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Updated: Sep 9, 2025
Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
Published on: August 1, 2018
Mapping the FOXA1 Interactome in ER+ Breast Cancer Cells Using Proximity Labeling Reveals Novel Interactions with the
Rosemary N Plagens1, Carla S Rodriquez Tirado2, Shen Li1
1Lineberger Comprehensive Cancer Center, Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
Abstract:
FOXA1 is a pioneer transcription factor essential for chromatin accessibility and transcriptional regulation in hormone-driven cancers. In breast cancer, FOXA1 plays a central role in facilitating nuclear receptor binding, reprogramming enhancer landscapes, and promoting transcriptional changes associated with therapy resistance. Whereas FOXA1's function has been primarily studied in the context of estrogen receptor-α (ER), its broader protein interaction network remains incompletely defined. In this study, we systematically map FOXA1-interacting proteins in ER-positive breast cancer cells using proximity-dependent biotin labeling (miniTurbo) combined with quantitative LC-MS/MS proteomics. We engineered MCF-7 cell lines stably expressing miniTurbo-tagged FOXA1 at either the N-terminus or C-terminus to ensure comprehensive coverage of interaction interfaces. This approach recovered known FOXA1 partners, including AR, MLL3, YAP1, and GATA3, and identified 157 previously unreported FOXA1 interactors. Notably, 42 of these novel partners, including NR2C2, were significantly associated with poor relapse-free survival in patients with ER-positive breast cancer. To demonstrate the utility of this resource, we characterized the FOXA1-NR2C2 interaction in depth. Integrating chromatin immunoprecipitation sequencing and RNA sequencing, we show that FOXA1 and NR2C2 co-occupy a subset of genomic regions and drive co-regulated transcriptional programs involved in tumor progression. Our study reveals an expanded FOXA1 interactome and new insights into its functional network in breast cancer, providing candidate proteins for further exploration as biomarkers or therapeutic targets.
Implications:
These findings expand the FOXA1 interactome in breast cancer and uncover new candidate proteins with potential as biomarkers and therapeutic targets in hormone-driven tumors.
Insights
Researchers mapped proteins interacting with FOXA1, a key factor in hormone-driven cancers. They discovered new FOXA1 partners, some linked to poor survival in breast cancer patients, offering potential therapeutic targets.
Area of Science:
- Oncology
- Molecular Biology
- Genomics
Background:
- FOXA1 is crucial for gene regulation in hormone-driven cancers, particularly breast cancer.
- Its role in estrogen receptor-positive (ER+) breast cancer involves nuclear receptor binding and therapy resistance.
- The full network of FOXA1 protein interactions is not well understood.
Purpose of the Study:
- To systematically map FOXA1-interacting proteins in ER+ breast cancer cells.
- To identify novel FOXA1 partners and understand their clinical relevance.
- To investigate the functional interaction between FOXA1 and NR2C2.
Main Methods:
- Proximity-dependent biotinylation (miniTurbo) coupled with quantitative LC-MS/MS proteomics.
- Engineering MCF-7 cell lines with N- or C-terminus miniTurbo-tagged FOXA1.
- ChIP-seq and RNA-seq for functional characterization of FOXA1-NR2C2 interaction.
Main Results:
- Successfully identified known FOXA1 partners and 157 novel interactors.
- Discovered that 42 new interactors, including NR2C2, correlate with poor relapse-free survival in ER+ breast cancer.
- Demonstrated co-occupancy of FOXA1 and NR2C2 at genomic regions, driving tumor progression-related transcription.
Conclusions:
- The study presents an expanded FOXA1 interactome in breast cancer.
- Identified novel candidate proteins, such as NR2C2, as potential biomarkers and therapeutic targets.
- Provides new insights into FOXA1's functional network in hormone-driven cancers.
