Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma [miRNA-seq]

Metabolic reprogramming is a hallmark of cancer that facilitates changes in many adaptive biological processes. Mutations in the tricarboxylic acid (TCA) cycle enzyme fumarate hydratase (FH) lead to fumarate accumulation and cause hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is a rare, inherited disease characterized by the development of non-cancerous smooth muscle tumors of the uterus and skin, and an increased risk of a highly metastatic and aggressive form of kidney cancer. Fumarate has been shown to inhibit 2-oxyglutarate-dependent dioxygenases (2OGDDs) involved in the hydroxylation of HIF1a, as well as in DNA and histone demethylation. However, the link between fumarate accumulation and changes in RNA post-transcriptional modifications has not been defined. Here, we determine the consequences of fumarate accumulation on the activity of different members of the 2OGDD family targeting RNA modifications. By evaluating multiple RNA modifications in patient-derived HLRCC cell lines, we show that mutation of FH selectively alters the activity of demethylases acting upon N6-methyladenosine (m6A), while the demethylases acting upon N1-methyladenosine (m1A) and 5-formylcytosine (f5C) in mitochondrial RNA are unaffected. The observation that metabolites may modulate specific subsets of RNA-modifying enzymes offers new insights into their gene regulatory effects and potential strategies for therapeutic intervention. Overall design: miRNA-seq

代谢重编程（Metabolic reprogramming）是癌症的标志性特征，可促进多种适应性生物学过程的重塑。三羧酸循环（tricarboxylic acid, TCA）酶延胡索酸水合酶（fumarate hydratase, FH）发生突变后会导致延胡索酸异常积累，并引发遗传性平滑肌瘤病和肾细胞癌（hereditary leiomyomatosis and renal cell cancer, HLRCC）。HLRCC是一种罕见的遗传性疾病，以子宫与皮肤出现良性平滑肌瘤为主要特征，且患者罹患高转移性、侵袭性肾细胞癌的风险显著升高。已有研究表明，延胡索酸可抑制参与缺氧诱导因子1α（HIF1α）羟化、以及DNA与组蛋白去甲基化的2-氧戊二酸依赖性双加氧酶（2-oxyglutarate-dependent dioxygenases, 2OGDDs）。然而，延胡索酸积累与RNA转录后修饰改变之间的关联尚未被阐明。本研究旨在明确延胡索酸积累对靶向RNA修饰的2OGDD家族不同成员活性的影响。通过在患者来源的HLRCC细胞系中检测多种RNA修饰类型，我们发现FH突变可选择性改变作用于N6-甲基腺苷（N6-methyladenosine, m6A）的去甲基化酶活性，而作用于线粒体RNA中N1-甲基腺苷（N1-methyladenosine, m1A）与5-甲酰基胞嘧啶（5-formylcytosine, f5C）的去甲基化酶则不受影响。代谢物能够调控RNA修饰酶的特定子集这一发现，为其基因调控效应及治疗干预的潜在策略提供了新的研究视角。整体实验设计：miRNA-seq