Chen Huadong, Sarah Letitia, Pucciarelli Daniela, Mao Ying, Diolaiti Morgan E, Fujimori Danica Galonić, Ashworth Alan
Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, California.
bioRxiv. 2024 Sep 25:2024.09.23.614494. doi: 10.1101/2024.09.23.614494.
Epigenetic factors, including lysine-specific demethylases such as the KDM5 paralogs KDM5A and KDM5B have been implicated in cancer and the regulation of immune responses. Here, we performed a comprehensive multiomic study in cells lacking KDM5A or KDM5B to map changes in transcriptional regulation and chromatin organization. RNA-seq analysis revealed a significant decrease in the expression of Krüppel-associated box containing zinc finger () genes in KDM5A or KDM5B knockout cell lines, which was accompanied by changes ATAC-seq and H3K4me3 ChIP-seq. Pharmacological inhibition of KDM5A and KDM5B catalytic activity with a pan-KDM5 inhibitor, CPI-455, did not significantly change KRAB-ZNF expression, raising the possibility that regulation of KRAB-ZNF expression does not require KDM5A and KDM5B demethylase activity. KRAB-ZNF are recognized suppressors of the transcription of endogenous retroviruses (ERVs) and HAP1 cells with or gene inactivation showed elevated ERV expression, increased dsRNA levels and elevated levels of immune response genes. Acute degradation of KDM5A using a dTAG system in HAP1 cells led to increased ERV expression, demonstrating that de-repression of ERV genes occurs rapidly after loss of KDM5A. Co-immunoprecipitation of KDM5A revealed an interaction with the Nucleosome Remodeling and Deacetylase (NuRD) complex suggesting that KDM5A and NuRD may act together to regulate the expression of ERVs through KRAB-ZNFs. These findings reveal roles of KDM5A and KDM5B in modulating ERV expression and underscore the therapeutic potential of using degraders of KDM5A and KDM5B to modulate tumor immune responses.
表观遗传因素，包括赖氨酸特异性去甲基化酶，如KDM5旁系同源物KDM5A和KDM5B，已被证明与癌症及免疫反应调节有关。在此，我们对缺乏KDM5A或KDM5B的细胞进行了全面的多组学研究，以绘制转录调控和染色质组织的变化图谱。RNA测序分析显示，在KDM5A或KDM5B基因敲除细胞系中，含锌指结构的Krüppel相关盒（KRAB-ZNF）基因的表达显著下降，同时伴随着ATAC测序和H3K4me3染色质免疫沉淀测序（ChIP-seq）的变化。用泛KDM5抑制剂CPI-455对KDM5A和KDM5B的催化活性进行药理抑制，并未显著改变KRAB-ZNF的表达，这增加了一种可能性，即KRAB-ZNF表达的调节不需要KDM5A和KDM5B的去甲基化酶活性。KRAB-ZNF是内源性逆转录病毒（ERVs）转录的公认抑制因子， 或 基因失活的HAP1细胞显示ERV表达升高、双链RNA水平增加以及免疫反应基因水平升高。在HAP1细胞中使用dTAG系统急性降解KDM5A导致ERV表达增加，表明KDM5A缺失后ERV基因的去抑制迅速发生。KDM5A的免疫共沉淀揭示了其与核小体重塑和去乙酰化酶（NuRD）复合物的相互作用，这表明KDM5A和NuRD可能共同作用，通过KRAB-ZNF调节ERV的表达。这些发现揭示了KDM5A和KDM5B在调节ERV表达中的作用，并强调了使用KDM5A和KDM5B降解剂调节肿瘤免疫反应的治疗潜力。
