3071–3084
https://clinicaltrials.gov/
Qu L et al. Circular RNA vaccines against SARS-CoV-2 and emerging variants. https://doi.org/10.1101/2021.03.16.435594.
Fischer JW, Leung AKL (2017) CircRNAs: a regulator of cellular stress. Crit Rev Biochem Mol Biol 52:220–233
Zhang Y et al (2021) Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying functional circRNAs. Genome Biol 22:41
Xia P et al (2018) A circular RNA protects dormant hematopoietic stem cells from DNA sensor cGAS-mediated exhaustion. Immunity 48:688–701.e7
Circular RNAs: methods and protocols. vol. 1724. Springer, New York, 2018.
Lu D et al (2022) A circular RNA derived from the insulin receptor locus protects against doxorubicin-induced cardiotoxicity. Eur Heart J. https://doi.org/10.1093/eurheartj/ehac337
Obi P, Chen YG (2021) The design and synthesis of circular RNAs. Methods 196:85–103
Wesselhoeft RA et al (2019) RNA circularization diminishes immunogenicity and can extend translation duration in vivo. Mol Cell 74:508–520.e4
Chen YG et al (2019) N6-methyladenosine modification controls circular RNA immunity. Mol Cell 76:96–109
Chen YG et al (2017) Sensing self and foreign circular RNAs by intron identity. Mol Cell 67:228–238.e5
Cheng CJ, Tietjen GT, Saucier-Sawyer JK, Saltzman WM (2015) A holistic approach to targeting disease with polymeric nanoparticles. Nat Rev Drug Discov 14:239–247
Evers MJW et al (2018) State-of-the-art design and rapid-mixing production techniques of lipid nanoparticles for nucleic acid delivery. Small Methods 2:1700375
Khalil IA, Younis MA, Kimura S, Harashima H (2020) Lipid nanoparticles for cell-specific in vivo targeted delivery of nucleic acids. Biol Pharm Bull 43:584–595
Polack FP et al (2020) Safety and efficacy of the BNT162b2 mRNA covid-19 vaccine. N Engl J Med 383:2603–2615
Schoenmaker L et al (2021) mRNA-lipid nanoparticle COVID-19 vaccines: structure and stability. Int J Pharm 601:120586
Anderson EJ et al (2020) Safety and immunogenicity of SARS-CoV-2 mRNA-1273 vaccine in older adults. N Engl J Med 383:2427–2438
Baden LR et al (2020) Efficacy and safety of the mRNA-1273 SARS-CoV-2 vaccine. N Engl J Med 384:403–416
Hou X, Zaks T, Langer R, Dong Y (2021) Lipid nanoparticles for mRNA delivery. Nat Rev Mater 6:1078–1094
Paunovska K, Loughrey D, Dahlman JE (2022) Drug delivery systems for RNA therapeutics. Nat Rev Genet 23:265–280
Ickenstein LM, Garidel P (2019) Lipid-based nanoparticle formulations for small molecules and RNA drugs. Expert Opin Drug Deliv 16:1205–1226
Hald Albertsen C et al (2022) The role of lipid components in lipid nanoparticles for vaccines and gene therapy. Adv Drug Deliv Rev 188:114416
Hassett KJ et al (2019) Optimization of lipid nanoparticles for intramuscular administration of mRNA vaccines. Mol Ther - Nucleic Acids 15:1–11
Stern ST, McNeil SE (2008) Nanotechnology safety concerns revisited. Toxicol Sci 101:4–21
Carrasco MJ et al (2021) Ionization and structural properties of mRNA lipid nanoparticles influence expression in intramuscular and intravascular administration. Commun Biol 4:956
Kularatne RN, Crist RM, Stern ST (2022) The future of tissue-targeted lipid nanoparticle-mediated nucleic acid delivery. Pharmaceuticals 15:897
Moderna Clinical Study Protocol (2020), Aug 20. https://covid19crc.org/wp-content/uploads/2020/09/mRNA-1273-P301-Protocol-2020.
