Dual Epigenetic and Chaperone Inhibition Disrupts Hypoxia Signaling and Tumor Progression in 3-D Models of
Meenal Datta1, Golnaz Asaadi Tehrani1, Maksym Zarodniuk2
1Notre Dame University.
Abstract:
Therapeutic resistance remains a major barrier to treating aggressive breast cancers, particularly triple-negative breast cancer (TNBC), in which hypoxia-associated stress adaptation within the tumor microenvironment limits treatment efficacy. Here, we investigated a multi-targeted therapeutic strategy combining histone deacetylase (HDAC) inhibition with blockade of hypoxia-associated chaperones HSP90β and mitochondrial TRAP1 in 3-D breast cancer models grown from TNBC human cells. HDAC inhibitors (HDACi; vorinostat [SAHA; pan-HDACi], valproic acid [VPA; HDAC1i], and CAY10603 [CAY; HDAC6i]; showed greater efficacy than paclitaxel at reducing viability and mammosphere formation in 3-D cultures, and induced apoptosis and G2/M cell cycle arrest in TNBC cells. Combined inhibition of HDACs with our novel agents targeting HSP90β (NDNB-25) or TRAP1 (NDNT-34) synergistically reduced mammosphere viability and disrupted spheroid architecture. Mechanistically, HSP90β and TRAP1 inhibition attenuated hypoxia-associated adaptive signaling by suppressing HIF-1α, VEGFA, HSP90β, and TRAP1 gene and protein expression. In co-cultures with HUVEC cells, these effects were accompanied by impaired endothelial network formation, tumor cell migration and invasion, mitotic progression, and clonogenic growth. Following Cleavage Under Targets and Release Using Nuclease (CUT&RUN) analysis, genome-wide HIF-1α occupancy analysis revealed extensive reprogramming of HIF-1α-associated regulatory programs under HDAC, HSP90β, and TRAP1 inhibition, including pathways linked to innate immunity, interferon signaling, redox balance, autophagy, mitochondrial function, and metabolic adaptation. Together, these findings identify hypoxia-associated stress adaptation as a therapeutically actionable vulnerability in aggressive breast cancer and support coordinated targeting of epigenetic regulation, proteostasis, and mitochondrial stress adaptation to enhance treatment response.
Insights
Targeting hypoxia-induced stress adaptation in triple-negative breast cancer (TNBC) with combined epigenetic and chaperone inhibition enhances treatment efficacy. This strategy overcomes therapeutic resistance by reprogramming key cancer pathways.
Area of Science:
- Oncology
- Molecular Biology
- Cancer Therapeutics
Background:
- Therapeutic resistance in aggressive breast cancers, especially triple-negative breast cancer (TNBC), is a significant clinical challenge.
- Tumor microenvironment hypoxia promotes stress adaptation, limiting the effectiveness of conventional treatments.
- Histone deacetylase (HDAC) inhibition and chaperone proteins like HSP90β and TRAP1 are implicated in cancer progression and survival.
Purpose of the Study:
- To investigate a multi-targeted therapeutic strategy combining HDAC inhibition with blockade of HSP90β and TRAP1 in TNBC models.
- To evaluate the synergistic effects of combined inhibition on TNBC cell viability, spheroid formation, and associated signaling pathways.
Main Methods:
- Utilized 3-D breast cancer models derived from human TNBC cells.
- Administered HDAC inhibitors (vorinostat, valproic acid, CAY10603) and novel agents targeting HSP90β (NDNB-25) and TRAP1 (NDNT-34).
- Performed co-culture experiments with HUVEC cells and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) analysis for genome-wide HIF-1α occupancy.
Main Results:
- HDAC inhibitors demonstrated superior efficacy over paclitaxel in reducing TNBC cell viability and mammosphere formation, inducing apoptosis and cell cycle arrest.
- Combined HDAC, HSP90β, and TRAP1 inhibition synergistically decreased spheroid viability, disrupted architecture, and attenuated hypoxia-associated signaling (HIF-1α, VEGFA).
- This combinatorial approach impaired endothelial network formation, tumor invasion, migration, and clonogenic growth, while genome-wide analysis revealed reprogramming of immunity, metabolism, and mitochondrial pathways.
Conclusions:
- Hypoxia-associated stress adaptation represents a therapeutically targetable vulnerability in aggressive breast cancer.
- Coordinated targeting of epigenetic regulation (HDACs), proteostasis (HSP90β), and mitochondrial stress (TRAP1) enhances treatment response in TNBC.
- This multi-targeted strategy holds promise for overcoming therapeutic resistance in aggressive breast cancers.
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