Koppenhafer Stacia L, Geary Elizabeth L, Thomas Mary V, Croushore Emma E, Zimmerman Jessica A O, Gedminas Jenna M, Quelle Dawn E, Dodd Rebecca D, Gordon David J
Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Iowa, Iowa City, Iowa.
Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, Iowa.
Cancer Res Commun. 2025 Jun 1;5(6):1034-1048. doi: 10.1158/2767-9764.CRC-25-0058.
Histone deacetylases (HDAC) regulate diverse pathways in cancer cells. Previously, we identified that Ewing sarcoma tumors, which are caused by a translocation between the EWSR1 and FLI1 genes (EWS::FLI1), are sensitive to drugs that target DNA replication, including the RRM1 and RRM2 subunits of ribonucleotide reductase, and the ATR-checkpoint kinase 1 (CHK1)-WEE1 signaling pathway. In this study, we identified that multiple HDAC inhibitors, including fimepinostat, romidepsin, and panobinostat, downregulate the levels of the RRM1, RRM2, CHK1, and WEE1 proteins in Ewing sarcoma cells and impair DNA replication. Moreover, transcriptome analyses identified that HDAC inhibitors downregulate the expression of multiple components of the prereplication complex, including the minichromosome maintenance complex 2-7 (MCM2-7) proteins and CDT1, that are essential for genomic DNA replication. Additionally, proteomic studies identified that HDAC inhibitors also downregulate the level of the BRD4 protein, a BET bromodomain protein that regulates both the transcriptional program of the EWS::FLI1 oncoprotein and DNA replication. Overall, these results provide novel insight into the molecular mechanisms by which HDAC inhibitors target cancer cells, regulate DNA replication, and inhibit the cellular response to DNA replication stress.
In this work, we identify that HDAC inhibitors broadly disrupt DNA replication and the response to replication stress in Ewing sarcoma cells by downregulating RRM1, RRM2, CHK1, and WEE1. Notably, HDAC inhibitors also reduce MCM2-7 proteins, which are essential for prereplication complex helicase function in replication initiation and elongation, and CDT1, which loads MCM2-7 onto DNA.
组蛋白去乙酰化酶（HDAC）调节癌细胞中的多种途径。此前，我们发现由EWSR1和FLI1基因易位（EWS::FLI1）引起的尤因肉瘤肿瘤对靶向DNA复制的药物敏感，包括核糖核苷酸还原酶的RRM1和RRM2亚基，以及ATR检查点激酶1（CHK1）-WEE1信号通路。在本研究中，我们发现多种HDAC抑制剂，包括非美司他、罗米地辛和帕比司他，可下调尤因肉瘤细胞中RRM1、RRM2、CHK1和WEE1蛋白的水平，并损害DNA复制。此外，转录组分析表明，HDAC抑制剂下调了预复制复合物多个组分的表达，包括对基因组DNA复制至关重要的微小染色体维持复合物2-7（MCM2-7）蛋白和CDT1。此外，蛋白质组学研究表明，HDAC抑制剂还下调了BRD4蛋白的水平，BRD4是一种BET溴结构域蛋白，可调节EWS::FLI1癌蛋白的转录程序和DNA复制。总体而言，这些结果为HDAC抑制剂靶向癌细胞、调节DNA复制以及抑制细胞对DNA复制应激反应的分子机制提供了新的见解。
在这项工作中，我们发现HDAC抑制剂通过下调RRM1、RRM2、CHK1和WEE1广泛破坏尤因肉瘤细胞中的DNA复制和对复制应激的反应。值得注意的是，HDAC抑制剂还减少了MCM2-7蛋白，其对复制起始和延伸中的预复制复合物解旋酶功能至关重要，以及将MCM2-7加载到DNA上的CDT1。
