Tumorigenic Herpesviruses: Kaposi sarcoma-associated herpesvirus and Epstein-Barr Virus

The gamma-herpesviruses Kaposi sarcoma-associated herpesvirus (KSHV) and Epstein-Barr Virus (EBV) are able to cause tumors in humans. Although these tumors are rare in the general population, they occur with increased frequency in immunodeficient individuals. In the wake of the AIDS pandemic, their incidence has risen dramatically such that today Kaposi sarcoma is one of the most frequent tumors in some regions of sub-saharan Africa.

KSHV- and EBV-associated tumors are caused by latently infected cells. Such cells do not produce viral progeny, but form a reservoir of viral infection in which the viral genome persist as a nuclear episomes that only express a very limited reservoir of viral genes. A primary goal of our work is the elucidation of the molecular mechanisms that govern establishment and maintenance of viral latency. Recently, we were able to show that a hallmark of primary KSHV latency is the establishment of complex histone modification patterns and recruitment of polycomb repressor complexes, which leads to the establishment of bivalent chromatin on key lytic promoters. We strongly suspect that KSHV actively induces this chromatin state. We employ experimental infection systems together with state-of-the-art analytical methods (e.g., ChIP-seq, RNA-seq) to identify latent gene products and genetic elements that control epigenetic patterns in KSHV and related viruses. In addition, we are investigating the functions of individual latency gene products, especially viral microRNAs, during viral infection and tumorigenesis.

FOR5200 DEEP-DV: Disrupt – Evade – Exploit

Nuclear entry of a non-chromatinized DNA molecule is a central event in all herpesvirus infections. Following nuclear delivery, epigenetically naïve episomes can either activate the lytic gene expression cascade, leading to production of viral progeny and host cell death, or acquire latent chromatin states that mediate selective and reversible silencing of lytic genes. Whereas latent chromatin allows the viral genome to persist in a dormant state until a reactivation signal is received, antiviral host defences promote constitutively repressive chromatin states to globally suppress invading DNA. If the virus fails to escape or manipulate these defences, viral episomes are permanently silenced or cleared. To date, the chromatin factors and epigenetic pathways governing successful establishment of latent chromatin are only partially understood. Given their evolutionary relationship, we hypothesize that as of yet undiscovered and fundamental principles are shared among different herpesviruses. To address this hypothesis, we will perform a comparative analysis of two human herpesviruses: The gammaherpesvirus Kaposi sarcoma-associated herpesvirus (KSHV) and the alphaherpesvirus varicella zoster virus (VZV). Based on our previous observations, we hypothesize that both viruses exploit default host pathways that have evolved to rapidly recruit polycomb repressive complexes (PRC) to CpG-rich DNA. Instead of constitutive heterochromatinization that may be imposed by PML nuclear bodies (PML-NBs), PRC recruitment allows viral episomes to acquire facultative heterochromatin states to establish and maintain latency. We therefore postulate PRC-mediated suppression to be a common denominator of latency, but also expect that initial assembly as well as maturation of viral chromatin proceed in a spatially and/or temporally distinct fashion for each virus. While this project aims to decipher the mechanisms that govern latent chromatin of KSHV and VZV chromatin, our long-term goal is to extend our findings to other viruses and develop a unified model of early chromatin regulation in DNA virus infection.

To reach our objectives, we will employ a variety of tools in appropriate latency and reactivation models, including epigenome (ChIP-Seq, MeDIP-Seq) and transcriptome (RNA-Seq) interrogation techniques, manipulation of sub-nuclear compartments and cellular repressor complexes by genome editing, and investigation of spatial and temporal episome dynamics by single molecule live cell imaging.

Tumorigenic Polyomaviruses: Merkel Cell Polyomavirus

Merkel cell carcinoma (MCC) is a rare but highly aggressive tumor that primarily afflicts the elderly or the immunosupressed. Recently, a novel polyomavirus, termed Merkel cell polyomavirus (MCPyV), was identified in MCC tissues. 80% of all MCC cases harbor monoclonally integrated, defective MCPyV genomes, strongly arguing for a causative role of abortive MCPyV infection during MCC pathogenesis. Using a synthetic consensus genome, we were able to establish a semi-permissive replication system. We now employ this system to investigate the role of T-antigens and a viral microRNA during the viral lifecycle as well as virally induced transformation, and to identify novel targets that may be exploited for therapeutic treatment of MCPyV-positive Merkel cell carcinoma.

Detection and analysis of infectious agents by high throughput sequencing

High throughput or next generation sequencing (NGS) has a unique potential to perform comprehensive metagenomic analyses of bacterial and viral pathogens in clinical specimen. A significant advantage of this technique is the ability to detect known as well as novel infectious agents. The development of NGS-based pathogen detection methods thus may contribute significantly to the ability to rapidly and efficiently react to future outbreaks. In order to optimally exploit the potential of this technology, we analyze different diagnostic entities by next generation sequencing with Illumina MiSeq and HiSeq 2500 machines, and systematically compare the results to conventional PCR-based detection methods. In addition, we are developing innovative bioinformatic solutions for the analysis of complex metagenomic data from clinical specimen.

SARS-CoV-2 - Hamburg Surveillance Platform

Against the background of the spread of variants with increased transmissibility and possibly increased ability to (re-)infect recovered or vaccinated individuals, a systematic overall surveillance of SARS-CoV-2 mutations is of great importance. With the support of the Hanseatic City of Hamburg, approximately 4,000 of the SARS-CoV-2 cases occurring in Hamburg will be sequenced over the next six months. The sequence data will be analyzed using computer-assisted methods and subsequently evaluated by a joint HPI/UKE team of experts in order to be able to detect at an early stage the spread of already known mutations, but also the emergence of possible new ones.

Since the beginning of the Corona pandemic, HPI and UKE have sequenced and analyzed more than 1,700 SARS-CoV-2 genomes. Sequence data have been collected from a systematic cross-section of all SARS-CoV-2 samples received by UKE to monitor virus arrivals in Hamburg, to track the spread of SARS-CoV-2 and, in particular, to closely monitor and evaluate genetic changes of the pathogen in the metropolitan region. Sequence analyses commissioned by Hamburg health departments and authorities have also already been able to make an important contribution in the investigation of local outbreaks in hospitals, schools and nursing homes.

The Hamburg-based viral genomics surveillance platform is also an important component of the collection of SARS-CoV-2 sequence data nationwide. The data is also forwarded to the Robert Koch Institute (RKI) in accordance with the federal regulation CorSuRV, which has been in force since January 18, 2021.

Here you can find current data on the spread of SARS-CoV-2 variants in Hamburg, collected by the Hamburg Surveillance Platform (in German)

SARS-CoV-2 Publications

Heyer et al. investigate SARS-CoV2 intra-host genomic diversity in longitudinal samples from 14 patients suffering from prolonged infection. Whereas viral populations are surprisingly stable overall, novel variant species can rapidly emerge in remdesivir-treated patients, suggesting that antiviral treatment can create evolutionary bottlenecks, which promote emergence of SARS-CoV2 variants.