Widespread dysregulation of long non-coding genes associated with fatty acid metabolism, cell division, and immune response gene networks in xenobiotic-exposed rat liver

Xenobiotic exposure dysregulates hundreds of protein-coding genes in mammalian liver, impacting many physiological processes and inducing diverse toxicological responses. Little is known about xenobiotic effects on long noncoding RNAs (lncRNAs), many of which have important regulatory functions. Here, we present a computational framework to discover liver-expressed, xenobiotic-responsive lncRNAs (xeno-lncs) with strong functional, gene regulatory potential and elucidate the impact of xenobiotic exposure on their gene regulatory networks. We assembled the long non-coding transcriptome of xenobiotic-exposed rat liver using RNA-seq datasets from male rats treated with 27 individual chemicals, representing seven mechanisms of action (MOAs). Ortholog analysis was combined with co-expression data and causal inference methods to infer lncRNA function and deduce gene regulatory networks, including causal effects of lncRNAs on protein-coding gene expression and biological pathways. We discovered >1,400 liver-expressed xeno-lncs, many with human and/or mouse orthologs. Xenobiotics representing different MOAs often regulated common xeno-lnc targets: 123 xeno-lncs were dysregulated by > 10 chemicals, and 5 xeno-lncs responded to > 20 of the 27 chemicals investigated; 81 other xeno-lncs served as MOA-selective markers of xenobiotic exposure. Xeno-lnc−protein-coding gene co-expression regulatory network analysis identified xeno-lncs closely associated with exposure-induced perturbations of hepatic fatty acid metabolism, cell division, or immune response pathways, and with apoptosis or cirrhosis. We also identified hub and bottleneck lncRNAs, which are expected to be key regulators of gene expression. This work elucidates extensive networks of xeno-lnc−protein-coding gene interactions and provides a framework for understanding the widespread transcriptome-altering actions of foreign chemicals in a key responsive mammalian tissue.

外源性化合物（xenobiotic）暴露会失调哺乳动物肝脏内数百个蛋白编码基因，进而影响诸多生理过程并诱发多样的毒理学反应。目前学界对外源性化合物对长链非编码RNA（long noncoding RNAs, lncRNAs）的调控影响知之甚少，而此类RNA中有许多承担着关键的生物学调控功能。本研究构建了一套计算分析框架，旨在筛选兼具强功能活性与基因调控潜力的肝脏表达型外源性化合物应答性长链非编码RNA（下称外源性应答lncRNA，xeno-lncs），并阐明外源性化合物暴露对其基因调控网络的影响。我们利用经27种单一化学物处理的雄性大鼠的RNA测序（RNA-seq）数据集，组装了外源性化合物暴露大鼠肝脏的长链非编码转录组；这些受试化学物涵盖7种作用机制（mechanisms of action, MOAs）。研究结合同源基因（ortholog）分析、共表达数据与因果推断方法，对lncRNA的功能进行推演，并推导其基因调控网络，包括lncRNA对蛋白编码基因表达及生物学通路的因果调控效应。本次研究共鉴定出超过1400个肝脏表达型外源性应答lncRNA，其中多数存在人类与/或小鼠同源基因。代表不同作用机制的外源性化合物往往可调控共同的外源性应答lncRNA靶点：123个外源性应答lncRNA可被超过10种化学物调控失调，而在本次研究涉及的27种化学物中，有5个外源性应答lncRNA可响应其中超过20种化学物；另有81个外源性应答lncRNA可作为外源性化合物暴露的作用机制特异性标志物。对外源性应答lncRNA与蛋白编码基因的共表达调控网络分析结果显示，部分外源性应答lncRNA与肝脏暴露诱导的脂肪酸代谢、细胞分裂或免疫应答通路扰动密切相关，同时还与细胞凋亡或肝硬化的发生发展存在关联。我们还鉴定出了枢纽与瓶颈型长链非编码RNA，此类RNA预计是基因表达调控的核心因子。本研究阐明了广泛存在的外源性应答lncRNA-蛋白编码基因互作网络，并为理解外源性化学物在关键响应性哺乳动物组织中引发的全转录组改变效应提供了标准化的研究框架。