UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs

The histone H3 Lys27-specific demethylase UTX (or KDM6A) is targeted by loss-of-function mutations in multiple cancers. Here, we demonstrate that UTX suppresses myeloid leukemogenesis through noncatalytic functions, a property shared with its catalytically inactive Y-chromosome paralog, UTY (or KDM6C). In keeping with this, we demonstrate concomitant loss/mutation of KDM6A (UTX) and UTY in multiple human cancers. Mechanistically, global genomic profiling showed only minor changes in H3K27me3 but significant and bidirectional alterations in H3K27ac and chromatin accessibility; a predominant loss of H3K4me1 modifications; alterations in ETS and GATA-factor binding; and altered gene expression after Utx loss. By integrating proteomic and genomic analyses, we link these changes to UTX regulation of ATP-dependent chromatin remodeling, coordination of the COMPASS complex and enhanced pioneering activity of ETS factors during evolution to AML. Collectively, our findings identify a dual role for UTX in suppressing acute myeloid leukemia via repression of oncogenic ETS and upregulation of tumor-suppressive GATA programs. Overall design: ChIP-Seq analysis for histone modification: H3K4Me1 and for PU.1 binding. Effect of Brg1 knockout on chromatine accessibility in Utx+/+ and Utx-/- HSPC cells (ATAC-Seq). ATAC-seq was also performed on Chd4 knockout Utx+/+ HSPC cells.组蛋白H3赖氨酸27特异性去甲基化酶UTX（KDM6A）在多种癌症中存在功能丧失性突变。本研究证实，UTX可通过非催化功能抑制髓系白血病发生，这一特性与其催化失活的Y染色体同源基因UTY（KDM6C）一致。与此一致，我们在多种人类癌症中发现KDM6A（UTX）与UTY同时发生缺失或突变。机制分析显示，Utx缺失后，全基因组检测结果表明H3K27me3仅存在微小变化，但组蛋白H3第27位赖氨酸乙酰化（H3K27ac）与染色质可及性则出现显著的双向改变；组蛋白H3第4位赖氨酸单甲基化（H3K4me1）修饰大量丢失；ETS与GATA家族转录因子的结合模式发生异常；同时基因表达谱亦出现显著改变。通过整合蛋白质组与基因组分析数据，我们将上述分子改变与UTX的调控功能建立关联：UTX可调控ATP依赖型染色质重塑过程、协调COMPASS复合物（COMPASS complex）的组装，并在向急性髓系白血病（AML）进展过程中增强ETS因子的先锋结合活性。综上，本研究揭示了UTX抑制急性髓系白血病的双重作用机制：通过抑制致癌性ETS通路、上调抑癌性GATA通路相关程序发挥抑癌作用。实验整体设计：针对组蛋白H3K4单甲基化（H3K4Me1）修饰以及转录因子PU.1的结合情况开展染色质免疫共沉淀测序（ChIP-Seq）分析；检测Brg1敲除对Utx野生型（Utx+/+）与Utx敲除型（Utx-/-）造血干祖细胞（HSPC）中染色质可及性的影响，该实验采用转座酶可及性测序（ATAC-Seq）；同时对Chd4敲除的Utx+/+造血干祖细胞开展ATAC-Seq分析。