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Updated: Jan 23, 2026
Generation of Prostate Cancer Cell Models of Resistance to the Anti-mitotic Agent Docetaxel
Published on: September 8, 2017
Integrative transcriptomic profiling reveals subtype-specific therapeutic vulnerabilities and resistance mechanisms
Wei Liu1,2, Weiyu Kong3, Silin Jiang1,2
1Department of Urology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, 210029, China.
Objective:
Advanced prostate cancer (PCa) remains therapeutically challenging due to heterogeneous mechanisms of resistance to androgen receptor (AR)-targeting agents. While AR signaling persists in castration-resistant PCa (CRPC), emerging evidence suggests AR-independent survival pathways may contribute to therapeutic escape. This study integrates transcriptomic data and clinical profiling to dissect AR dependency and resistance mechanisms in PCa, aiming to identify subtype-specific vulnerabilities and therapeutic targets.
Methods:
We performed CRISPR-Cas9 screens in AR-dependent (VCaP, LNCaP, 22Rv1) and AR-independent (DU145, PC-3, WPE1-NA22, P4E6, Shmac5) cell lines to identify core essential genes. RNA sequencing data from TCGA-PRAD, Changhai, and DKFZ cohorts were integrated to define molecular subtypes using consensus clustering. Spatial transcriptomics (ST) and single-cell RNA sequencing (scRNA-seq) were employed to validate gene expression patterns in primary tumors and metastatic samples. Temporal expression dynamics were analyzed using fuzzy clustering to identify resistance mediators, with a focus on MCL1. Drug sensitivity analysis revealed that AR-dependent cells were more sensitive to MCL1 inhibitor UMI-77, and MCL1 expression was higher in Enzalutamide-resistant cell lines. Functional validation via MCL1 knockdown confirmed its role in supporting the proliferation and inhibiting apoptosis of resistant cells.
Results:
CRISPR screening identified 952 shared essential genes in prostate cancer, with 157 AR-high essential signature and 130 AR-low essential signature genes. AR-high essential signature genes enriched in cell cycle/polycomb pathways, while AR-low essential signature genes correlated with oxidative phosphorylation/mTOR signaling. Consensus clustering of TCGA-PRAD data revealed three molecular subtypes (Clusters 1-3); Cluster 3 showed worst prognosis (shorter PFI/OS) and advanced clinical features (higher T/N stage, Gleason grade). External validation confirmed Cluster 3's aggressive phenotype and independent prognostic value (meta-cohort HR = 1.98, 95% CI: 1.19-3.27). Cluster 3 signature genes were upregulated in metastatic/CRPC tissues and spatially enriched in CRPC epithelium. Notably, Cluster 3 shared essential gene expression decreased after Enzalutamide treatment, whereas AR-high essential signature genes remained stable. MCL1 emerged as a key resistance driver, demonstrating persistent upregulation in Enzalutamide-resistant cells and CRPC models.
Conclusions:
This study elucidates distinct AR dependency landscapes in PCa, revealing AR-independent survival pathways and a clinically actionable molecular subtype (Cluster 3) linked to therapy resistance. MCL1 emerges as a critical mediator of adaptive resistance, highlighting the need for combination therapies targeting both AR-driven and AR-independent programs to improve outcomes in advanced PCa.
Insights
This study reveals distinct androgen receptor (AR) dependency in prostate cancer (PCa), identifying a therapy-resistant subtype and MCL1 as a key driver. Combination therapies targeting AR-driven and AR-independent pathways are crucial for advanced PCa.
Area of Science:
- Oncology
- Molecular Biology
- Genomics
Background:
- Advanced prostate cancer (PCa) presents therapeutic challenges due to resistance to androgen receptor (AR)-targeting agents.
- While AR signaling is key, AR-independent pathways may drive therapeutic escape in castration-resistant PCa (CRPC).
Purpose of the Study:
- To integrate transcriptomic data and clinical profiling to dissect AR dependency and resistance mechanisms in PCa.
- To identify subtype-specific vulnerabilities and therapeutic targets for advanced prostate cancer.
Main Methods:
- CRISPR-Cas9 screens were performed in AR-dependent and AR-independent cell lines.
- RNA sequencing, spatial transcriptomics (ST), and single-cell RNA sequencing (scRNA-seq) analyzed tumor samples.
- Consensus clustering defined molecular subtypes, and temporal expression dynamics identified resistance mediators like MCL1.
Main Results:
- Three molecular subtypes were identified; Cluster 3 exhibited the worst prognosis and advanced clinical features.
- Cluster 3 signature genes were upregulated in metastatic/CRPC tissues and enriched in CRPC epithelium.
- MCL1 was identified as a key resistance driver, upregulated in Enzalutamide-resistant cells and CRPC models.
Conclusions:
- Distinct AR dependency landscapes and AR-independent survival pathways were elucidated in PCa.
- A clinically actionable molecular subtype (Cluster 3) linked to therapy resistance was identified.
- MCL1 is a critical mediator of adaptive resistance, suggesting combination therapies for advanced PCa.
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