RiboSTS – Ribosome Signatures Targeted by High-Throughput Single-Cell Sequencing

Challenge

scRNA-seq of mRNA is the dominant high-throughput method to study cellular heterogeneity because polyadenylated transcripts are easy to capture and amplify. In diseases such as cancer and viral infection, key changes in ribosome regulation, abundance, and heterogeneity are missed. Ribosomal RNAs (>85% of cellular RNA), which form the ribosome’s core, are excluded due to extreme abundance and complex structure and sequence, leaving rRNA-based signals and biomarkers inaccessible at single-cell resolution.
 

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Technology

RiboSTS (Ribosome Signatures Targeted by high-throughput single-cell Sequencing) is a novel scRNA-seq workflow with four key features. Multi-RNA capture: it quantifies multiple RNA classes per cell, currently rRNA and mRNA, and is extendable to additional classes. Titrated, target-specific balancing: selective amplification PCR (saPCR) rebalances RNA classes with extreme abundance differences, enabling joint sequencing when mRNA is <5% and rRNA >95% while preserving quantitative ribosome abundance and diversity information. Generalizability: it works in complex cell mixtures across species from prokaryotes to eukaryotes without extensive protocol re-optimization. Scalability: a one-tube, 384-well automation–ready workflow scalable to large cell numbers for cohort-scale studies and industrial screening.

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Commercial Opportunity

RiboSTS has completed proof-of-concept validation and is protected by a patent, creating a clear path toward commercialization in biotech and clinical single-cell markets. At the present stage, three complementary exploitation routes provide short- and mid-/long-term commercial opportunities:

1. Licensing of the core technology (short-term): RiboSTS can be licensed in its current form to established biotechnology and genomics companies active in scRNA-seq library preparation and NGS services. It complements existing scRNA-seq platforms by including rRNA.
2. Co-development and method extension with industry partners (mid- to long-term): Together with industrial partners, RiboSTS can be adapted from the current well-based format to higher-throughput microwell- or droplet-based workflows and combined with complementary modalities (e.g., Ribo-seq or SLAMseq).
3. Platform expansion to additional molecular targets (mid- to long-term): Beyond rRNA and mRNA, RiboSTS can be extended to capture additional non-coding RNAs (mitochondrial rRNAs, telomerase RNA, spliceosome RNA, and signal recognition particle RNA) and viral RNAs.
    

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Development Status

RiboSTS was systematically validated—first in vitro. In a proof-of-concept study on mouse embryonic neocortex development, RiboSTS was applied across multiple developmental stages and profiled >4,000 single cells, recovering expected cell-state phenotypes and revealing previously unknown lineage- and stage-specific ribosome-abundance features (manuscript submitted). RiboSTS is currently implemented as a one-tube, one-cell-per-well workflow compatible with 384-well automation, with cell barcoding introduced at the final stage. The next development milestone is to improve throughput and cost efficiency by adapting RiboSTS to microwell- or droplet-based partitioning with cell barcodes and UMIs introduced during reverse transcription, enabling early pooling and reducing dependence on large sets of unique dual indices. Further optimization of barcoded RT primer sets targeting both rRNA and mRNA (solution- or bead-immobilized) is a key step toward a product-ready workflow. 
 

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Patent Situation

Patent Application EP25184315.7, filed on 20th of June 2025 
 

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Further Reading

PMID: 32375039, 34312084, 36482253.
 

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