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Updated: Jul 4, 2026
Implementation of In Vitro Drug Resistance Assays: Maximizing the Potential for Uncovering Clinically Relevant Resistance Mechanisms
Published on: December 9, 2015
High-content microscopy reveals a morphological signature of bortezomib resistance
M E Kelley1, A Y Berman1, D R Stirling2
1Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.
Abstract:
Drug resistance is a challenge in anticancer therapy, particularly with targeted therapeutics and cytotoxic compounds. In many cases, cancers can be resistant to the drug prior to exposure, i.e., possess intrinsic drug resistance. However, we lack target-independent methods to anticipate resistance in cancer cell lines or characterize intrinsic drug resistance without a priori knowledge of its cause. We hypothesized that cell morphology could provide an unbiased readout of drug sensitivity prior to treatment. We therefore isolated clonal cell lines that were either sensitive or resistant to bortezomib, a well-characterized proteasome inhibitor and anticancer drug to which many cancer cells possess intrinsic resistance. We then measured high-dimensional single-cell morphology profiles using Cell Painting, a high-content microscopy assay. Our imaging- and computation-based profiling pipeline identified morphological features typically different between resistant and sensitive clones. These features were compiled to generate a morphological signature of bortezomib resistance, which correctly predicted the bortezomib treatment response in seven of ten cell lines not included in the training dataset. This signature of resistance was specific to bortezomib over other drugs targeting the ubiquitin-proteasome system. Our results provide evidence that intrinsic morphological features of drug resistance exist and establish a framework for their identification.
Insights
Cell morphology can predict anticancer drug resistance. Researchers identified a unique cell shape signature linked to bortezomib resistance, offering a new way to anticipate treatment effectiveness in cancer cells.
Area of Science:
- Oncology
- Cell Biology
- Biophysics
Background:
- Drug resistance, particularly intrinsic resistance, poses a significant challenge in anticancer therapy, limiting the efficacy of targeted and cytotoxic drugs.
- Current methods for characterizing intrinsic drug resistance often require prior knowledge of resistance mechanisms, lacking a target-independent approach.
- Predicting and understanding intrinsic drug resistance in cancer cell lines remains a critical unmet need in oncology.
Approach:
- Investigated cell morphology as an unbiased predictor of drug sensitivity using Cell Painting, a high-content microscopy assay.
- Isolated clonal cancer cell lines with intrinsic sensitivity or resistance to bortezomib, a proteasome inhibitor.
- Developed an imaging- and computation-based pipeline to identify morphological features distinguishing resistant from sensitive cells.
Key Points:
- Identified a distinct set of morphological features associated with bortezomib resistance in cancer cell lines.
- Generated a 'morphological signature' of bortezomib resistance that accurately predicted treatment response in independent cell lines.
- Demonstrated that this resistance signature was specific to bortezomib and not observed with other drugs targeting the ubiquitin-proteasome system.
Conclusions:
- Intrinsic cell morphology can serve as a reliable indicator of anticancer drug resistance.
- Established a novel framework for identifying target-independent morphological signatures of drug resistance.
- This approach offers a promising strategy for anticipating drug response and overcoming resistance in cancer therapy.
