Cell-type-agnostic differential gene expression uncovers conserved principles of cellular regulation

Abstract

Cellular responses to perturbagens--including pharmacological compounds and genetic manipulations--remain incompletely characterized, as conventional approaches are constrained by cell-type-specific biases. Here, we derive consensus signatures (CS) that uncover conserved principles not of gene expression, but of fundamental cellular regulation. Quantified by aggregating differential gene expression responses across diverse cell types, time points, and doses, these CS retain the core features of individual experiments while preserving biological relevance. As proof of concept, genome-wide CS screening identified three knockdown-resistant genes--CCNA1, ORC1, and SOX2--that also engage in their reciprocal up-regulation. Expression of this network is modulated by the factor E2F2, revealing a mechanism by which proliferative signaling persists despite diverse genetic and chemical perturbations. Crucially, we identify that ORC1 down-regulation by specific CDK4/6 inhibitors singularly disrupts this feedback loop, providing a direct route to suppress E2F2-driven proliferation. More generally, we demonstrate for the first time that CS can accurately predict RNA-seq responses in novel cell lines, uncovering evolutionarily conserved mechanisms that regulate fundamental biological processes beyond context-specific variability.