Campos-León Karen, Ferguson Jack, Günther Thomas, Wood C David, Wingett Steven W, Pekel Selin, Varghese Christy S, Jones Leanne S, Stockton Joanne D, Várnai Csilla, West Michelle J, Beggs Andrew, Grundhoff Adam, Noyvert Boris, Roberts Sally, Parish Joanna L
Department of Cancer and Genomic Sciences, College of Medicine and Health, University of Birmingham, Birmingham, United Kingdom.
Leibniz Institute of Virology, Hamburg, Germany.
PLoS Pathog. 2025 Jan 27;21(1):e1012506. doi: 10.1371/journal.ppat.1012506. eCollection 2025 Jan.
Upon infection, human papillomavirus (HPV) manipulates host cell gene expression to create an environment that is supportive of a productive and persistent infection. The virus-induced changes to the host cell's transcriptome are thought to contribute to carcinogenesis. Here, we show by RNA-sequencing that oncogenic HPV18 episome replication in primary human foreskin keratinocytes (HFKs) drives host transcriptional changes that are consistent between multiple HFK donors. We have previously shown that HPV18 recruits the host protein CTCF to viral episomes to control the differentiation-dependent viral transcriptional programme. Since CTCF is an important regulator of host cell transcription via coordination of epigenetic boundaries and long-range chromosomal interactions, we hypothesised that HPV18 may also manipulate CTCF to contribute to host transcription reprogramming. Analysis of CTCF binding in the host cell genome by ChIP-Seq revealed that while the total number of CTCF binding sites is not altered by the virus, there are a sub-set of CTCF binding sites that are either enriched or depleted of CTCF. Many of these altered sites are clustered within regulatory elements of differentially expressed genes, including the tumour suppressor gene cell adhesion molecule 1 (CADM1), which supresses epithelial cell growth and invasion. We show that HPV18 establishment results in reduced CTCF binding at the CADM1 promoter and upstream enhancer. Loss of CTCF binding is coincident with epigenetic repression of CADM1, in the absence of CpG hypermethylation, while adjacent genes including the transcriptional regulator ZBTB16 are activated. These data indicate that the CADM1 locus is subject to topological rearrangement following HPV18 establishment. We tested this hypothesis using 4C-Seq (circular chromosome confirmation capture-sequencing) and show that HPV18 establishment causes a loss of long-range chromosomal interactions between the CADM1 transcriptional start site and the upstream transcriptional enhancer. These data show that HPV18 manipulates host cell promoter-enhancer interactions to drive transcriptional reprogramming that may contribute to HPV-induced disease progression.
感染后，人乳头瘤病毒（HPV）会操纵宿主细胞基因表达，营造一个有利于高效且持续感染的环境。病毒诱导的宿主细胞转录组变化被认为与致癌作用有关。在此，我们通过RNA测序表明，致癌性HPV18在原代人包皮角质形成细胞（HFK）中的游离型复制驱动宿主转录变化，这种变化在多个HFK供体之间是一致的。我们之前已经表明，HPV18会将宿主蛋白CTCF招募到病毒游离型上，以控制依赖分化的病毒转录程序。由于CTCF通过协调表观遗传边界和长距离染色体相互作用，是宿主细胞转录的重要调节因子，我们推测HPV18也可能操纵CTCF，以促成宿主转录重编程。通过ChIP-Seq分析宿主细胞基因组中的CTCF结合情况发现，虽然病毒不会改变CTCF结合位点的总数，但有一部分CTCF结合位点的CTCF富集或减少。这些改变的位点中有许多聚集在差异表达基因的调控元件内，包括肿瘤抑制基因细胞黏附分子1（CADM1），它可抑制上皮细胞生长和侵袭。我们表明，HPV18的建立导致CADM1启动子和上游增强子处的CTCF结合减少。在没有CpG高甲基化的情况下，CTCF结合的丧失与CADM1的表观遗传抑制同时发生，而包括转录调节因子ZBTB16在内的相邻基因被激活。这些数据表明，HPV18建立后，CADM1基因座会发生拓扑重排。我们使用4C-Seq（环状染色体构象捕获测序）验证了这一假设，结果表明HPV18的建立导致CADM1转录起始位点与上游转录增强子之间的长距离染色体相互作用丧失。这些数据表明，HPV18操纵宿主细胞启动子-增强子相互作用，以驱动转录重编程，这可能有助于HPV诱导的疾病进展。
