Contributed by Robert Langer, January 3, 2017 (sent for review October 28, 2016; reviewed by Charles A. Gersbach and David Putnam)
The effectiveness of nucleic acid drugs is limited by inefficient delivery to target tissues and cells and by unwanted accumulation in off-target organs. Although thousands of chemically distinct nanoparticles can be synthesized, nanoparticles designed to deliver nucleic acids in vivo were first tested in cell culture, yielding poor predictions for delivery in vivo. To facilitate testing of many nanoparticles in vivo, we designed and optimized a high-throughput DNA barcoding system to simultaneously measure nucleic acid delivery mediated by dozens of distinct nanoparticles in a single mouse. This nano-barcoding system can be used to study hundreds, or even thousands, of nanoparticles directly in vivo and could dramatically accelerate the discovery and understanding of nanoparticle drug delivery systems.
Nucleic acid therapeutics are limited by inefficient delivery to target tissues and cells and by an incomplete understanding of how nanoparticle structure affects biodistribution to off-target organs. Although thousands of nanoparticle formulations have been designed to deliver nucleic acids, most nanoparticles have been tested in cell culture contexts that do not recapitulate systemic in vivo delivery. To increase the number of nanoparticles that could be tested in vivo, we developed a method to simultaneously measure the biodistribution of many chemically distinct nanoparticles. We formulated nanoparticles to carry specific nucleic acid barcodes, administered the pool of particles, and quantified particle biodistribution by deep sequencing the barcodes. This method distinguished previously characterized lung- and liver- targeting nanoparticles and accurately reported relative quantities of nucleic acid delivered to tissues. Barcode sequences did not affect delivery, and no evidence of particle mixing was observed for tested particles. By measuring the biodistribution of 30 nanoparticles to eight tissues simultaneously, we identified chemical properties promoting delivery to some tissues relative to others. Finally, particles that distributed to the liver also silenced gene expression in hepatocytes when formulated with siRNA. This system can facilitate discovery of nanoparticles targeting specific tissues and cells and accelerate the study of relationships between chemical structure and delivery in vivo.
↵1J.E.D., K.J.K., and Y.X. contributed equally to this work.
Author contributions: J.E.D., K.J.K., Y.X., T.E.S., F.F.M., R.L., D.G.A., and E.T.W. designed research; J.E.D., K.J.K., Y.X., T.E.S., F.F.M., C.C.D., and E.T.W. performed research; J.E.D., K.J.K., Y.X., R.L., D.G.A., and E.T.W. contributed new reagents/analytic tools; J.E.D., K.J.K., Y.X., T.E.S., C.C.D., R.L., D.G.A., and E.T.W. analyzed data; and J.E.D., K.J.K., R.L., D.G.A., and E.T.W. wrote the paper.
Reviewers: C.A.G., Duke University; and D.P., Cornell University.
The authors declare no conflict of interest.
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1620874114/-/DCSupplemental.
