The SAGA acetyltransferase module is required for the maintenance of MAF and MYC oncogenic gene expression programs in multiple myeloma [CUT&RUN]

Despite recent advances in therapeutic treatments, multiple myeloma (MM) remains an incurable malignancy. Epigenetic factors contribute to the initiation, progression, relapse, and clonal heterogeneity in MM, but our knowledge on epigenetic mechanisms underlying MM development is far from complete. The SAGA complex serves as a coactivator in transcription and catalyzes acetylation and deubiquitylation. Analyses of datasets in the Cancer Dependency Map Project revealed many SAGA components are selective dependencies in MM. To define SAGA-specific functions, we focused on ADA2B, the only subunit in the lysine acetyltransferase (KAT) module that specifically functions in SAGA. Integration of RNA-seq, ATAC-seq, and CUT&RUN results identified pathways directly regulated by ADA2B include MTORC1 signaling, MYC, E2F, and MM-specific MAF oncogenic programs. We discovered that ADA2B is recruited to MAF and MYC gene targets, and that MAF shares a majority of its targets with MYC in MM cells. Furthermore, we found the SANT domain of ADA2B is required for interaction with both GCN5 and PCAF acetyltransferases, incorporation into SAGA, and ADA2B protein stability. Our findings uncover previously unknown SAGA KAT module-dependent mechanisms controlling MM cell growth, revealing a vulnerability that might be exploited for future development of MM therapy. CUT&RUN was performed on MM.1S cells harboring either FLAG-3xHA-ADA2B or FLAG-3xHA using HA, H3K9ac, or IgG antibodies.

尽管治疗手段近年来取得进展，多发性骨髓瘤（multiple myeloma, MM）仍是一种无法治愈的恶性肿瘤。表观遗传因子参与MM的发生、进展、复发及克隆异质性，但我们对MM发生背后的表观遗传机制的认知仍远未完善。SAGA复合物（SAGA complex）作为转录共激活因子，可催化乙酰化与去泛素化反应。对癌症依赖性图谱项目（Cancer Dependency Map Project）数据集的分析显示，多种SAGA复合物组分是MM中的选择性依赖基因。为明确SAGA复合物的特异性功能，我们聚焦于ADA2B——赖氨酸乙酰转移酶模块（lysine acetyltransferase, KAT）中唯一仅在SAGA复合物中发挥功能的亚基。整合RNA测序（RNA-seq）、转座酶可及性测序（ATAC-seq）及CUT&RUN技术的结果，发现ADA2B直接调控的通路包括MTORC1信号通路、MYC、E2F以及MM特异性MAF致癌程序。我们发现ADA2B被招募至MAF与MYC的基因靶点，且在MM细胞中，MAF的大部分靶点与MYC重合。此外，我们证实ADA2B的SANT结构域（SANT domain）是其与GCN5、PCAF乙酰转移酶结合、整合进入SAGA复合物以及维持ADA2B蛋白质稳定性所必需的。本研究揭示了此前未被阐明的、依赖于SAGA复合物KAT模块的MM细胞生长调控机制，发现了可用于未来MM治疗开发的潜在治疗靶点。本实验中，我们对携带FLAG-3xHA-ADA2B或仅携带FLAG-3xHA的MM.1S细胞，分别使用HA、H3K9ac或IgG抗体进行了CUT&RUN实验。