Drug-Seq combines drug studies with gene sequencing to understand how cells respond to compounds. This platform integrates drug testing with RNA sequencing, providing insights into cellular function at a genetic level. It transforms how therapeutics are identified and evaluated by linking genomic analysis with pharmacological testing.
Understanding Drug-Seq
Drug-Seq profiles how drugs affect gene activity within cells by examining the entire transcriptome, including all RNA molecules. It reveals which genes are turned on or off, or have altered activity, after drug exposure. Understanding these genetic changes helps uncover molecular pathways and biological processes a drug influences, providing a precise understanding of its intended actions and any “off-target” effects.
Drug-Seq offers a high-resolution view, detecting subtle molecular changes traditional methods, which average responses across many cells, might miss. This approach is valuable for understanding cellular response heterogeneity, where individual cells react differently to treatment. It helps develop effective, targeted therapies by clarifying how drugs interact with biological systems.
How Drug-Seq Works
The Drug-Seq process begins by exposing cells to drugs in multi-well plates (e.g., 384- or 1536-well). After treatment, cells are directly lysed, eliminating separate RNA purification. This streamlines workflow and reduces RNA degradation risk.
Following cell lysis, RNA serves as a template for reverse transcription. Specialized primers with unique well barcodes and unique molecular identifiers (UMIs) are incorporated into the newly synthesized cDNA. These barcodes allow multiple samples to be pooled for processing. This multiplexing strategy reduces the cost and hands-on time of traditional RNA sequencing.
After pooling, second-strand cDNA synthesis and library construction are performed. This involves fragmenting cDNA and adding Illumina adaptors. Plate-level barcodes track multiple plates simultaneously. Prepared libraries are quality-checked, quantified, normalized, and pooled for sequencing on Illumina platforms. The resulting data is analyzed using bioinformatics pipelines to identify changes in gene expression patterns in response to drugs.
Where Drug-Seq is Applied
Drug-Seq applies across drug discovery and development stages. In early phases, it accelerates novel compound identification by revealing molecular effects, enabling faster selection of promising candidates. It can also reduce reliance on animal models. The technology helps uncover unexpected links between gene expression patterns and drug effects, leading to new molecular target discovery.
It is used to understand drug mechanism of action (MoA). By comparing gene expression profiles before and after treatment, researchers view how drugs interact with gene networks. This reveals specific pathways and genes influenced by a drug, and identifies “off-target” effects contributing to side effects or toxicity. Drug-Seq can group compounds with similar MoAs based on transcriptional signatures, even if their specific molecular targets vary.
In toxicology, Drug-Seq helps assess side effects or toxicity of new compounds early in development. By detecting subtle changes in gene expression linked to toxicity, it can reduce drug candidate failures in later, more expensive stages. It also uncovers gene signatures indicative of treatment response, useful in biomarker discovery. This helps predict how tumors might respond to specific therapies, such as immune checkpoint inhibitors.
Drug-Seq is valuable in personalized medicine by predicting how individuals or their cells respond to a drug, enabling tailored treatments based on unique genetic profiles. Its ability to study how different cell populations within a tumor respond to treatment is useful in oncology, given cancers’ diverse molecular profiles. It can also study human primary cell types, offering insights into drug action in physiologically relevant systems and supporting systems-level models of drug response.
The Impact of Drug-Seq
Drug-Seq has transformed scientific research and drug development by providing a cost-effective, high-throughput method for comprehensive gene expression profiling. It advances understanding of drug action by enabling researchers to generate vast data on how compounds affect cellular transcription. This allows for more thorough and broad compound screening than previously possible.
The method’s ability to process samples in 384- or 1536-well formats increases throughput, allowing many chemicals to be profiled simultaneously. This high-throughput nature, combined with reduced costs per sample, accelerates compound screening and lowers drug development expenses. Drug-Seq detects transcriptional changes with fewer sequencing reads per well than traditional methods, further reducing costs while maintaining high data quality.
This innovation supports compound repurposing and facilitates sophisticated genetic network studies by providing unbiased activity readouts. It offers direct measurement of over 10,000 genes with comprehensive transcriptome coverage and better clustering accuracy than some existing platforms. Insights from Drug-Seq contribute to making drug discovery more efficient and data-driven, accelerating the identification and optimization of new therapies.