Immunoproteasome function maintains oncogenic gene expression in KMT2a-rearranged leukemia [RNA-seq II]

Pharmacologic targeting of epigenetic protein complexes has shown significant in vitro responses in AML. Early clinical trials in MLL-rearranged leukemia indicate rather transient responses and development of resistance. In an effort to define functional dependencies of MLL-fusions in acute myeloid leukemia, we identify the catalytic immunoproteasome subunit PSMB8 as an oncogene-specific vulnerability. Genetic and pharmacologic inactivation of PSMB8 results in impaired proliferation of murine and human leukemic cells while normal hematopoietic cells remain unaffected. Disruption of immunoproteasome function results in cellular enrichment of transcription factor BASP1, and consecutive repression of MLL-target genes. Pharmacologic targeting of PSMB8 improves efficacy of Menin-inhibitors, eradicates leukemia in primary human xenografts and shows preserved activity against Menin-inhibitor resistance mutations. This identifies and validates a cell-intrinsic mechanism whereby selectivity of proteostasis results in altered transcription factor abundance and repression of oncogene-specific transcriptional networks. Therapeutic targeting of PSMB8-dependent transcription in combination with Menin-inhibition could thus eradicate AML harboring MLL-rearrangements. Overall design: Comparative gene expression profiling analysis of RNA-seq data for MOLM-13 cells treated with 1 µM MI-503, a combination of 1 µM MI-503 and 100nM PR-957 (ONX-0914) or diluent treated controls.

表观遗传蛋白复合物（epigenetic protein complexes）的药理学靶向已在急性髓系白血病（Acute Myeloid Leukemia, AML）中展现出显著的体外应答。针对MLL重排白血病（MLL-rearranged leukemia）的早期临床试验显示，此类疗法的应答较为短暂且易产生耐药性。为明确急性髓系白血病中MLL融合基因（MLL-fusions）的功能依赖特性，我们鉴定出催化型免疫蛋白酶体亚基PSMB8（immunoproteasome subunit PSMB8）为一种癌基因特异性脆弱位点。对PSMB8进行遗传与药理学失活，可抑制小鼠及人源白血病细胞的增殖，而正常造血细胞则不受影响。免疫蛋白酶体功能的破坏会导致细胞内转录因子BASP1（transcription factor BASP1）富集，并依次抑制MLL靶基因（MLL-target genes）的表达。对PSMB8进行药理学靶向可增强Menin抑制剂（Menin-inhibitors）的疗效，可在原代人源移植瘤（primary human xenografts）模型中彻底根除白血病，且对携带Menin抑制剂耐药突变（Menin-inhibitor resistance mutations）的样本仍保有活性。本研究鉴定并验证了一种细胞内在机制：蛋白质稳态（proteostasis）的选择性调控可改变转录因子的丰度，并抑制癌基因特异性的转录调控网络。因此，靶向PSMB8依赖的转录通路并联合Menin抑制疗法，有望根除携带MLL重排的急性髓系白血病。
整体实验设计：对经1 μM MI-503处理、1 μM MI-503与100 nM PR-957（ONX-0914）联合处理，以及溶剂对照处理的MOLM-13细胞的RNA测序（RNA-seq）数据开展比较基因表达谱分析。