Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in...

Area of Science:

• Oncology
• Genomics
• Bioengineering

Background:

• Anti-cancer therapies often have limited efficacy due to acquired drug resistance, leading to tumor relapse.
• Drug combinations offer a promising strategy to overcome resistance, but identifying optimal combinations is complex.
• Current high-throughput screening methods require substantial biological material, often unavailable from patient biopsies.

Purpose of the Study:

• To develop a scalable microfluidic workflow, Combi-Seq, for high-throughput screening of drug combinations.
• To utilize single-cell transcriptome changes as a readout for drug effects.
• To enable drug combination screening using limited patient-derived samples.

Main Methods:

• A microfluidic system was designed to screen hundreds of drug combinations in picoliter droplets.
• A deterministic combinatorial DNA barcoding method was developed to encode treatment conditions.
• Single-cell RNA sequencing was employed to analyze transcriptome-wide gene expression changes.

Main Results:

• Combi-Seq successfully screened 420 drug combinations using approximately 250 single-cell droplets per condition.
• The workflow accurately predicted synergistic and antagonistic drug pairs.
• Pathway activities influenced by drug combinations were identified.

Conclusions:

• Combi-Seq provides a scalable and material-efficient approach for drug combination screening.
• This method enables gene expression-based analysis of drug effects in a highly multiplexed manner.
• Combi-Seq has the potential to accelerate the discovery of effective combination therapies for cancer treatment.