Biology of Virus-associated Cancers

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

Polyomaviruses are ubiquitous pathogens that establish subclinical lifelong infections. In immunosuppressed individuals, these viruses can cause a number of serious diseases and are linked to cancer development. Our research interests primarily focus on how viruses (predominantly BK polyomavirus and Merkel cell polyomavirus) cause DNA damage/mutations in the host genome and integrate, which is a dead-end to the normal virus lifecycle. To experimentally study the interplay between BK polyomavirus (BKPyV) and urinary diseases, such as bladder cancer and hemorrhagic cystitis (HC), we've utilized a spontaneously immortalized urothelial cell line (HBLAK), which retains a normal morphology and ability to differentiate into stratified urothelium, to study virus infections in three dimensions. In one project, we treated these cells with low-dose genotoxic agents commonly used as immune conditioning drugs in bone marrow transplant recipients and identified that these greatly amplify BKPyV genome replication, which may contribute to the development of HC in these patients. We have partnered with the NIH clinical center and other clinicians to evaluate mutations in BKPyV in urine of patients receiving these drugs as an early detection for disease development. A manuscript describing these findings is in progress. We have also engineered bladder cells to remove the primary mutagenic enzymes responsible for the somatic mutations observed in bladder cancer and in BKPyV evolution (APOBEC3A and APOBEC3B). Preliminary data from these lines have confirmed that APOBEC host mutagenesis happens during BKPyV infection and is abolished in the KO cells. Further experiments also suggest that APOBEC enzymes suppress the development of pathogenic variants of BKPyV and validation of these findings is ongoing. In the above-mentioned cellular models, we are also using chromatin conformation sequencing in conjunction with knockdown of factors that control chromatin looping (CTCF, WAPL, RAD21) to study how these affect polyomavirus replication and erroneous integration into the host genome. While these models are used to study events prior and during integration, we are using newly derived virus-positive Merkel cell carcinoma (MCC) cell lines to study how integrated viral DNAs in established cancers interact with host chromatin and affect cellular gene expression and chromatin conformation. These data are being combined with substantial sequencing data from patient-derived specimens to identify clinically relevant and important factors. A manuscript summarizing our findings from these patient-derived specimens on novel mutagenic processes and their relative timing in MCC is in preparation. This work is being further expanded to understand how various epigenetic marks (DNA methylation, histone modifications, and chromatin conformation) contribute to the development of MCC. Lastly, we are also involved in a number of collaborative team projects on lesser studied cancers to accurately identify virus involvement as well as their integration locations. From these collaborations, we have published two studies on HPV integration and involvement in the development of sinonasal carcinomas and in skin squamous cell carcinoma in an individual with rare germline immune deficiency.