ZNF397 Deficiency Triggers TET2-Driven Lineage Plasticity and AR-Targeted Therapy Resistance in Prostate Cancer

Academic Background and Research Motivation

Existing research evidence suggests that cancer cell lineage plasticity and epigenetic reprogramming enable them to evade lineage-dependent targeted therapy by adopting lineage plasticity. However, the mechanisms behind how these cancer cells utilize epigenetic regulation to gain lineage plasticity and treatment resistance remain largely unknown. The authors of this paper identify Zinc Finger Protein 397 (ZNF397) as a genuine androgen receptor (AR) coactivator, playing a crucial role in maintaining the luminal lineage in AR-driven prostate cancer cells. Loss of ZNF397 promotes a transition from an AR-driven luminal lineage to a TET2-driven plastic state, eventually leading to resistance to AR signaling inhibition therapy. Interestingly, the study finds that TET2 inhibitors can eliminate the resistance to AR-targeted therapy in tumors lacking ZNF397. These findings unveil a novel mechanism by which prostate cancer acquires lineage plasticity through epigenetic remodeling and propose a clinical intervention strategy to overcome therapy resistance caused by lineage plasticity.

Research Source and Author Information

This article was jointly written by several scholars including Yaru Xu, Yuqiu Yang, and Zhaoning Wang. The authors are primarily affiliated with institutions such as the University of Texas Southwestern Medical Center, University of California San Francisco, Baylor College of Medicine, and the University of Texas MD Anderson Cancer Center. The article was published in the journal Cancer Discovery in 2024.

Research Content and Workflow

a) Research Workflow

The research involved multiple steps. Initially, ZNF397 was identified as a key AR coactivator, followed by investigating how ZNF397 deficiency affects lineage plasticity in prostate cancer cells and their resistance to AR-targeted therapy. Various experimental methods and techniques were utilized, including CRISPR/Cas9 gene knockout, Chromatin Immunoprecipitation Sequencing (ChIP-seq), RNA sequencing (RNA-seq), and gene expression profile analysis.

Research Subjects and Sample Processing

The subjects of the study were different types of prostate cancer cell lines (such as LNCaP/AR, CWR22PC, MDA-PCa-2b) and mouse xenograft models. These cells underwent ZNF397 gene knockout through the CRISPR/Cas9 technology, and detailed analysis of gene expression and epigenetic characteristics was performed using multiple omics techniques.

Experimental Methods and Techniques

1. Gene Knockout and Functional Validation: CRISPR/Cas9 technology was used to knock out the ZNF397 gene to validate its role in anti-AR therapy.
2. Chromatin Immunoprecipitation Sequencing (ChIP-seq): This was used to study the binding sites of ZNF397 and AR and their effect on target gene expression.
3. Gene Expression and Transcriptome Sequencing (RNA-seq): This was employed to analyze changes in gene expression and explore transcriptional programs related to lineage plasticity.
4. Extreme Limiting Dilution Analysis (ELDA) and Xenograft Tumor Models: These were used to validate in vivo the lineage plasticity and therapy resistance caused by ZNF397 deficiency.

b) Main Research Results

1. ZNF397 is a key coactivator of the AR signaling pathway: ChIP-seq results showed that the loss of ZNF397 led to the loss of over 40% of AR binding peaks, significantly suppressing AR signal transduction.
2. ZNF397 deficiency leads to lineage plasticity: RNA-seq analysis revealed that the loss of ZNF397 drives prostate cancer cells toward a mixed, multi-lineage gene expression program, including EMT-like, stem-like, and neuronal-like lineages.
3. TET2 plays a crucial role in ZNF397 deficiency: The loss of ZNF397 activates a TET2-driven epigenetic program, promoting lineage plasticity and resistance to AR-targeted treatment.
4. TET2 inhibitors significantly reduce resistance: In vitro and in vivo experiments showed that using TET2 inhibitors could significantly inhibit the growth of ZNF397-deficient prostate cancer cells and restore sensitivity to AR-targeted therapy.

c) Research Conclusions and Significance

This study reveals the mechanism by which ZNF397 deficiency promotes lineage plasticity and therapy resistance through TET2-driven epigenetic remodeling. This not only enhances understanding of drug resistance but also identifies therapeutic strategies targeting TET2, especially for prostate cancer patients lacking ZNF397. ZNF397 and TET2 can serve as potential biomarkers for predicting resistance, helping in the early identification and intervention of resistant patients.

d) Highlights

1. Innovative Mechanism: The dual role of ZNF397 as an AR coactivator and repressor of lineage plasticity was revealed for the first time.
2. Clinical Significance: The potential of TET2 as a therapeutic target is highlighted, where targeting TET2 might reverse resistance.
3. Treatment Strategy: The use of TET2 inhibitors provides a novel approach to overcoming resistance to AR-targeted therapy.

e) Other Valuable Information

The study comprehensively validated the critical roles of ZNF397 and TET2 in prostate cancer through various models and analytical methods, providing a solid foundation for future clinical trials. The interaction between ZNF397 and TET2 and its impact on epigenetic modifications fill a significant knowledge gap on cancer epigenetic regulation and therapy resistance.

The paper not only deepens the theoretical understanding of lineage plasticity and therapy resistance in prostate cancer but also provides feasible scientific evidence for the development of practical treatment strategies.