In a groundbreaking study that could redefine our understanding of virus-driven cancer progression, researchers have uncovered the intricate ways in which viral genomes interact with human chromatin to restructure the three-dimensional architecture of the genome. This revelation uncovers new layers of complexity in the malignancy of nasopharyngeal carcinoma (NPC), a cancer strongly associated with Epstein-Barr virus (EBV) infection, and highlights the viral hijacking of epigenetic machinery as a driver of metastatic potential.
Nasopharyngeal carcinoma remains a formidable clinical challenge, given its aggressive nature and propensity for early metastasis. Although the role of EBV in NPC has long been recognized, the molecular underpinnings by which the virus manipulates host cellular machinery to promote cancer progression have remained elusive. The new research sheds light on the physical and functional interactions between viral DNA and human chromatin, revealing how these interactions provoke a reorganization of chromatin topology, thus remodeling gene expression patterns in favor of cancer dissemination.
Central to these findings is the virus’s ability to hijack KDM5B, a histone demethylase known to play pivotal roles in chromatin remodeling and gene regulation. KDM5B, by demethylating specific histone marks, affects the transcriptional landscape, thereby influencing cellular fate decisions. The study demonstrates that EBV co-opts KDM5B’s epigenetic regulatory functions to establish a permissive chromatin environment, facilitating the activation of oncogenic pathways and suppression of tumor suppressor networks that collectively enhance NPC metastasis.
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The researchers employed state-of-the-art chromatin conformation capture techniques alongside sophisticated viral genome mapping to illuminate the spatial proximity and interactions between the viral episome and human chromatin domains. Their data reveals that EBV DNA localizes preferentially to regions of the human genome that are rich in regulatory elements, including enhancers and promoters of metastasis-related genes. This viral tethering induces the formation of novel chromatin loops which physically juxtapose distant genomic loci, fundamentally altering gene regulatory circuits.
Moreover, the study reveals that this virus-induced 3D genome reorganization is not a passive consequence of infection but an active and strategic manipulation to reprogram the host epigenome. EBV exploits KDM5B to selectively erase H3K4me3 marks—histone modifications typically associated with active transcription—thereby dynamically silencing tumor suppressive genes and enhancing the expression of genes that promote cell motility and invasion. This epigenetic remodeling underlies the aggressive phenotype observed in metastatic NPC cases.
Importantly, the viral-human chromatin interface identified in this research presents an unprecedented target for therapeutic intervention. Disrupting the physical communication between EBV DNA and host chromatin or inhibiting KDM5B’s enzymatic activity could restore normal gene expression patterns and halt NPC progression. This insight opens new avenues for epigenetic drugs and antiviral strategies that are desperately needed in the clinical management of EBV-associated malignancies.
The implications of these findings extend beyond nasopharyngeal carcinoma, as they exemplify a viral strategy that may be conserved across other oncogenic viruses. By orchestrating three-dimensional genome reconfiguration, viruses can finely tune host gene expression resources to favor their own replication and survival while simultaneously driving oncogenesis. This paradigm encourages a revisitation of viral-host genome interplay in other cancers, potentially offering universal principles of virus-induced tumorigenesis.
The research team conducted comprehensive bioinformatics analyses to integrate chromatin interaction datasets with transcriptomic and epigenomic profiles. This integrated approach validated that viral chromatin loops correlate with changes in host gene expression relevant to metastatic traits, providing both spatial and functional perspectives on viral oncogenesis. The multi-omics perspective enhances confidence in the causal relationships proposed between viral genome insertion sites, chromatin structure alteration, and metastatic gene activation.
Such meticulous mapping of viral-human chromatin landscapes emphasizes the importance of 3D genome organization in cancer biology, moving beyond linear DNA sequence alterations to embrace higher-order genome folding as a determinant of disease phenotype. The concept that viruses can remodel nuclear architecture to induce cancer expands conceptual frameworks and prompts the exploration of nuclear structure as a therapeutic target.
An additional layer of complexity is conferred by the finding that the recruitment of KDM5B by EBV is mediated through viral proteins that tether the enzyme to specific host genome regions. This interaction facilitates the formation of repressive chromatin states in targeted loci, offering mechanistic insight into how viral components selectively reengineer epigenetic marks. The molecular basis of this recruitment provides critical clues for the development of inhibitors that could uncouple KDM5B from viral effectors.
In experimental models, reduction of KDM5B expression or function attenuated the invasive characteristics of NPC cells, reinforcing the enzyme’s crucial role in mediating viral-driven metastasis. These functional validations underscore KDM5B as a linchpin in the pathological crosstalk between EBV and the host genome, making it a compelling biomarker and drug target candidate.
This work represents a significant step forward in the effort to delineate the molecular choreography by which a virus manipulates host genome architecture to tip the balance toward malignancy. The dynamic and multifaceted relationship between viral infection, epigenetic remodeling, and three-dimensional genome reorganization elucidated here paves the way for a new class of anti-cancer therapeutics rooted in the manipulation of nuclear topology.
Future research inspired by these findings will likely delve into the temporal dynamics of viral-chromatin interactions during the NPC progression timeline, exploring whether interruption at specific genomic entry points can prevent chromatin rewiring and metastasis. The potential for early detection of these virus-mediated chromatin alterations could revolutionize diagnostic strategies.
The narrative emerging from this study challenges us to reconsider the nucleus not just as a container for genomic information, but as a battleground for viral-host conflict influencing cancer outcomes. It invites an expanded view of oncogenesis where viral genomes are active architects of the nuclear environment in favor of disease progression.
In conclusion, this research underscores the sophistication of viral strategies to weaponize host epigenetic machineries and genome architecture, illuminating potential vulnerabilities that can be pharmacologically exploited. As nasopharyngeal carcinoma remains a leading cause of cancer mortality in affected regions, these insights offer hope for more effective, targeted treatments that disrupt the viral manipulation of human chromatin.
Subject of Research: Virus-human chromatin interactions and their role in reorganization of the 3D genome architecture in nasopharyngeal carcinoma.
Article Title: Virus-human chromatin interactions reorganise 3D genome and hijack KDM5B for promoting metastasis in nasopharyngeal carcinoma.
Article References:
Chung, D.LS., Hou, Z., Wang, Y. et al. Virus-human chromatin interactions reorganise 3D genome and hijack KDM5B for promoting metastasis in nasopharyngeal carcinoma. Nat Commun 16, 7149 (2025). https://doi.org/10.1038/s41467-025-61597-1
Image Credits: AI Generated
Tags: cancer dissemination mechanismschromatin remodeling in cancerepigenetic hijacking by virusesEpstein-Barr virus and nasopharyngeal carcinomagene expression changes in cancerhistone demethylation and cancerKDM5B role in metastasismolecular interactions between virus and genomenasopharyngeal carcinoma metastasisviral genomes and chromatin architectureviral manipulation of host machineryvirus-driven cancer progression