Integrated Interactomics Reveals Novel Protein Associations: The FOXA1-PBX1 Complex as a Case Study

Area of Science:

• Molecular Biology
• Proteomics
• Cellular Signaling

Background:

• Protein-protein interactions (PPIs) are crucial for cellular functions but are often incompletely mapped by single methods.
• Technical limitations hinder the detection of many transient or weak PPIs.

Purpose of the Study:

• To systematically map the interaction landscapes of six key regulatory proteins.
• To overcome limitations of individual affinity purification techniques by integrating multiple methods.

Main Methods:

• An integrated proteomics workflow combining native immunoprecipitation, crosslinking-assisted capture, and proximity labeling.
• Systematic mapping of PPIs for six regulatory proteins (three transcription factors, three kinases).

Main Results:

• The integrated approach revealed distinct yet overlapping PPI profiles, identifying numerous novel interactors.
• Known interactions were robustly recovered, and PPI networks were substantially extended.
• A previously unrecognized physical interaction between FOXA1 and PBX1 transcription factors was discovered and validated.

Conclusions:

• Integrated proteomics workflows enhance PPI network coverage and uncover previously undetected interactions.
• The FOXA1-PBX1 complex plays a role in regulating transcriptional programs and cell fitness in ER-positive breast cells.
• The FOXA1-PBX1 complex may act as a regulatory node integrating chromatin accessibility and ER signaling.