Automated image-based profiling of complex drug induced phenotypes in patient-derived organoids

Study ID Alternative Stable ID Type
EGAS00001003140 Other

Study Description

We established a platform for high-throughput confocal fluorescence microscopy and automated image analysis to perform large-scale drug response profiling with patient derived organoids (PDOs). Using PDO lines newly established from colorectal cancer patients with a standardized workflow, we performed chemical perturbations with more than 500 experimental and clinically used compounds. Subsequently, we captured approx. six million images by confocal microscopy. To analyze drug-induced PDO re-organization on a single organoid level we developed SCOPE, a software framework for automated PDO high-throughput image analysis. We observed a rich variety of divergent and reoccurring compound induced phenotypes in organoids. Perturbation of cellular processes, including signaling by MEK, GSK3β, cyclin dependent kinases (CDKs) and others, led to recurring and distinct architectural changes. Highlighting the clinical relevance, PDO viability was heterogeneous after perturbation with anticancer drugs and matched clinical response of corresponding colorectal cancer patients. Our work opens new ... (Show More)

Study Datasets 1 dataset.

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Dataset ID Description Technology Samples
The dataset includes 13 bam files. Each bam file is a different colorectal cancer patient organoid.
Illumina MiSeq 13

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