SCOPE: Revealing Hidden Mechanisms in Phenotypic Screens Through Target and Pathway Enrichment

Area of Science:

• Computational biology
• Pharmacology
• Systems biology

Background:

• Phenotypic screening identifies bioactive compounds but struggles with mechanistic interpretation due to complex cellular pathways and polypharmacology.
• Understanding the molecular basis of phenotypic changes is crucial for drug discovery and development.

Purpose of the Study:

• To develop and validate SCOPE (Screening Compound Ontology for Pathway Enrichment), a computational framework to elucidate molecular mechanisms underlying phenotypic screening results.
• To identify key pathways and targets involved in endoplasmic reticulum (ER) stress-induced exodosis.

Main Methods:

• SCOPE integrates compound screening data with multi-source target annotations and pathway databases (e.g., KEGG).
• Statistical enrichment analysis is employed to identify significantly associated pathways and targets.
• The framework was applied to a high-throughput screen for modulators of ER-stress induced exodosis.

Main Results:

• SCOPE identified calcium signaling as a key pathway regulating exodosis without prior biological assumptions.
• Enrichment analysis highlighted G protein-coupled receptors (GPCRs) and inositol 1,4,5-trisphosphate receptors (IP3Rs)-mediated signaling.
• A novel role for the histamine receptor HRH1 in exodosis regulation was uncovered and validated.

Conclusions:

• SCOPE effectively deconvolutes complex phenotypic screening data to reveal underlying molecular mechanisms.
• The histamine receptor HRH1 is implicated in ER stress and exodosis, representing a potential therapeutic target for related disorders.
• This framework facilitates the identification of actionable biological insights from high-throughput screening campaigns.