Noninvasive nanoparticle barcoding demonstrated in nonhuman primates

Lipid nanoparticles (LNPs) have become one of the most important delivery technologies in modern medicine, helping transport messenger RNA into cells for vaccines, protein replacement therapies and experimental treatments. Yet a formulation that performs well in mice can behave very differently in humans. This species gap makes nonhuman primate studies an important step in drug development, but conventional methods for comparing multiple nanoparticles often require euthanasia and extensive tissue collection. A new study reports a way to measure the functional activity of several LNPs in the same animal using only a small blood sample.

Published in Nature Biotechnology, the work introduces a non-invasive nanoparticle barcoding platform called snapCodes. The method is designed to determine which LNP formulation successfully delivers its mRNA cargo and prompts cells to produce the encoded protein. Rather than relying on tissue harvesting, the researchers identify delivery events through DNA barcodes that can be recovered from serum and analyzed by sequencing. The approach could allow scientists to compare many candidate nanoparticles in a single nonhuman primate while reducing both animal use and the logistical burden of downstream analysis.

The central challenge addressed by the study is that nanoparticle delivery is not adequately described by measuring where an LNP travels. An LNP may reach an organ or circulate in the bloodstream without releasing its mRNA in a form that cells can translate. The new system instead records functional mRNA delivery. Each nanoparticle is associated with a distinctive DNA sequence, and the mRNA cargo is engineered to encode a fusion protein containing nanoluciferase and a SNAP-tag. Nanoluciferase is a compact enzyme that produces light in the presence of its substrate, while the SNAP-tag is a protein module capable of forming a covalent bond with specific chemical groups.

For the barcode to become a permanent molecular record of delivery, the researchers modified the DNA tags with benzylguanine. When a cell receives an mRNA molecule encoding the nanoluciferase–SNAP-tag fusion, the resulting protein can react with a benzylguanine-bearing snapCode. This creates a stable DNA–protein complex. The complexes are then exported from cells into the circulation, where they can be isolated from a small serum sample. Sequencing the recovered DNA reveals which barcoded LNPs produced the fusion protein and therefore achieved functional mRNA delivery.

The design turns transient protein expression into a measurable signal that can be collected without sacrificing the animal. This is particularly valuable in studies involving nonhuman primates, where tissue-based nanoparticle profiling can require euthanasia and can limit the number of formulations tested in each subject. A blood-based assay also makes it possible to monitor delivery over time, potentially showing how the activity of a formulation changes after dosing. The study used just 30 microliters of serum, a volume small enough to support repeated sampling and longitudinal measurements.

Before comparing nanoparticle performance, the researchers validated the molecular components of the system, including the activity of the snapCode chemistry and the ability of the fusion protein to participate in the intended covalent reaction. These steps were necessary to establish that the barcode signal reflected genuine expression of the delivered mRNA rather than nonspecific interactions. Once the platform had been characterized, the team used it to evaluate multiple chemically distinct LNPs in living animals.

The investigators intravenously administered six snapCoded LNP formulations to mice and nonhuman primates. Each formulation carried its own molecular identity, allowing all six candidates to be assessed in parallel. Serum collected after administration was analyzed for the DNA–fusion protein complexes, and sequencing was used to quantify the relative delivery activity associated with each barcode. By testing the same barcoded set across species, the researchers could directly examine whether patterns observed in mice were reproduced in nonhuman primates.

Such cross-species comparisons are crucial because LNP composition strongly influences biological behavior. Changes in ionizable lipids, helper lipids, cholesterol, polyethylene glycol-lipid components or particle structure can affect stability, organ distribution, cellular uptake and endosomal escape. These properties may differ substantially between rodents and primates because of differences in blood proteins, immune responses, tissue physiology and cellular trafficking. A method that measures expression from several formulations in the same animal may therefore reveal species-specific delivery patterns more efficiently than traditional one-formulation-per-animal experiments.

The snapCode strategy does not replace every form of nanoparticle analysis. It reports successful expression of a particular engineered mRNA and depends on the recovery and sequencing of the associated molecular complexes. It does not, by itself, provide a complete map of tissue distribution, long-term safety or therapeutic efficacy. Nevertheless, it adds a functional layer to LNP evaluation: scientists can ask not only where particles go, but which particles actually release mRNA that cells translate. In early development, that distinction can help prioritize candidates before more resource-intensive studies begin.

By combining multiplexed dosing with low-volume serum sampling, the researchers aim to make nonhuman primate testing more informative while using fewer animals. The platform could be adapted for screening delivery systems designed for different organs or therapeutic proteins, provided that the encoded reporter and barcode chemistry remain compatible with the intended experiment. As mRNA medicines expand beyond vaccines into gene editing, immunotherapy and protein replacement, tools that connect nanoparticle chemistry to real biological output may become increasingly important. Non-invasive barcoding offers a way to track those differences in living subjects and could help narrow the path from promising LNP design to clinically relevant drug candidate.