Limonciel Alice, van Breda Simone G, Jiang Xiaoqi, Tredwell Gregory D, Wilmes Anja, Aschauer Lydia, Siskos Alexandros P, Sachinidis Agapios, Keun Hector C, Kopp-Schneider Annette, de Kok Theo M, Kleinjans Jos C S, Jennings Paul
Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, Netherlands.
Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, Innsbruck, Austria.
Front Genet. 2018 Dec 3;9:558. doi: 10.3389/fgene.2018.00558. eCollection 2018.
The discovery of the epigenetic regulation of transcription has provided a new source of mechanistic understanding to long lasting effects of chemicals. However, this information is still seldom exploited in a toxicological context and studies of chemical effect after washout remain rare. Here we studied the effects of two nephrocarcinogens on the human proximal tubule cell line RPTEC/TERT1 using high-content mRNA microarrays coupled with miRNA, histone acetylation (HA) and DNA methylation (DM) arrays and metabolomics during a 5-day repeat-dose exposure and 3 days after washout. The mycotoxin ochratoxin A (OTA) was chosen as a model compound for its known impact on HA and DM. The foremost effect observed was the modulation of thousands of mRNAs and histones by OTA during and after exposure. In comparison, the oxidant potassium bromate (KBrO) had a milder impact on gene expression and epigenetics. However, there was no strong correlation between epigenetic modifications and mRNA changes with OTA while with KBrO the gene expression data correlated better with HA for both up- and down-regulated genes. Even when focusing on the genes with persistent epigenetic modifications after washout, only half were coupled to matching changes in gene expression induced by OTA, suggesting that while OTA causes a major effect on the two epigenetic mechanisms studied, these alone cannot explain its impact on gene expression. Mechanistic analysis confirmed the known activation of Nrf2 and p53 by KBrO, while OTA inhibited most of the same genes, and genes involved in the unfolded protein response. A few miRNAs could be linked to these effects of OTA, albeit without clear contribution of epigenetics to the modulation of the pathways at large. Metabolomics revealed disturbances in amino acid balance, energy catabolism, nucleotide metabolism and polyamine metabolism with both chemicals. In conclusion, the large impact of OTA on transcription was confirmed at the mRNA level but also with two high-content epigenomic methodologies. Transcriptomic data confirmed the previously reported activation (by KBrO) and inhibition (by OTA) of protective pathways. However, the integration of omic datasets suggested that HA and DM were not driving forces in the gene expression changes induced by either chemical.
转录表观遗传调控的发现为理解化学物质的长期影响提供了新的机制来源。然而，在毒理学背景下，这些信息仍很少被利用，关于化学物质洗脱后的效应研究仍然很少。在这里，我们使用高内涵mRNA微阵列结合miRNA、组蛋白乙酰化（HA）和DNA甲基化（DM）阵列以及代谢组学，研究了两种肾致癌物对人近端肾小管细胞系RPTEC/TERT1在5天重复剂量暴露期间和洗脱后3天的影响。霉菌毒素赭曲霉毒素A（OTA）因其对HA和DM的已知影响而被选为模型化合物。观察到的最主要影响是OTA在暴露期间和暴露后对数千种mRNA和组蛋白的调节。相比之下，氧化剂溴酸钾（KBrO）对基因表达和表观遗传学的影响较小。然而，OTA的表观遗传修饰与mRNA变化之间没有很强的相关性，而对于KBrO，无论是上调还是下调的基因，基因表达数据与HA的相关性都更好。即使关注洗脱后具有持续表观遗传修饰的基因，只有一半与OTA诱导的基因表达匹配变化相关，这表明虽然OTA对所研究的两种表观遗传机制有重大影响，但仅这些机制无法解释其对基因表达的影响。机制分析证实了KBrO对Nrf2和p53的已知激活作用，而OTA抑制了大多数相同的基因以及参与未折叠蛋白反应的基因。一些miRNA可能与OTA的这些效应有关，尽管表观遗传学对整个通路的调节没有明显贡献。代谢组学揭示了两种化学物质都会导致氨基酸平衡、能量分解代谢、核苷酸代谢和多胺代谢紊乱。总之，OTA对转录的巨大影响在mRNA水平以及两种高内涵表观基因组学方法中都得到了证实。转录组学数据证实了先前报道的保护通路的激活（由KBrO）和抑制（由OTA）。然而，组学数据集的整合表明，HA和DM不是两种化学物质诱导基因表达变化的驱动力。
