In a recent study reported in the journal Molecular Therapy, a team led by researchers from the University of Science and Technology of China, Hefei, presents a groundbreaking approach to improving natural killer (NK) cell-based immunotherapy for hepatocellular carcinoma (HCC) by targeting the epigenetic factor BPTF (bromodomain PHD-finger containing transcription factor). The study demonstrates that BPTF plays a critical role in immune evasion by HCC cells and that its degradation using a proteolysis-targeting chimera (PROTAC) can enhance NK cell-mediated cytotoxicity against HCC. This essay will delve into the key findings, methodologies, and implications of this research, highlighting its significance in the field of cancer immunotherapy.

NK cells, BPTF and Their Role in hepatocellular carcinoma (HCC) HCC Immune Evasion

Hepatocellular carcinoma (HCC) is one of the most aggressive and lethal forms of cancer, particularly in its advanced stages. Traditional treatments, such as surgery, chemotherapy, and radiation, often have limited efficacy, especially in advanced HCC. Immunotherapy has emerged as a promising alternative, leveraging the body’s immune system to combat cancer. Among the immune cells, NK cells are particularly important in HCC due to their significant presence in the liver and their ability to directly kill tumor cells without prior sensitization. However, HCC cells often evade NK cell-mediated immunosurveillance by downregulating the expression of ligands that are crucial for NK cell recognition.
The study focuses on BPTF, an epigenetic reader overexpressed in various cancers, including HCC. By recognizing H3K4me3 marks, BPTF regulates gene expression, including heparanase (HPSE), an enzyme that degrades heparan sulfate proteoglycans (HSPGs), key ligands for NK cell receptors. BPTF overexpression in HCC correlates with advanced disease and poor survival, promoting immune evasion by reducing NCR ligand availability and weakening NK cell-mediated cytotoxicity.

Design and Synthesis of BPTF-Targeting PROTACs

Given the limitations of small-molecule inhibitors that only target specific domains of BPTF, PROTACs offer a more effective strategy by promoting complete degradation of the protein through the ubiquitin-proteasome pathway. The study describes the development of four candidate BPTF-specific PROTAC degraders (8a-d), synthesized via click chemistry. Computational molecular dynamics simulations were performed to assess their binding affinities, revealing that compound 8d exhibited the strongest interaction with BPTF and E3 ligase, making it the most potent degrader.

BPTF-Targeting PROTACs Selectively Degrades BPTF and Enhances NK Cell Cytotoxicity

The BPTF-targeting PROTAC, 8d, selectively degraded BPTF in HCC cells, reducing HPSE expression and increasing NCR ligand abundance, enhancing NK cell-mediated cytotoxicity. Western blot confirmed its effectiveness, with a DC50 of ~10 µM, while proteomics showed similar effects to BPTF knockdown, increasing HSPGs for NK cell recognition.

In vitro, BPTF-specific PROTAC significantly boosted NK cell killing of HCC cells, outperforming deactivated degraders and TP238. It also upregulated NK cell receptors (NKp30, NKp46, NKG2D) and effector markers (perforin, granzyme B, IFN-γ), enhancing anti-tumor activity. Mechanistically, BPTF-targeting PROTAC required E3 ligase-mediated ubiquitination, as inhibitors blocked degradation. A washout experiment confirmed its reversible action, ensuring specificity.

In Vivo Efficacy of BPTF-Targeting PROTACs

To assess the translational potential of BPTF-targeting PROTAC, the study employed orthotopic and subcutaneous HCC mouse models. In an orthotopic HCC mouse model, treatment with BPTF-targeting PROTAC significantly reduced tumor growth and improved survival, with its anti-tumor effects relying on NK cells, as their depletion abolished BPTF-targeting PROTAC’s therapeutic benefits. In a human hepatoma model using immunodeficient mice, BPTF-targeting PROTAC treatment combined with adoptive transfer of human NK cells effectively controlled tumor growth, further confirming its potential as an NK cell-enhancing immunotherapeutic strategy.

