ArticleNature communications2022
Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 27 citations in OpenAlex.
- Review
- Discovering anticancer drug target combinations via network-informed signaling-based approach.Communications medicine · 2025Article
- Barcodes based on nucleic acid sequences: Applications and challenges (Review).Molecular medicine reports · 2025Review
- State-of-the-Art Liver Cancer Organoids: Modeling Cancer Stem Cell Heterogeneity for Personalized Treatment.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2025Review
- Towards an interpretable deep learning model of cancer.NPJ precision oncology · 2025Review
- Article
- Targeted barcoding of variable antibody domains and individual transcriptomes of the human B-cell repertoire using Link-Seq.PNAS nexus · 2025Article
- Robust Double Emulsions for Multicolor Fluorescence-Activated Cell Sorting.Analytical chemistry · 2024Article
- Understanding genomic medicine for thoracic aortic disease through the lens of induced pluripotent stem cells.Frontiers in cardiovascular medicine · 2024Review
- Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq.Nature communications · 2023Article
- High-throughput transcriptional profiling of perturbations byJournal of pharmaceutical analysis · 2023Article
- Application of perturbation gene expression profiles in drug discovery-From mechanism of action to quantitative modelling.Frontiers in systems biology · 2023Review
- A microfluidic Braille valve platform for on-demand production, combinatorial screening and sorting of chemically distinct droplets.Nature protocols · 2022Review
- Combi-seq for multiplexed transcriptome-based profiling of drug combinations using deterministic barcoding in single-cell droplets.Nature communications · 2022Article
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.