Non-canonical immune response to inhibition of DNA methylation via stabilization of dsRNAs from endogenous retroviruses

5-Aza-2'-deoxycytidine, also known as decitabine, is a DNA hypomethylating agent (HMA) used to treat acute myeloid leukemia (AML) and pre-leukemic disorder myelodysplastic syndrome (MDS). Decitabine activates the transcription of endogenous retroviruses (ERV), which can induce immune response by acting as cellular double-stranded RNAs. Here, we employ an image-based screening system to identify dsRNA-binding factors that mediate the downstream effect of ERV induction. We find that STAUFEN1 (STAU1) knockdown decreases the interferon signature and rescues decitabine-mediated cell death. Our subsequent analyses reveal that STAU1 directly binds to ERV RNAs and stabilizes the RNAs together with a long noncoding RNA, TINCR. Analysis of a clinical patient cohort further supports that MDS and AML patients with low STAU1 and TINCR expressions exhibited poor response to the HMA therapy. Our study reveals that decitabine-mediated cell death is a consequence of complex interactions among different dsRNA binding proteins for access to their common dsRNA targets. Overall design: ncRNA and total RNA profiles of WT HCT116 and Staufen1-deficient HCT116.

5-氮杂-2'-脱氧胞苷（5-Aza-2'-deoxycytidine）又名地西他滨（decitabine），是一种DNA去甲基化药物（DNA hypomethylating agent, HMA），用于治疗急性髓系白血病（acute myeloid leukemia, AML）与癌前血液病骨髓增生异常综合征（myelodysplastic syndrome, MDS）。地西他滨可激活内源性逆转录病毒（endogenous retroviruses, ERV）的转录，后者可通过充当细胞内双链RNA（double-stranded RNAs）诱导免疫应答。本研究采用基于图像的筛选系统（image-based screening system），以鉴定介导ERV诱导下游效应的双链RNA结合因子（dsRNA-binding factors）。研究发现，Staufen1（STAU1）敲低可削弱干扰素特征（interferon signature）信号，并减轻地西他滨介导的细胞死亡。后续分析显示，STAU1可直接结合ERV RNA，并与长链非编码RNA（long noncoding RNA）TINCR共同稳定此类RNA分子。对临床患者队列（clinical patient cohort）的进一步分析证实，低表达STAU1与TINCR的MDS及AML患者对HMA疗法的应答效果不佳。本研究揭示，地西他滨介导的细胞死亡是多种双链RNA结合蛋白竞争结合共同双链RNA靶标所形成的复杂相互作用的结果。总体实验设计：野生型HCT116细胞及Staufen1敲除型HCT116细胞的非编码RNA（ncRNA）与总RNA转录谱。