Deconvolution of cell types from bulk gene expression profiling in a nonalcoholic steatohepatitis model of mice liver reveals global alteration of macrophages and hepatic stellate cells

Nonalcoholic fatty liver disease (NAFLD) is a common cause of chronic liver disease due to the accumulation of excess fat in the liver cells. The two histological categories of NAFLD are NASH (nonalcoholic steatohepatitis) and NAFL (nonalcoholic fatty liver). While NASH is typically considered a disorder of the hepatocytes, the role of other liver cell types in its pathophysiology and progression is becoming more established. Bioinformatics analytic approaches can now incorporate single cell RNA transcriptomics (sc-RNA-Seq) as a reference to deconvolute cell type profiles and proportions in bulk /RNA-Seq data. This technique can be inferred to investigate the changes in cellular compositions in tissues across multiple disease states. This study performed deconvolution analysis using CIBERSORTx, by integrating the bulk/RNA-Seq data with single-cell transcriptomic data to identify changes in cell composition associated with NASH. This study aimed to observe the changes in cell types among healthy and NASH mouse liver. The result of the analyses revealed a general increase in the fraction of HSC (Hepatic Stellate cells), liver macrophages, and cholangiocytes in NASH samples. Hepatocytes had a higher proportion in healthy samples compared with NASH, however, no significant observable difference was established in the endothelial cell proportions. We gained insight on the cell-type proportions profiles of NASH mice models, which highly mimics the human NASH. Comparative gene expression analysis between wild-type whole liver homogenate, and NASH whole liver homogenate

非酒精性脂肪性肝病（Nonalcoholic fatty liver disease, NAFLD）是因肝细胞内过量脂肪堆积引发的常见慢性肝病。NAFLD的两大组织学分类为非酒精性脂肪性肝炎（nonalcoholic steatohepatitis, NASH）与非酒精性脂肪肝（nonalcoholic fatty liver, NAFL）。尽管既往多将NASH视作肝细胞的病变，但其他肝细胞类型在其病理生理过程与疾病进展中的作用正逐渐得到证实。当前生物信息学分析手段可将单细胞RNA转录组学（sc-RNA-Seq）作为参考基准，以解析批量RNA测序（bulk RNA-seq）数据中的细胞类型谱及其占比。该技术可用于探究多种疾病状态下组织内细胞组成的变化。本研究采用CIBERSORTx工具开展细胞反卷积分析，将批量RNA测序数据与单细胞转录组数据进行整合，以识别与NASH相关的细胞组成变化。本研究旨在观察健康小鼠与NASH模型小鼠的肝脏细胞类型差异。分析结果显示，NASH样本中肝星状细胞（Hepatic Stellate cells, HSC）、肝巨噬细胞及胆管上皮细胞的占比普遍升高。与NASH样本相比，健康样本内肝细胞的占比更高；但内皮细胞的占比未观察到显著差异。本研究揭示了高度模拟人类NASH的NASH模型小鼠的细胞类型占比谱。本研究开展了野生型全肝匀浆与NASH模型全肝匀浆之间的比较基因表达分析。