Abstract：
Cyclosporine A (CsA) has shown efficacy against immunity-related diseases despite its toxicity in various organs, including the liver, emphasizing the need to elucidate its underlying hepatotoxicity mechanism. This study aimed to capture the alterations in genome-wide expression over time and the subsequent perturbations of corresponding pathways across species. Six data from humans, mice, and rats, including animal liver tissue, human liver microtissues, and two liver cell lines exposed to CsA toxic dose, were used. The microtissue exposed to CsA for 10 d was analyzed to obtain dynamically differentially expressed genes (DEGs). Single-time points data at 1, 3, 5, 7, and 28 d of different species were used to provide additional evidence. Using liver microtissue-based longitudinal design, DEGs that were consistently up- or down-regulated over time were captured, and the well-known mechanism involved in CsA toxicity was elucidated. Thirty DEGs that consistently changed in longitudinal data were also altered in 28-d rat in-house data with concordant expression. Some genes (e.g. TUBB2A, PLIN2, APOB) showed good concordance with identified DEGs in 1-d and 7-d mouse data. Pathway analysis revealed up-regulations of protein processing, asparagine N-linked glycosylation, and cargo concentration in the endoplasmic reticulum. Furthermore, the down-regulations of pathways related to biological oxidations and metabolite and lipid metabolism were elucidated. These pathways were also enriched in single-time-point data and conserved across species, implying their biological significance and generalizability. Overall, the human organoids-based longitudinal design coupled with cross-species validation provides temporal molecular change tracking, aiding mechanistic elucidation and biologically relevant biomarker discovery.
摘要：
环孢菌素A（CsA）尽管在各种器官中具有毒性，但仍显示出对免疫相关疾病的功效。包括肝脏,强调需要阐明其潜在的肝毒性机制。这项研究旨在捕获全基因组表达随时间的变化以及随后跨物种的相应途径的扰动。来自人类的六个数据，老鼠,和老鼠,包括动物肝脏组织,人类肝脏微组织，和两种暴露于CsA毒性剂量的肝细胞系，被使用。分析暴露于CsA10d的微组织，以获得动态差异表达基因（DEGs）。使用不同物种的1、3、5、7和28d的单时间点数据来提供其他证据。采用基于肝脏微组织的纵向设计，捕获了随时间持续上调或下调的DEG，并阐明了CsA毒性的众所周知的机制。在28d大鼠内部数据中，纵向数据一致变化的30个DEG也发生了变化，表达一致。一些基因（例如TUBB2A，PLIN2，APOB）在1-d和7-d小鼠数据中与鉴定的DEG表现出良好的一致性。路径分析揭示了蛋白质加工的上调，天冬酰胺N-连接糖基化，和内质网中的货物浓度。此外，阐明了与生物氧化，代谢产物和脂质代谢相关的途径的下调。这些途径也在单时间点数据中得到了丰富，并在物种之间得到了保守，暗示它们的生物学意义和普遍性。总的来说,基于人类类器官的纵向设计与跨物种验证相结合，提供了时间分子变化跟踪，帮助机械阐明和生物学相关的生物标志物发现。
