Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.
mBio. 2021 Oct 26;12(5):e0206221. doi: 10.1128/mBio.02062-21.
Fusobacterium nucleatum is a ubiquitous opportunistic pathogen with an emerging role as an oncomicrobe in colorectal cancer and other cancer settings. F. nucleatum can adhere to and invade host cells in a manner that varies across F. nucleatum strains and host cell phenotypes. Here, we performed pairwise cocultures between three F. nucleatum strains and two immortalized primary host cell types (human colonic epithelial [HCE] cells and human carotid artery endothelial [HCAE] cells) followed by transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to investigate transcriptional and epigenetic host cell responses. We observed that F. nucleatum-induced host cell transcriptional modulation involves strong upregulation of genes related to immune migration and inflammatory processes, such as , , , and . Furthermore, we identified genes strongly upregulated in a cell line-specific manner. In HCE cells, overexpressed genes included and /, associated with p53 degradation-mediated proliferation and intestinal reactive oxygen species (ROS) production, respectively. In HCAE cells, overexpressed genes included and , two genes commonly upregulated in colorectal cancer and associated with poor patient outcomes, and (), a gene associated with the protective effect of aspirin in the colorectal cancer setting. Interestingly, we also observed downregulation of numerous histone modification genes upon F. nucleatum exposure. We used the ChIP-seq data to annotate chromatin states genome wide and found significant chromatin remodeling following F. nucleatum exposure in HCAE cells, with increased frequencies of active enhancer and low-signal/quiescent states. Thus, our results highlight increased inflammation and chemokine gene expression as conserved host cell responses to F. nucleatum exposure and extensive host cell epigenomic changes specific to host cell type. Fusobacterium nucleatum is a bacterium normally found in the healthy oral cavity but also has an emerging role in colorectal cancer and other cancer settings. The host-microbe interactions of F. nucleatum and its involvement in tumor initiation, progression, and treatment resistance are not fully understood. We explored host cell changes that occur in response to F. nucleatum. We identified key genes differentially expressed in response to various conditions of F. nucleatum exposure and determined that the conserved host cell response to F. nucleatum was dominated by increased inflammation and chemokine gene expression. Additionally, we found extensive host cell epigenomic changes as a novel aspect of host modulation associated with F. nucleatum exposure. These results extend our understanding of F. nucleatum as an emerging pathogen and highlight the importance of considering strain heterogeneity and host cell phenotypic variation when exploring pathogenic mechanisms of F. nucleatum.
具核梭杆菌是一种普遍存在的机会致病菌，它在结直肠癌和其他癌症环境中作为致癌微生物的作用正在不断显现。具核梭杆菌可以以菌株和宿主细胞表型差异的方式黏附和侵入宿主细胞。在这里，我们进行了三株具核梭杆菌菌株与两种永生化原代宿主细胞类型（人结肠上皮细胞[HCE]和人颈动脉内皮细胞[HCAE]）之间的两两共培养，随后进行转录组测序（RNA-seq）和染色质免疫沉淀测序（ChIP-seq），以研究转录和表观遗传的宿主细胞反应。我们观察到，具核梭杆菌诱导的宿主细胞转录调节涉及与免疫迁移和炎症过程相关的基因的强烈上调，例如、、和。此外，我们还鉴定了以细胞系特异性方式强烈上调的基因。在 HCE 细胞中，过表达的基因包括和/，分别与 p53 降解介导的增殖和肠道活性氧（ROS）产生有关。在 HCAE 细胞中，过表达的基因包括和，这两个基因在结直肠癌中共同上调，并与患者预后不良有关，以及（），这是一个与阿司匹林在结直肠癌环境中保护作用相关的基因。有趣的是，我们还观察到具核梭杆菌暴露后许多组蛋白修饰基因的下调。我们使用 ChIP-seq 数据对全基因组的染色质状态进行注释，并发现 HCAE 细胞中具核梭杆菌暴露后染色质重塑显著，增强了活性增强子和低信号/静止状态的频率。因此，我们的研究结果强调了炎症和趋化因子基因表达的增加是宿主细胞对具核梭杆菌暴露的保守反应，并强调了宿主细胞类型特异性的广泛的宿主细胞表观基因组变化。 具核梭杆菌是一种正常存在于健康口腔中的细菌，但在结直肠癌和其他癌症环境中也具有新兴作用。具核梭杆菌与宿主的相互作用及其在肿瘤起始、进展和治疗耐药性中的作用尚不完全清楚。我们探讨了宿主细胞在响应具核梭杆菌时发生的变化。我们鉴定了对各种具核梭杆菌暴露条件下差异表达的关键基因，并确定具核梭杆菌对宿主细胞的保守反应是以炎症和趋化因子基因表达的增加为主。此外，我们还发现了广泛的宿主细胞表观基因组变化，这是与具核梭杆菌暴露相关的宿主调节的一个新方面。这些结果扩展了我们对具核梭杆菌作为一种新兴病原体的理解，并强调了在探索具核梭杆菌的致病机制时考虑菌株异质性和宿主细胞表型变异的重要性。
