Nanocoding: Lipid Nanoparticle Barcoding for Multiplexed Single-Cell RNA Sequencing

Sample multiplexing is an emerging method in single-cell RNA sequencing (scRNA-seq) that addresses high costs and batch effects. Current multiplexing schemes use DNA labels to barcode cell samples but are limited in their stability and extent of labeling of heterogeneous cell populations. Here, we describe nanocoding, a technology that applies lipid nanoparticles (LNPs) for high barcode labeling density in multiplexed scRNA-seq. LNPs reduce dependencies on cell surface labeling mechanisms due to multiple controllable means of cell uptake, amplifying barcode loading 10-100-fold and allowing both protection and efficient release by upon cell lysis. In cultured cell lines and heterogeneous cells from tissue digests, nanocoding occurs in 40 min with stability after sample mixing and requires only commercially available reagents without complex chemical modifications. In spleen digests, 6-plex barcoded samples show minimal unlabeled cells, with all barcodes giving bimodal count distributions. Challenging samples from adipose tissue of obese rodents containing lipid-rich debris and heterogeneous cells show more than 95% labeling with all known subtypes identified. Using nanocoding, we investigate gene expression changes related to aging in adipose tissue, profiling cells that could not be readily identified with current direct conjugate methods using lipid or antibody conjugates. The ease of generating and tuning these constructs may afford efficient and robust sample multiplexing with minimal crosstalk.