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Updated: Jul 4, 2025
A Multiplexed Luciferase-based Screening Platform for Interrogating Cancer-associated Signal Transduction in Cultured Cells
Published on: July 3, 2013
Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy
José L McFaline-Figueroa1, Sanjay Srivatsan2, Andrew J Hill3
1Department of Biomedical Engineering, Columbia University, New York, NY, USA; Department of Genome Sciences, University of Washington, Seattle, WA, USA.
Abstract:
Chemical genetic screens are a powerful tool for exploring how cancer cells' response to drugs is shaped by their mutations, yet they lack a molecular view of the contribution of individual genes to the response to exposure. Here, we present sci-Plex-Gene-by-Environment (sci-Plex-GxE), a platform for combined single-cell genetic and chemical screening at scale. We highlight the advantages of large-scale, unbiased screening by defining the contribution of each of 522 human kinases to the response of glioblastoma to different drugs designed to abrogate signaling from the receptor tyrosine kinase pathway. In total, we probed 14,121 gene-by-environment combinations across 1,052,205 single-cell transcriptomes. We identify an expression signature characteristic of compensatory adaptive signaling regulated in a MEK/MAPK-dependent manner. Further analyses aimed at preventing adaptation revealed promising combination therapies, including dual MEK and CDC7/CDK9 or nuclear factor κB (NF-κB) inhibitors, as potent means of preventing transcriptional adaptation of glioblastoma to targeted therapy.
Insights
This study introduces sci-Plex-Gene-by-Environment (sci-Plex-GxE) for large-scale single-cell genetic and chemical screening. It identifies combination therapies to prevent glioblastoma adaptation to targeted treatments.
Area of Science:
- Cancer Biology
- Genomics
- Pharmacology
Background:
- Chemical genetic screens offer insights into cancer drug response but lack gene-level molecular detail.
- Understanding gene contributions is crucial for optimizing targeted cancer therapies.
Purpose of the Study:
- To develop and apply a scalable platform for combined single-cell genetic and chemical screening.
- To elucidate the role of individual genes in glioblastoma response to receptor tyrosine kinase pathway inhibitors.
Main Methods:
- Introduction of sci-Plex-Gene-by-Environment (sci-Plex-GxE) for high-throughput screening.
- Probing 522 human kinases across 14,121 gene-by-environment combinations in glioblastoma cells.
- Analysis of 1,052,205 single-cell transcriptomes to identify adaptive signaling pathways.
Main Results:
- Identified an expression signature of compensatory adaptive signaling dependent on MEK/MAPK.
- Discovered that glioblastoma cells adapt to targeted therapy through transcriptional changes.
- Revealed promising combination therapies, including MEK inhibitors with CDC7/CDK9 or NF-κB inhibitors, to overcome adaptation.
Conclusions:
- sci-Plex-GxE enables large-scale, unbiased screening for molecular insights into drug response.
- Targeted therapies can be enhanced by inhibiting compensatory signaling pathways.
- Combination therapies targeting MEK/MAPK and other pathways show potential for treating glioblastoma.
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