Ultrasensitive and High-Throughput Single Cell RNA Sequencing Technology

NU 2024-199

INVENTORS

• Yogesh Goyal*
• Emanuelle Grody
• Elena Martinelli

SHORT DESCRIPTION

Single-cell Amplified Libraries for Variant isoform Enrichment sequencing (SALVEseq), is an innovative experimental and computational workflow designed to detect rare RNA isoforms, such as viral RNA, in single cells.

BACKGROUND

Standard single-cell RNA sequencing (scRNA-seq) technologies have revolutionized our understanding of cellular heterogeneity, yet they remain severely limited in their ability to sensitively and cost-effectively detect rare, low-abundance RNA transcripts within individual cells, such as latent viral genomes or specific disease-associated isoforms. Because conventional high-throughput droplet-based platforms sequence the entire transcriptome indiscriminately, highly abundant host transcripts dominate the sequencing depth, frequently leaving rare target transcripts undetected. To address this, existing targeted enrichment methods often rely on specialized, proprietary on-bead capture chemistries early in the library preparation workflow, which restricts customization, increases costs, and limits compatibility with standard laboratory protocols. Alternatively, other specialized sequencing platforms that capture both host and viral RNA suffer from lower throughput and high operational complexity, preventing researchers from seamlessly and affordably profiling both high-dimensional host transcriptomes and rare variant isoforms simultaneously.

ABSTRACT

SALVEseq is a single-cell RNA sequencing workflow designed to detect rare RNA isoforms. By utilizing a valuable byproduct of single-cell RNA sequencing workflows, SALVEseq offers a cost-effective and adaptable solution that maintains the high throughput nature of single-cell RNA-seq while enabling high sensitivity for extremely rare isoforms. The technology has been applied in various viral infections to detect elusive viral RNAs in the context of the host cell transcriptome, allowing for unprecedented resolution in studying infection dynamics and optimizing latency reversal treatments. Furthermore, SALVEseq can be easily adapted outside of viral infections, such as neuronal degeneration, cancer, and liver regeneration, and therefore has potential as a diagnostic tool in wide-ranging fields.

APPLICATIONS

• Antiviral drug discovery and development - enables highly sensitive detection of rare viral transcripts within single cells (HIV, EBV, CMV, HSV, etc.)
• Precision medicine and clinical diagnostics - for example, detection of rare mutations, splice variants, or CAR-T monitoring to inform individual treatment strategies 
• Single-cell sequencing research tools and kits - supplemental laboratory kit for existing platforms

ADVANTAGES

• Higher sensitivity - recovers rare RNAs isoforms from single cells not detectable with current methods
• User friendly and cost-effective - standard workflow provides simple implementation and high throughput efficiency
• Flexible - customization for target enrichment adapts to a variety of disease indications

IP STATUS

PCT Patent Application WO2026090533A1 Filed.