SCOPE-based target and pathway enrichment identifies the histamine H1 receptor as a regulator of exodosis

Abstract

Phenotypic screening enables discovery of small molecules without requiring predefined targets, but mechanistic interpretation remains challenging due to polypharmacology and pathway complexity. We developed SCOPE (Screening Compound Ontology for Pathway Enrichment), a KNIME-based computational framework that links compound-level screening data to annotated targets and pathways to facilitate generation of mechanistic hypotheses. SCOPE integrates multi-source target annotations and performs sequential target- and pathway-level statistical enrichment using the screened compound library as the background to prioritize shared mechanisms of action. Applied to a previously established high-throughput screen for modulators of endoplasmic reticulum (ER)-stress induced secretion of ER resident proteins, a process known as exodosis, SCOPE identified calcium signaling as the most enriched KEGG pathway without prior biological context. Its target enrichment revealed several G protein-coupled receptors (GPCRs) linked to inositol 1,4,5-trisphosphate receptors (IP3Rs)-mediated calcium signaling, with widespread antagonism of these receptors among compounds that reduced exodosis, implicating this pathway in the regulation of exodosis. Notably, SCOPE uncovered a novel role for the histamine receptor HRH1 in exodosis, which was validated by RNAi knockdown, gene knockout, and pharmacological modulation, implicating HRH1 as a potential therapeutic target for modulating exodosis. These results highlight SCOPE’s potential to prioritize experimentally testable targets and pathways from phenotypic screening data.