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

Area of Science:

• Biotechnology
• Genomics
• Molecular Biology

Background:

• Single-cell RNA sequencing (scRNA-seq) is powerful but costly and susceptible to batch effects.
• Current sample multiplexing methods using DNA labels have limitations in stability and labeling efficiency for diverse cell types.
• Efficient multiplexing is crucial for reducing costs and improving data quality in scRNA-seq.

Purpose of the Study:

• To introduce nanocoding, a novel technology utilizing lipid nanoparticles (LNPs) for enhanced barcoding in multiplexed scRNA-seq.
• To demonstrate the efficiency, stability, and broad applicability of nanocoding across various cell types and sample origins.
• To showcase nanocoding's utility in investigating complex biological questions, such as aging-related gene expression changes.

Main Methods:

• Development of nanocoding technology employing LNPs for high barcode labeling density in scRNA-seq.
• Optimization of LNP uptake mechanisms for efficient and stable cell barcoding.
• Application of nanocoding to cultured cell lines, tissue digests (spleen, adipose), and challenging sample types.

Main Results:

• Nanocoding achieves high barcode loading (10-100x amplification) and stability within 40 minutes using commercial reagents.
• Successful labeling of over 95% of cells in challenging adipose tissue samples from obese rodents.
• Identification of cell subtypes and gene expression changes related to aging, including cells missed by conventional methods.

Conclusions:

• Nanocoding offers a robust, efficient, and versatile solution for sample multiplexing in scRNA-seq.
• The LNP-based approach overcomes limitations of DNA-based methods, enabling deeper and more accurate cellular profiling.
• Nanocoding facilitates the study of complex biological systems and disease states with improved data quality and reduced cost.