An <i>in silico</i> toxicogenomic approach in constructing the aflatoxin B1-mediated regulatory network of hub genes in hepatocellular carcinoma

Aflatoxin B1 (AFB1) can cause hepatocellular carcinoma (HCC) through a mutagenic mode of action but can also lead to global changes in gene expression; however, the AFB1 network of molecular pathways involved in HCC is not known. Here, we used toxicogenomic data from human liver cells exposed to AFB1 to infer the network of AFB1-responsive molecular pathways involved in HCC. The following computational tools: STRING, MCODE, cytoHubba, iRegulon, kinase enrichment tool KEA3, and DAVID were used to identify protein-protein interaction network, hub genes, transcription factors (TFs), upstream kinases, and biological processes (BPs). Predicted molecular events were validated with an external dataset, whereas the hub genes in HCC were validated using the UALCAN database. The results revealed an association between AFB1 and the hub genes involved in the cell cycle. We identified TFs that regulate the hub genes and linked them with upstream kinases including cyclin-dependent kinases, mitogen-activated protein kinase 1, and AKT. This approach enabled the construction of the AFB1-mediated regulatory network consisting of upstream kinases, TFs, hub genes, and BPs, thus revealing the signaling hierarchy and information flow that may contribute to AFB1-induced HCC. This could be a useful tool in predicting the molecular mechanisms involved in chemical-induced diseases when available toxicogenomic data exist.

黄曲霉毒素B1（Aflatoxin B1，AFB1）可通过诱变作用模式引发肝细胞癌（hepatocellular carcinoma，HCC），同时还可诱导基因表达发生全局性改变；然而，AFB1诱导HCC所涉及的分子通路调控网络尚未明确。本研究利用暴露于AFB1的人肝细胞的毒理基因组学数据，推断AFB1应答的、参与HCC发生的分子通路调控网络。本研究采用STRING、MCODE、cytoHubba、iRegulon、激酶富集工具KEA3以及DAVID等计算工具，分别鉴定蛋白质相互作用网络、核心基因、转录因子（transcription factors，TFs）、上游激酶以及生物学过程（biological processes，BPs）。研究通过外部数据集对预测的分子事件进行验证，并借助UALCAN数据库验证HCC中的核心基因。研究结果显示，AFB1与细胞周期相关的核心基因存在关联。本研究鉴定出调控核心基因的转录因子，并将其与上游激酶（包括细胞周期蛋白依赖性激酶、丝裂原活化蛋白激酶1以及AKT）建立关联。本研究借此构建了由上游激酶、转录因子、核心基因以及生物学过程组成的AFB1介导的调控网络，进而揭示了可能参与AFB1诱导HCC发生的信号层级与信息流动机制。当存在可用的毒理基因组学数据时，本研究方法可作为预测化学诱导疾病分子机制的有效工具。