化学肝癌发生中癌基因蛋白丧失引发的基因组与转录组分析

Genomic and transcriptomic analyses of chemical hepatocarcinogenesis aggravated by oncoprotein loss

HEPATOLOGY

影响因子:15.8

分区:医学1区 Top / 胃肠肝病学1区

发表日期:2025 Apr 01

作者: Xinyi Wang, Yingluo Liu, Shuo Zhang, Jiemeng Zhang, Xiaoxue Lin, Yan Liang, Min Zong, Kaisa L Hanley, Jin Lee, Michael Karin, Gen-Sheng Feng

DOI: 10.1097/HEP.0000000000001037

摘要

二乙基亚硝胺（DEN）是一种常用的诱导小鼠肝细胞癌（HCC）的化学致癌剂。奇怪的是，多个实验室报道去除肝细胞中的癌基因蛋白反而加剧了 DEN 诱导的 HCC，机制尚不清楚。本研究旨在揭示癌基因蛋白的肿瘤抑制作用的分子机制。我们构建了肝细胞特异性删除 Met、Ptpn11 / Shp2、Ikkβ 或 Ctnnb1 / β-连环蛋白的突变小鼠系，并评估了野生型及突变小鼠中的 DEN 诱导肿瘤发生情况。通过全外显子测序和RNA测序，分析了癌前阶段及已建立肿瘤阶段的肝脏样本。虽然 DEN 诱导的肿瘤突变谱在野生型与突变小鼠中差异不大，但癌基因蛋白的缺失增加了 DEN 诱导的突变负荷，尤其在 Shp2 缺失肿瘤中表现明显。RNA测序显示多条信号通路发生变化，特别是上调上皮-间质转化、细胞迁移和肿瘤转移，同时小分子代谢途径被下调。我们识别出与肝脏固有免疫相关的关键分子和通路，并在人体肝细胞癌数据库中发现少数 miRNA 表达显著变化。癌基因蛋白缺失引起的 DEN 诱导 HCC 进展加剧，可能由共同或不同的基因组和信号通路变化引起。本研究揭示了肝细胞癌发生的复杂性新层面，并阐明了肿瘤演变与复发的分子机制。

Abstract

The chemical carcinogen diethylnitrosamine (DEN) is often used to induce HCC in mice. Curiously, several labs have reported that the removal of oncoproteins from hepatocytes exacerbated DEN-induced HCC, with mechanisms unknown. This study aimed at deciphering molecular mechanisms underlying the tumor suppressive effect of oncoproteins.We generated mutant mouse lines with hepatocyte-specific deletions of Met , Ptpn11 / Shp2 , Ikkβ , or Ctnnb1/β-catenin and assessed DEN-induced tumorigenesis in the wild-type and mutant mice. To systematically examine genetic and molecular signaling alterations, we performed whole exome and RNA-sequencing on liver samples collected at the pre-cancer and established cancer stages. Although the mutational profiles of DEN-induced tumors were barely different in wild-type and mutant mice, oncoprotein ablation increased DEN-induced mutational burdens, especially in Shp2-deficient tumors. RNA-sequencing revealed multiple changes in signaling pathways, in particular, upregulated epithelial-mesenchymal transition, cell migration, and tumor metastasis, as well as downregulated small molecule metabolism that was affected by oncoprotein ablation. We identified key molecules and pathways that are associated with hepatic innate immunity and implicated in liver tumorigenesis. In addition, we unveiled markedly changed expression of a few miRNAs in the human HCC database.The aggravation of DEN-induced HCC progression seen on oncoprotein ablation could be caused by common and distinct genomic and signaling alterations. This study reveals a new level of complexity in hepatocarcinogenesis and elucidates molecular mechanisms underlying tumor evolution and recurrence.