Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic Acid on rat kidneys

RNA-Seq has been increasingly used for the quantification and characterization of transcriptomes. The ongoing development of the technology promises the more accurate measurement of gene expression. However, its benefits over widely accepted microarray technologies have not been adequately assessed, especially in toxicogenomics studies. The goal of this study is to enhance the scientific community's understanding of the advantages and challenges of RNA-Seq in the quantification of gene expression by comparing analysis results from RNA-Seq and microarray data on a toxicogenomics study. A typical toxicogenomics study design was used to compare the performance of an RNA-Seq approach (Illumina Genome Analyzer II) to a microarray-based approach (Affymetrix Rat Genome 230 2.0 arrays) for detecting differentially expressed genes (DEGs) in the kidneys of rats treated with aristolochic acid (AA), a carcinogenic and nephrotoxic chemical most notably used for weight loss. We studied the comparability of the RNA-Seq and microarray data in terms of absolute gene expression, gene expression patterns, differentially expressed genes, and biological interpretation. We found that RNA-Seq was more sensitive in detecting genes with low expression levels, while similar gene expression patterns were observed for both platforms. Moreover, although the overlap of the DEGs was only 40-50%, the biological interpretation was largely consistent between the RNA-Seq and microarray data. RNA-Seq maintained a consistent biological interpretation with time-tested microarray platforms while generating more sensitive results. However, there is clearly a need for future investigations to better understand the advantages and limitations of RNA-Seq in toxicogenomics studies and environmental health research.RNA测序（RNA-Seq）已愈发广泛地应用于转录组的定量分析与特征表征。该技术的持续迭代有望实现更为精准的基因表达量检测。然而，相较于已被广泛接纳的微阵列技术，其优势尚未得到充分评估，在毒理基因组学（toxicogenomics）研究中尤为凸显。本研究旨在通过对比毒理基因组学研究中RNA测序与微阵列数据的分析结果，提升科学界对RNA测序在基因表达定量领域的优势与挑战的认知。研究采用典型的毒理基因组学研究设计方案，对比RNA测序平台（Illumina Genome Analyzer II）与基于微阵列的检测平台（Affymetrix Rat Genome 230 2.0 arrays）在检测经马兜铃酸（aristolochic acid, AA）处理的大鼠肾脏组织中差异表达基因（differentially expressed genes, DEGs）的性能差异。马兜铃酸是一种兼具致癌性与肾毒性的化学物质，曾主要用于减重用途。本研究从绝对基因表达量、基因表达模式、差异表达基因以及生物学解读四个维度，探究RNA测序与微阵列数据的可比性。研究发现，RNA测序在检测低表达基因时灵敏度更高，而两种平台的基因表达模式整体相似。此外，尽管差异表达基因的重叠比例仅为40%~50%，但RNA测序与微阵列数据的生物学解读结果基本一致。RNA测序在生成灵敏度更优的检测结果的同时，可与经过长期验证的微阵列平台保持一致的生物学解读结论。不过，未来仍需开展更多研究，以更全面地阐明RNA测序在毒理基因组学研究与环境健康研究中的优势与局限性。