Application of singe nuclei RNA sequencing to assess the hepatic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin

Cell-specific transcriptional responses are lost in the averages of bulk RNA sequencing. We performed single nuclei RNA sequencing (snSeq) on frozen liver samples from male C57BL/6 mice in response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Approximately 19,907 hepatic genes were detected across 16,015 sequenced nuclei from control and treated samples. Eleven cell-(sub)types were identified including distinct hepatocyte sub-populations, consistent with the cell diversity of the liver. TCDD increased macrophages from 0.5% to 24.7%, while neutrophils were only present in treated samples. The number of differentially expressed genes correlated with the basal expression level of Ahr. In addition to expected functional enrichments within each cell-(sub)type, RAS signaling was enriched in nonparenchymal cells. snSeq also identified a Kupffer cell subtype highly expressing Gpnmb, consistent with a dietary NASH model. Overall, snSeq distinguished cell-specific transcriptional changes and population shifts consistent with the hepatotoxicity of TCDD.

批量RNA测序的均值数据会丢失细胞特异性的转录应答反应。我们针对雄性C57BL/6小鼠的冰冻肝脏样本开展单细胞核RNA测序（single nuclei RNA sequencing, snSeq），以探究其暴露于2,3,7,8-四氯二苯并对二噁英（2,3,7,8-tetrachlorodibenzo-p-dioxin, TCDD）后的转录应答效应。在来自对照组与处理组的16015个测序细胞核中，共检测到约19907个肝脏基因。共鉴定出11种细胞（亚）型，包括特征明确的肝细胞亚群，这与肝脏的细胞多样性特征相符。TCDD可将巨噬细胞占比从0.5%提升至24.7%，而中性粒细胞仅在处理组样本中存在。差异表达基因的数量与芳香烃受体（Ahr）的基础表达水平相关。除各细胞（亚）型中预期的功能富集结果外，RAS信号通路在非实质细胞中出现富集。snSeq还鉴定出一种高表达Gpnmb的库普弗细胞（Kupffer cell）亚群，这与膳食诱导的非酒精性脂肪性肝炎（NASH）模型的研究结果一致。总体而言，snSeq可分辨出细胞特异性的转录组变化以及细胞群体比例偏移，这些变化与TCDD的肝毒性效应相符。

搜集汇总

背景与挑战

背景概述

该数据集应用单核RNA测序技术研究2,3,7,8-四氯二苯并对二噁英（TCDD）对小鼠肝脏的毒性影响，通过分析约19,907个基因和16,015个核，识别出11种细胞类型，并揭示TCDD导致巨噬细胞比例显著增加等细胞特异性转录变化。数据集包含4个小鼠肝脏样本的转录组测序数据，总大小295.62 GB，旨在探索肝毒性物质的细胞异质性和转录组学响应。