DRUG-seq for miniaturized high-throughput transcriptome profiling in drug discovery.

Area of Science:

• Biotechnology
• Genomics
• Drug Discovery

Background:

• High-throughput screening is crucial for pharmaceutical discovery but current platforms have limited readouts.
• Standard RNA sequencing (RNA-seq) offers powerful transcriptome analysis but is cost-prohibitive for large-scale screening.

Purpose of the Study:

• To introduce Digital RNA with pertUrbation of Genes (DRUG-seq), a novel high-throughput platform for cost-effective drug discovery.
• To demonstrate DRUG-seq's capability in capturing transcriptional changes for mechanism of action (MoA) elucidation and on/off-target activity assessment.

Main Methods:

• DRUG-seq was developed as a high-throughput platform to capture transcriptional changes at a significantly reduced cost compared to standard RNA-seq.
• Proof-of-concept experiments involved profiling 433 compounds across 8 doses using DRUG-seq.

Main Results:

• DRUG-seq successfully grouped compounds into functional clusters based on their intended targets and MoAs.
• Transcriptome changes detected by DRUG-seq reflected perturbation differences for compounds targeting the same gene.
• DRUG-seq identified common mechanisms and differences between compound treatments and CRISPR perturbations on the same target.

Conclusions:

• DRUG-seq provides a powerful and economical tool for comprehensive transcriptome readout in high-throughput screening environments.
• This platform facilitates a deeper understanding of drug effects, including on-target and off-target activities, accelerating pharmaceutical discovery.