The Histone Methyltransferase KMT2D is a Critical Mediator of Lineage Plasticity and Therapeutic Response in Castration Resistant Prostate Cancer [LNCaP Bulk RNA-Seq]

Castration-resistant prostate cancer (CRPC) is largely dependent on the androgen receptor (AR) for growth and often exhibits hyperactive PI3K signaling, most frequently due to PTEN loss. Therapeutic pressure from anti-AR therapies can induce trans-differentiation toward an AR-independent phenotype. Recently, different subtypes of AR-independent CRPC have been redefined, with the stem cell-like (SCL) subtype emerging as one of the most prevalent. Elucidation of the epigenetic mechanisms controlling the maintenance of these distinct CRPC cell states could pave the way for effective combinatorial therapies for CRPC. In this study, we identified a key role for the histone methyltransferase KMT2D in establishing the chromatin competence necessary for the recruitment of AR and FOXA1 transcription factors (TFs) that are essential for the AR transcriptional output in AR-dependent CRPC cell lines, patient derived organoids, and patient samples. Unexpectedly, KMT2D maintained the identity of the AR-low CRPC-SCL subtype and controlled activity of AP-1 TFs such as FOSL1, which acts as a master regulator of this subtype. Single cell transcriptomics and chromatin assays underscored the role of KMT2D in sustaining a mixed lineage cell state via AP-1 and FOXA1. The combined suppression of PI3K/AKT and KMT2D reduced cell proliferation in prostate cancer cells and patient-derived organoids in both CRPC-AR and CRPC-SCL subtypes. Altogether, these results unveil KMT2D as a major mediator of the epigenetic landscape in subtype-specific CRPC, contributing to tumor growth and therapeutic response. Overall design: Bulk RNA-Seq was performed in LNCAP AR-high prostate cancer cells with doxycycline-inducible knockdown of KMT2D

去势抵抗性前列腺癌（Castration-resistant prostate cancer, CRPC）的生长主要依赖雄激素受体（androgen receptor, AR），且常伴随过度激活的PI3K信号通路，该现象最常见的分子机制为PTEN缺失。抗雄激素治疗带来的治疗筛选压力可诱导肿瘤细胞转分化为AR非依赖表型。近年来，学界已重新界定多种AR非依赖型CRPC亚型，其中干细胞样（stem cell-like, SCL）亚型已成为最常见的亚型之一。阐明维持这些不同CRPC细胞状态的表观遗传机制，可为CRPC的高效联合治疗开辟新路径。
本研究中，我们在AR依赖型CRPC细胞系、患者来源类器官及患者样本中，鉴定出组蛋白甲基转移酶KMT2D在建立染色质适配能力中的关键作用——该能力是招募AR与FOXA1转录因子（transcription factors, TFs）所必需的，而这两种转录因子是AR转录调控输出的核心要素。令人意外的是，KMT2D可维持AR低表达的CRPC-SCL亚型的细胞身份，并调控AP-1转录因子（如FOSL1）的活性，而FOSL1是该亚型的核心调控因子。单细胞转录组学与染色质分析实验证实，KMT2D可通过AP-1与FOXA1维持混合谱系细胞状态。同时抑制PI3K/AKT通路与KMT2D，可降低CRPC-AR与CRPC-SCL亚型的前列腺癌细胞及患者来源类器官的细胞增殖能力。综上，本研究结果揭示KMT2D是亚型特异性CRPC表观遗传调控网络的核心介导因子，其参与调控肿瘤生长与治疗响应。
整体实验设计：对携带多西环素诱导性KMT2D敲低系统的LNCAP AR高表达前列腺癌细胞系开展批量RNA测序（Bulk RNA-Seq）。