Loss of the Y chromosome (LOY) is observed in multiple cancer types, including 10–40% of bladder cancers^1,2,3,4,5,6, but its clinical and biological significance is unknown. Here, using genomic and transcriptomic studies, we report that LOY correlates with poor prognoses in patients with bladder cancer. We performed in-depth studies of naturally occurring LOY mutant bladder cancer cells as well as those with targeted deletion of Y chromosome by CRISPR–Cas9. Y-positive (Y⁺) and Y-negative (Y^–) tumours grew similarly in vitro, whereas Y⁻ tumours were more aggressive than Y⁺ tumours in immune-competent hosts in a T cell-dependent manner. High-dimensional flow cytometric analyses demonstrated that Y⁻ tumours promote striking dysfunction or exhaustion of CD8⁺ T cells in the tumour microenvironment. These findings were validated using single-nuclei RNA sequencing and spatial proteomic evaluation of human bladder cancers. Of note, compared with Y⁺ tumours, Y⁻ tumours exhibited an increased response to anti-PD-1 immune checkpoint blockade therapy in both mice and patients with cancer. Together, these results demonstrate that cancer cells with LOY mutations alter T cell function, promoting T cell exhaustion and sensitizing them to PD-1-targeted immunotherapy. This work provides insights into the basic biology of LOY mutation and potential biomarkers for improving cancer immunotherapy.

在多种癌症类型中观察到 Y 染色体 （LOY） 的缺失，包括 10-40% 的膀胱癌^1,2,3,4,5,6，但其临床和生物学意义尚不清楚。在这里，使用基因组和转录组学研究，我们报告了 LOY 与膀胱癌患者的不良预后相关。我们对天然存在的 LOY 突变膀胱癌细胞以及 CRISPR-Cas9 靶向缺失 Y 染色体的细胞进行了深入研究。Y 阳性 （Y⁺） 和 Y 阴性 （Y^–） 肿瘤在体外生长相似，而 Y ^- 肿瘤在免疫功能正常的宿主中以 T 细胞依赖性方式比 Y⁺ 肿瘤更具侵袭性。高维流式细胞术分析表明，Y⁻ 肿瘤促进肿瘤微环境中 CD8⁺ T 细胞的显著功能障碍或耗竭。这些发现使用单核 RNA 测序和人膀胱癌的空间蛋白质组学评估进行了验证。值得注意的是，与 Y⁺ 肿瘤相比，Y^-肿瘤在小鼠和癌症患者中对抗 PD-1 免疫检查点阻断治疗的反应增加。总之，这些结果表明，具有 LOY 突变的癌细胞会改变 T 细胞功能，促进 T 细胞耗竭并使它们对 PD-1 靶向免疫疗法敏感。这项工作提供了对 LOY 突变的基础生物学和改善癌症免疫治疗的潜在生物标志物的见解。