Cells that were previously described as homogeneous are composed of subsets with distinct transcriptional states. However, it remains unclear whether this cell heterogeneity influences the efficiency with which lipid nanoparticles (LNPs) deliver messenger RNA therapies in vivo. To test the hypothesis that cell heterogeneity influences LNP-mediated mRNA delivery, we report here a new multiomic nanoparticle delivery system called single-cell nanoparticle targeting-sequencing (SENT-seq). SENT-seq quantifies how dozens of LNPs deliver DNA barcodes and mRNA into cells, the subsequent protein production and the transcriptome, with single-cell resolution. Using SENT-seq, we have identified cell subtypes that exhibit particularly high or low LNP uptake as well as genes associated with those subtypes. The data suggest that cell subsets have distinct responses to LNPs that may affect mRNA therapies.
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All raw sequencing data (GEO: GSE186395) are available online. All other data are provided in the main text or the Supplementary Information.
The custom code used is available at https://github.com/Jack-Feldman/barcode_count.
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We thank K. Tiegren for copyediting the manuscript. Funding was provided by the National Institutes of Health (grant nos. UG3-TR002855 (J.E.D. and P.J.S.) and R01DE026941 (J.E.D.)).
C.D., K.P. and J.E.D. have filed intellectual property related to SENT-seq. J.E.D. is an advisor for GV. All other authors declare no competing interests.
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Dobrowolski, C., Paunovska, K., Schrader Echeverri, E. et al. Nanoparticle single-cell multiomic readouts reveal that cell heterogeneity influences lipid nanoparticle-mediated messenger RNA delivery. Nat. Nanotechnol. 17, 871–879 (2022). https://doi.org/10.1038/s41565-022-01146-9
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