biostudies-literatureUnknown13(1)Mathur LAnti-cancer therapies often exhibit only short-term effects. Tumors typically develop drug resistance causing relapses that might be tackled with drug combinations. Identification of the right combination is challenging and would benefit from high-content, high-throughput combinatorial screens directly on patient biopsies. However, such screens require a large amount of material, normally not available from patients. To address these challenges, we present a scalable microfluidic workflow, called Combi-Seq, to screen hundreds of drug combinations in picoliter-size droplets using transcriptome changes as a readout for drug effects. We devise a deterministic combinatorial DNA barcoding approach to encode treatment conditions, enabling the gene expression-based readout of drug effects in a hiNature communications4450https://www.ebi.ac.uk/biostudies/studies/S-EPMC9343464biostudies-literatureCombi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets.PMC9343464Landry JJMSzalai BUtharala RSaez-Rodriguez JMathur LDu NHBallinger MBenes VMerten CARyckelynck MfalseCombi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets.Anti-cancer therapies often exhibit only short-term effects. Tumors typically develop drug resistance causing relapses that might be tackled with drug combinations. Identification of the right combination is challenging and would benefit from high-content, high-throughput combinatorial screens directly on patient biopsies. However, such screens require a large amount of material, normally not available from patients. To address these challenges, we present a scalable microfluidic workflow, called Combi-Seq, to screen hundreds of drug combinations in picoliter-size droplets using transcriptome changes as a readout for drug effects. We devise a deterministic combinatorial DNA barcoding approach to encode treatment conditions, enabling the gene expression-based readout of drug effects in a hi2022-01-01T00:00:00Z2022 Aug2025-04-22T01:49:45.167Z2025-04-05T20:04:45.035ZS-EPMC93434643591510810.1038/s41467-022-32197-0