Combining time-resolved transcriptomics and proteomics data for Adverse Outcome Pathway refinement in ecotoxicology

Conventional Environmental Risk Assessment (ERA) of pesticide pollution is
based on soil concentrations and apical endpoints, such as the
reproduction of test organisms, but disregards information along the
organismal response cascade leading to an adverse outcome. The Adverse
Outcome Pathway (AOP) framework, on the other hand, facilitates the use of
response information at any level of biological organization.
Transcriptomic and proteomic data can provide thousands of data points on
the response to toxic exposure. Combining multiple omics data types is
necessary for a comprehensive overview of the response cascade and,
therefore, AOP development. However, it is unclear if transcript and
protein responses are synchronized in time or time-lagged. To understand
if analysis of multi-omics data obtained at the same timepoint reveals one
synchronized response cascade, we studied time-resolved shifts in gene
transcript and protein abundance in the springtail Folsomia candida, a
soil ecotoxicological model, after exposure to the neonicotinoid
insecticide imidacloprid. We analyzed transcriptome and proteome data
every 12 hours up to 72 hours after onset of exposure. The most pronounced
shift in both transcript and protein abundances was observed after 48
hours of exposure. Moreover, cross-correlation analyses indicate that most
genes displayed the highest correlation between transcript and protein
abundances without a time-lag. This demonstrates that a combined analysis
of transcriptomic and proteomic data can be used for AOP improvement. This
data will promote the development of biomarkers for neonicotinoid
insecticide pollution in soils or chemicals with a similar mechanism of
action.

传统农药污染的环境风险评估（Environmental Risk Assessment, ERA）通常以土壤污染物浓度及试验生物繁殖等顶端终点为依据，但忽略了通往不良结局的生物响应级联相关信息。而不良结局途径（Adverse Outcome Pathway, AOP）框架则支持使用任意生物组织层级的响应信息。转录组学与蛋白质组学数据可提供毒性暴露响应的数千个数据节点。为全面解析响应级联并推进AOP构建，整合多组学数据类型实属必要。然而目前尚不明确转录本与蛋白质的响应是否存在时间同步性，抑或存在时间滞后。为探明同一时间点获取的多组学数据分析是否可揭示同步的响应级联，本研究以土壤生态毒理学模式生物——弹尾虫（Folsomia candida）为研究对象，探究其暴露于新烟碱类杀虫剂吡虫啉后，基因转录本与蛋白质丰度的时序变化。本研究在暴露开始后每12小时采集一次样本，直至72小时，对转录组与蛋白质组数据进行分析。结果显示，暴露48小时后，转录本与蛋白质丰度均出现最为显著的变化。此外，互相关分析表明，绝大多数基因的转录本与蛋白质丰度之间不存在时间滞后的最高相关性。本研究证实，整合转录组与蛋白质组数据可用于优化AOP构建。本数据集将助力土壤中新烟碱类杀虫剂污染或作用机制相似的化学品的生物标志物开发。