Testing thousands of nanoparticles in vivo using DNA barcodes

Lokugamage, Melissa P.; Sago, Cory D.; Dahlman, James E.

doi:10.1016/j.cobme.2018.08.001

Cited by 58 publications

(52 citation statements)

References 58 publications

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“…We reasoned that measuring hundreds of distinct LNPs in vivo would provide the best chance of identifying nanoparticles that deliver mRNA to new cell types. Using DNA barcodes ( 17 , 20 – 22 ), we previously quantified how >350 LNPs distributed in vivo. However, biodistribution is necessary, but not sufficient, for functional RNA delivery.…”

mentioning

confidence: 99%

High-throughput in vivo screen of functional mRNA delivery identifies nanoparticles for endothelial cell gene editing

Sago

Lokugamage

Paunovska

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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236

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SignificanceNanoparticle-mediated delivery of siRNA to hepatocytes has treated disease in humans. However, systemically delivering RNA drugs to nonliver tissues remains an important challenge. To increase the number of nanoparticles that could be studied in vivo, we designed a high-throughput method to measure how >100 nanoparticles delivered mRNA that was translated into functional protein in vivo. We quantified how >250 lipid nanoparticles (LNPs) delivered mRNA in vivo, identifying two LNPs that deliver mRNA to endothelial cells. One of the LNPs codelivered Cas9 mRNA and single-guide RNA in vivo, leading to endothelial cell gene editing. This approach can identify nanoparticles that target new cells.

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mentioning

confidence: 99%

High-throughput in vivo screen of functional mRNA delivery identifies nanoparticles for endothelial cell gene editing

Sago

Lokugamage

Paunovska

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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236

209

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“…More specifically, we found that a rationally designed ddPCR-based barcode system can quantify delivery with very high sensitivity. Previous DNA barcode technologies designed to track nanoparticle biodistribution could only compare relative biodistribution within the same cell type, but could not be used to compare biodistribution between different cell types 71 . We anticipate future studies further improving the design of QUANT barcodes by incorporating different patterns of chemical modification.…”

Section: Discussionmentioning

confidence: 99%

Modifying a Commonly Expressed Endocytic Receptor Retargets Nanoparticles in Vivo

et al. 2018

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Nanoparticles are often targeted to receptors expressed on specific cells, but few receptors are (i) highly expressed on one cell type and (ii) involved in endocytosis. One unexplored alternative is manipulating an endocytic gene expressed on multiple cell types; an ideal gene would inhibit delivery to cell type A more than cell type B, promoting delivery to cell type B. This would require a commonly expressed endocytic gene to alter nanoparticle delivery in a cell type-dependent manner in vivo; whether this can occur is unknown. Based on its microenvironmental regulation, we hypothesized Caveolin 1 (Cav1) would exert cell type-specific effects on nanoparticle delivery. Fluorescence was not sensitive enough to investigate this question, and as a result, we designed a platform named QUANT to study nanoparticle biodistribution. QUANT is 10× more sensitive than fluorescence and can be multiplexed. By measuring how 226 lipid nanoparticles (LNPs) delivered nucleic acids to multiple cell types in vivo in wild-type and Cav1 knockout mice, we found Cav1 altered delivery in a cell-type specific manner. Cav1 knockout did not alter LNP delivery to lung and kidney macrophages but substantially reduced LNP delivery to Kupffer cells, which are liver-resident macrophages. These data suggest caveolin-mediated endocytosis of nanomedicines by macrophages varies with tissue type. These results suggest manipulating receptors expressed on multiple cell types can tune drug delivery.

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“…The different nanoformulations were pooled together and injected into a single mouse. The nucleic acid barcodes were recovered at a different time point from different tissues or cells, then Illumina deep sequencing was performed to accurately quantify the distinct barcodes and thus the biodistribution of different nanoparticles [ 188 , 190 ]. Careful dosing studies demonstrated that DNA barcode LNPs can be measured at a low dose, which confirms the feasibility of multiplexing hundreds of nanoparticles in a single experiment [ 188 ].…”

Section: Barcoding—a New Mode To Apply Sequences For Finding In VImentioning

confidence: 99%

Non-Viral Targeted Nucleic Acid Delivery: Apply Sequences for Optimization

Wang

Wagner

2020

Pharmaceutics

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In nature, genomes have been optimized by the evolution of their nucleic acid sequences. The design of peptide-like carriers as synthetic sequences provides a strategy for optimizing multifunctional targeted nucleic acid delivery in an iterative process. The optimization of sequence-defined nanocarriers differs for different nucleic acid cargos as well as their specific applications. Supramolecular self-assembly enriched the development of a virus-inspired non-viral nucleic acid delivery system. Incorporation of DNA barcodes presents a complementary approach of applying sequences for nanocarrier optimization. This strategy may greatly help to identify nucleic acid carriers that can overcome pharmacological barriers and facilitate targeted delivery in vivo. Barcode sequences enable simultaneous evaluation of multiple nucleic acid nanocarriers in a single test organism for in vivo biodistribution as well as in vivo bioactivity.

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Testing thousands of nanoparticles in vivo using DNA barcodes

Cited by 58 publications

References 58 publications

High-throughput in vivo screen of functional mRNA delivery identifies nanoparticles for endothelial cell gene editing

High-throughput in vivo screen of functional mRNA delivery identifies nanoparticles for endothelial cell gene editing

Modifying a Commonly Expressed Endocytic Receptor Retargets Nanoparticles in Vivo

Non-Viral Targeted Nucleic Acid Delivery: Apply Sequences for Optimization

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