snFLARE-seq and mrFRIGID for the transcriptomic and metabolomic landscape of prostate cancer with different anatomical origins

Prostate cancer cells of different anatomical locations display remarkable heterogeneity. This poses a challenge to the clinical relevance of pre-clinical models and the efficacy of contemporary therapeutic approaches. Here we developed the snFLARE-seq and mrFRIGID methodologies to directly investigate the transcriptomic and metabolomic landscape of prostate cancer patients utilizing formalin-fixed paraffin-embedded (FFPE) specimens. A retrospective analysis revealed the clinical disparities of prostate cancer from peripheral zone (PZ), transition zone (TZ), and across PZ and TZ. The snFLARE-seq, refined for enhanced single-nucleus sequencing, unveiled distinct cell type distributions and signaling pathways between PZ and TZ samples. Hormone therapy substantially affected cancer cells and microenvironment, leading to a polarized feature of epithelial cells and a subverted immune microenvironment. With improvements on metabolite extraction, mrFRIGID revealed unique metabolic features of prostate cancer from different origins. The metabolomic results indicate that PZ cancer cells were in a metabolic-dormant status, which were probably awaken by hormone therapy. Integrative analysis of results from snFLARE-seq, mrFRIGID, and TCGA database uncovered four metabolic pathways and related genes associated with disease aggressiveness. Our work would accelerate investigations on disease heterogeneity and evolution in real-world clinical settings, stimulating patient-specific precision healthcare solutions.不同解剖部位的前列腺癌细胞展现出显著的异质性，这给临床前模型的临床相关性以及当前治疗方案的疗效带来了挑战。本研究开发了snFLARE-seq与mrFRIGID技术方法，利用福尔马林固定石蜡包埋（formalin-fixed paraffin-embedded, FFPE）样本，直接探究前列腺癌患者的转录组与代谢组图谱。本研究通过回顾性分析，揭示了源自外周带（peripheral zone, PZ）、移行带（transition zone, TZ）以及同时累及PZ与TZ的前列腺癌的临床差异。经优化以提升单核测序性能的snFLARE-seq技术，揭示了PZ与TZ样本间截然不同的细胞类型分布与信号通路特征。激素治疗可显著影响癌细胞与肿瘤微环境，导致上皮细胞呈现极化表型，并使免疫微环境发生重塑。通过优化代谢物提取流程，mrFRIGID技术揭示了不同起源前列腺癌的独特代谢特征。代谢组学分析结果显示，PZ来源的癌细胞处于代谢休眠状态，而该状态可能被激素治疗激活。通过整合snFLARE-seq、mrFRIGID以及癌症基因组图谱（The Cancer Genome Atlas, TCGA）数据库的分析结果，本研究鉴定出四条与疾病侵袭性相关的代谢通路及对应基因。本研究将加速真实世界临床场景下的肿瘤异质性与演化机制研究，助力开发个体化精准医疗解决方案。