Rurik JG et al (2022) CAR T cells produced in vivo to treat cardiac injury. Science 375:91–96
Tombácz I et al (2021) Highly efficient CD4+ T cell targeting and genetic recombination using engineered CD4+ cell-homing mRNA-LNPs. Mol Ther 29:3293–3304
Ramishetti S et al (2015) Systemic gene silencing in primary T lymphocytes using targeted lipid nanoparticles. ACS Nano 9:6706–6716
Nakamura T et al (2020) The effect of size and charge of lipid nanoparticles prepared by microfluidic mixing on their lymph node transitivity and distribution. Mol Pharm 17:944–953
Cheng Q et al (2020) Selective organ targeting (SORT) nanoparticles for tissue-specific mRNA delivery and CRISPR–Cas gene editing. Nat Nanotechnol 15:313–320
Wang X et al (2023) Preparation of selective organ-targeting (SORT) lipid nanoparticles (LNPs) using multiple technical methods for tissue-specific mRNA delivery. Nat Protoc 18:265–291
Johnson LT et al (2022) Lipid nanoparticle (LNP) chemistry can endow unique in vivo RNA delivery fates within the liver that alter therapeutic outcomes in a cancer model. Mol Pharm 19:3973–3986
Genvoy User Manual. https://www.precisionnanosystems.com/docs/default-source/pni-files/user-guides/genvoy-user-guide-2020-final-emailsize.pdf.
Walsh C et al (2014) In: Jain KK (ed) Microfluidic-based manufacture of siRNA-lipid nanoparticles for therapeutic applications BT - drug delivery system. Springer, New York, pp 109–120. https://doi.org/10.1007/978-1-4939-0363-4_6
Miltenyi- Neonatal Heart Dissociation Kit, mouse and rat. https://www.miltenyibiotec.com/DE-en/products/neonatal-heart-dissociation-kit-mouse-and-rat.html#gref.
Thermofischer- Lipofectamine 2000. https://www.thermofisher.com/de/de/home/references/protocols/cell-culture/transfection-protocol/lipofectamine-2000.html.
Qiagen- RNeasy Mini Kit. https://www.qiagen.com/us/resources/resourcedetail?id=14e7cf6e-521a-4cf7-8cbc-bf9f6fa33e24&lang=en.
Biorad- iScript. https://www.bio-rad.com/sites/default/files/webroot/web/pdf/lsr/literature/10001023.pdf.
QIAquick® Gel Extraction Kit. https://www.qiagen.com/us/resources/resourcedetail?id=1426dbb4-da09-487c-ae01-c587c2be14c3&lang=en.
Ni H et al (2022) Piperazine-derived lipid nanoparticles deliver mRNA to immune cells in vivo. Nat Commun 13:4766
Lorenzer C, Dirin M, Winkler A-M, Baumann V, Winkler J (2015) Going beyond the liver: progress and challenges of targeted delivery of siRNA therapeutics. J Control Release 203:1–15
Sago CD et al (2018) High-throughput in vivo screen of functional mRNA delivery identifies nanoparticles for endothelial cell gene editing. Proc Natl Acad Sci 115:E9944–E9952
Roces CB et al (2020) Manufacturing considerations for the development of lipid nanoparticles using microfluidics. Pharmaceutics 12:1095
Acknowledgments
This work was supported by funding from the German Research Foundation, DFG (SFB/Transregio TRR267, to C.B. and T.T.) and the European Research Council, ERC (ERC Advanced Grant REVERSE, to T.T.).
Disclosure
TT is a founder and shareholder of Cardior Pharmaceuticals GmbH (outside of this book chapter). D.L., C.B., and T.T. have filed and partly licensed patents for non-coding RNAs including for Circ-INSR.
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Juchem, M., Cushman, S., Lu, D., Chatterjee, S., Bär, C., Thum, T. (2024). Encapsulating In Vitro Transcribed circRNA into Lipid Nanoparticles Via Microfluidic Mixing. In: Dieterich, C., Baudet, ML. (eds) Circular RNAs. Methods in Molecular Biology, vol 2765. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3678-7_14
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DOI: https://doi.org/10.1007/978-1-0716-3678-7_14
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