Abstract

High-throughput phenotypic screens using biochemical perturbations
and high-content readouts are constrained by limitations of scale. To
address this, we establish a method of pooling exogenous perturbations
followed by computational deconvolution to reduce required sample size,
labor and cost. We demonstrate the increased efficiency of compressed
experimental designs compared to conventional approaches through
benchmarking with a bioactive small-molecule library and a high-content
imaging readout. We then apply compressed screening in two biological
discovery campaigns. In the first, we use early-passage pancreatic cancer
organoids to map transcriptional responses to a library of recombinant
tumor microenvironment protein ligands, uncovering reproducible
phenotypic shifts induced by specific ligands distinct from canonical
reference signatures and correlated with clinical outcome. In the second, we
identify the pleotropic modulatory effects of a chemical compound library
with known mechanisms of action on primary human peripheral blood
mononuclear cell immune responses. In sum, our approach empowers
phenotypic screens with information-rich readouts to advance drug
discovery efforts and basic biological inquiry.