Drugs targeting chromatin-modifying enzymes have entered clinical trials for myeloid malignancies, including INCB059872, a selective irreversible inhibitor of Lysine-Specific Demethylase 1 (LSD1). While initial studies of LSD1 inhibitors suggested these compounds may be used to induce differentiation of acute myeloid leukemia (AML), the mechanisms underlying this effect and dose-limiting toxicities are not well understood. Here, we used precision nuclear run-on sequencing (PRO-seq) and ChIP-seq in AML cell lines to probe for the earliest regulatory events associated with INCB059872 treatment. The changes in nascent transcription could be traced back to a loss of CoREST activity and activation of GFI1-regulated genes. INCB059872 is in phase I clinical trials, and we evaluated a pre-treatment bone marrow sample of a patient who showed a clinical response to INCB059872 while being treated with azacitidine. We used single-cell RNA-sequencing (scRNA-seq) to show that INCB059872 caused a shift in gene expression that was again associated with GFI1/GFI1B regulation. Finally, we treated mice with INCB059872 and performed scRNA-seq of lineage-negative bone marrow cells, which showed that INCB059872 triggered accumulation of megakaryocyte early progenitor cells with gene expression hallmarks of stem cells. Accumulation of these stem/progenitor cells may contribute to the thrombocytopenia observed in patients treated with LSD1 inhibitors.

中文翻译：

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新生转录本和单细胞 RNA-seq 分析定义了 LSD1 抑制剂 INCB059872 在髓系白血病中的作用机制。

靶向染色质修饰酶的药物已进入髓系恶性肿瘤的临床试验，包括 INCB059872，一种赖氨酸特异性脱甲基酶 1 (LSD1) 的选择性不可逆抑制剂。虽然对 LSD1 抑制剂的初步研究表明这些化合物可用于诱导急性髓系白血病 (AML) 的分化，但这种作用和剂量限制性毒性的潜在机制尚不清楚。在这里，我们在 AML 细胞系中使用精确核连续测序 (PRO-seq) 和 ChIP-seq 来探测与 INCB059872 治疗相关的最早调节事件。新生转录的变化可以追溯到 CoREST 活性的丧失和 GFI1 调节基因的激活。INCB059872 处于 I 期临床试验，我们评估了一名患者的治疗前骨髓样本，该患者在接受阿扎胞苷治疗时对 INCB059872 表现出临床反应。我们使用单细胞 RNA 测序 (scRNA-seq) 显示 INCB059872 引起基因表达的变化，这再次与 GFI1/GFI1B 调节相关。最后，我们用 INCB059872 处理小鼠并对谱系阴性骨髓细胞进行 scRNA-seq，结果表明 INCB059872 触发了具有干细胞基因表达标志的巨核细胞早期祖细胞的积累。这些干/祖细胞的积累可能导致在接受 LSD1 抑制剂治疗的患者中观察到的血小板减少症。我们使用单细胞 RNA 测序 (scRNA-seq) 显示 INCB059872 引起基因表达的变化，这再次与 GFI1/GFI1B 调节相关。最后，我们用 INCB059872 处理小鼠并对谱系阴性骨髓细胞进行 scRNA-seq，结果表明 INCB059872 触发了具有干细胞基因表达标志的巨核细胞早期祖细胞的积累。这些干/祖细胞的积累可能导致在接受 LSD1 抑制剂治疗的患者中观察到的血小板减少症。我们使用单细胞 RNA 测序 (scRNA-seq) 显示 INCB059872 引起基因表达的变化，这再次与 GFI1/GFI1B 调节相关。最后，我们用 INCB059872 处理小鼠并对谱系阴性骨髓细胞进行 scRNA-seq，结果表明 INCB059872 触发了具有干细胞基因表达标志的巨核细胞早期祖细胞的积累。这些干/祖细胞的积累可能导致在接受 LSD1 抑制剂治疗的患者中观察到的血小板减少症。