Histological and biochemical analyses confirmed that BPTF-Targeting PROTAC effectively downregulated BPTF and HPSE while increasing HSPG expression within tumors. Importantly, BPTF-targeting PROTAC treatment did not induce significant systemic toxicity, as evidenced by stable body weight, organ weights, and histological integrity of the kidneys and spleen.

Proteomic Profiling Reveals Broader Anti-Tumor Effects

Proteomic analysis of primary HCC cells treated with BPTF-targeting PROTAC showed a downregulation of tumor-promoting proteins such as ATG9A, IMPA1, SF3B4, and LRG1, along with an upregulation of tumor-suppressor pathways, including nicotine pharmacodynamics and GABA-B receptor signaling. These findings suggest that BPTF-targeting PROTAC not only enhances NK cell activity but also directly reduces the tumorigenic potential of HCC cells, further supporting its therapeutic potential.

 

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Expanding PROTAC Applications: From HCC to Broad-Spectrum Cancer Immunotherapy

This study presents several key implications for cancer immunotherapy. The development of BPTF-targeting PROTAC introduces a novel approach to enhancing NK cell-based immunotherapy by inducing complete protein degradation rather than merely inhibiting target function.

NK cell-based therapies have emerged as a promising approach in cancer immunotherapy due to their innate ability to recognize and eliminate tumor cells without prior sensitization. Unlike T cell-based therapies, NK cells exhibit a lower risk of graft-versus-host disease and cytokine release syndrome, making them a safer and highly effective option for treating various malignancies. Advances in adoptive NK cell transfer, CAR-NK cell engineering, and cytokine-induced memory-like NK cells have further improved their persistence, cytotoxicity, and adaptability in targeting tumors. However, a major challenge in NK cell therapy is tumor immune evasion, where cancer cells downregulate activating ligands and alter their microenvironment to escape NK cell-mediated destruction.

The discovery of BPTF-targeting PROTACs represents a breakthrough in overcoming this limitation by targeting BPTF, a key epigenetic regulator that suppresses NK cell recognition in HCC. By selectively degrading BPTF, BPTF-targeting PROTACs restores NCR ligand expression on tumor cells, making them more susceptible to NK cell-mediated cytotoxicity. This approach not only enhances the efficacy of NK cell-based therapies but also reprograms the tumor microenvironment to favor immune activation. Unlike conventional NK cell therapies that focus on direct modifications to NK cells, this strategy amplifies their natural function by altering tumor cell susceptibility. Moreover, the study suggests that BPTF degradation could be applied beyond HCC, extending its therapeutic potential to other malignancies with high BPTF expression, such as lung and breast cancer.

Additionally, the findings highlight the potential of integrating PROTAC-based strategies with existing immunotherapies, including immune checkpoint inhibitors and adoptive NK cell therapies, to further enhance anti-tumor responses. This study establishes targeted protein degradation as a powerful tool in immunotherapy, paving the way for more effective NK cell-based treatments that could revolutionize cancer immunotherapy.

Conclusion

In conclusion, this study provides compelling evidence that targeting BPTF with a PROTAC degrader can enhance NK cell-based immunotherapy for HCC. By elucidating the role of BPTF in immune evasion and demonstrating the efficacy of BPTF-targeting PROTACs in both in vitro and in vivo models, the study opens new avenues for the development of epigenetic-based immunotherapies. The findings underscore the potential of PROTAC technology to overcome the limitations of traditional cancer treatments and pave the way for more effective and targeted therapies in the fight against cancer.

Reference

Li Y, Bai L, Liang H, Yan P, Chen H, Cao Z, Shen Y, Wang Z, Huang M, He B, Hao Q, Mei Y, Wei H, Ding C, Jin J, Wang Y. A BPTF-specific PROTAC degrader enhances NK cell-based cancer immunotherapy. Mol Ther. 2025 Feb 11:S1525-0016(25)00103-0. doi: 10.1016/j.ymthe.2025.02.013. Epub ahead of print. PMID: 39935175.

Disclaimer: This information is intended solely for research purposes and does not serve as medical advice.

 

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