Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets

Nature Communications, vol. 13, pp. 4450

Abstract

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 highly multiplexed fashion. We apply Combi-Seq to screen the effect of 420 drug combinations on the transcriptome of K562 cells using only ~250 single cell droplets per condition, to successfully predict synergistic and antagonistic drug pairs, as well as their pathway activities.

Authors 10

1. Lukas Mathur

   Heidelberg University · European Molecular Biology Laboratory · European Molecular Biology Laboratory

   Affiliation as printed

   Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany

   Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

2. Bence Szalai

   Semmelweis University · Institute of Molecular Life Sciences · HUN-REN Research Centre for Natural Sciences

   Affiliation as printed

   Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary

   Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary

   Turbine Simulated Cell Technologies Ltd, Budapest, Hungary

3. N. H. Du

   École Polytechnique Fédérale de Lausanne

   Affiliation as printed

   Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

4. Ramesh Utharala

   European Molecular Biology Laboratory · European Molecular Biology Laboratory

   Affiliation as printed

   Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

5. Martine Ballinger

   European Molecular Biology Laboratory · European Molecular Biology Laboratory

   Affiliation as printed

   Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

6. Jonathan J. M. Landry

   European Molecular Biology Laboratory · European Molecular Biology Laboratory

   Affiliation as printed

   Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

7. Michaël Ryckelynck

   Centre National de la Recherche Scientifique · Architecture et Réactivité de l'arN · Institut de Biologie Moléculaire et Cellulaire · Université de Strasbourg

   Affiliation as printed

   Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR, 9002, Strasbourg, France

   Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR, 9002, Strasbourg, France

8. Vladimı́r Beneš

   European Molecular Biology Laboratory · European Molecular Biology Laboratory

   Affiliation as printed

   Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany

9. Julio Sáez-Rodríguez corresponding Aachen Faculty of Medicine Joint Research Centre for Computational Biomedicine (JRC-COMBINE)

   Heidelberg University · University Hospital Heidelberg · RWTH Aachen University

   Affiliation as printed

   Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany. pub.saez@uni-heidelberg.de

   Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany. pub.saez@uni-heidelberg.de

   Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany

10. Christoph A. Merten corresponding

    European Molecular Biology Laboratory · École Polytechnique Fédérale de Lausanne

    Affiliation as printed

    Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. christoph.merten@epfl.ch

    Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland. christoph.merten@epfl.ch

    Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland