DCLK1 drives malignant progression and chemoresistance of bladder cancer by deubiquitinating HDAC6.

BACKGROUND: Bladder cancer (BC) is the most common malignancy of the urinary system, with rising incidence and mortality. Advanced BC frequently recurs or metastasizes and is often refractory to curative surgical intervention. Although cisplatin-based chemotherapy remains the standard first-line treatment, its clinical efficacy is frequently compromised by the development of drug resistance. Elucidating the molecular mechanisms underlying chemoresistance and metastasis is therefore critical for improving therapeutic strategies. METHODS: Single-cell RNA sequencing (scRNA-seq) was conducted to assess intratumoral heterogeneity and identify expression programs associated with bladder cancer progression. DCLK1 emerged as a key cancer-related hub gene. Its role in metastasis, cisplatin resistance, and immune evasion was evaluated using sphere formation, CCK-8, Transwell, CFSE staining, and flow cytometry assays. The interaction between DCLK1, USP10, and HDAC6 was confirmed through RNA pull-down, co-immunoprecipitation, mass spectrometry, cell localization, and molecular docking. Finally, the therapeutic potential of DCLK1, cisplatin, and ACY-1215 (an HDAC6 inhibitor) was tested in vivo. RESULTS: We identified multiple cell types, including cancer cells, lymphocytes, myeloid cells, fibroblasts, and other stromal components. In cancer cells, six biologically relevant expression programs were revealed. Among key cancer-related genes, DCLK1 was notably enriched and promoted bladder cancer metastasis, cisplatin resistance, and stemness. Mechanistically, DCLK1 activated the Notch pathway to upregulate PD-L1, suppress CD8⁺ T cell activity, and promote immune evasion. It also facilitated USP10-HDAC6 interaction, removing K48-linked ubiquitin at Lys116 to prevent HDAC6 degradation. Importantly, HDAC6 depletion abrogated the oncogenic effects of DCLK1, whereas inhibition of DCLK1 suppressed tumor progression and enhanced the antitumor efficacy of combined cisplatin and ACY-1215 treatment. CONCLUSIONS: DCLK1 is a critical driver of bladder cancer progression, chemoresistance, and immune escape. Single-cell analysis and functional assays revealed that DCLK1 enhances metastasis and stemness by activating the Notch/PD-L1 axis and stabilizing HDAC6 through USP10 interaction. Targeting DCLK1, alone or in combination with cisplatin and HDAC6 inhibition, represents a promising therapeutic strategy for advanced bladder cancer. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12943-025-02560-y.