Molecular basis oh herpes simplex virus entry into the cell and retargeting of the viral tropism for the design of oncolytic herpesviruses

Herpes simplex virus 1 (HSV-1) infects oral epitelial cells, then spreads to the nerve endings and estabilishes latency in sensory ganglia, from where it may, or may not reactivate. Diseases caused by virus reactivation include mild diseases such as muco-cutaneous lesions, and more severe, and even life-threatening encephalitis, or systemic infections affecting diverse organs. Herpes simplex virus represents the most comprehensive example of virus receptor interaction in Herpesviridae family, and the prototype virus encoding multipartite entry genes. In fact, it encodes 11-12 glycoproteins and a number of additional membrane proteins: five of these proteins play key roles in virus entry into subsceptible cells. Thus, glycoprotein B (gB) and glycoprotein C (gC) interact with heparan sulfate proteoglycan to enable initial attachment to cell surfaces. In the next step, in the entry cascade, gD binds a specific surface receptor such as nectin1 or HVEM. The interaction of glycoprotein D with the receptor alters the conformation of gD to enable the activation of gB, glycoprotein H, and glycoprotein L, a trio of glycoproteins that execute the fusion of the viral envelope with the plasma membrane. In this thesis, I described two distinct projects: I. The retargeting of viral tropism for the design of oncolytic Herpesviruses: • capable of infecting cells through the human epitelial growth factor receptor 2 (HER2), overexpressed in highly malignant mammary and ovarian tumors and correlates with a poor prognosis; • detargeted from its natural receptors, HVEM and nectin1. To this end, we inserted a ligand to HER2 in gD. Because HER2 has no natural ligand, the selected ligand was a single chain antibody (scFv) derived from MAb4D5 (monoclonal antibody to HER2), herein designated scHER2. All recombinant viruses were targeted to HER2 receptor, but only two viruses (R-LM113 and R-LM249) were completely detargeted from HVEM and nectin1. To engineer R-LM113, we removed a large portion at the N-terminus of gD (from aa 6 to aa 38) and inserted scHER2 sequence plus 9-aa serine-glycine flexible linker at position 39. On the other hand, to engineer R-LM249, we replaced the Ig-folded core of gD (from aa 61 to aa 218) with scHER2 flanked by Ser-Gly linkers. In summary, these results provide evidence that: i. gD can tolerate an insert almost as big as gD itself; ii. the Ig-like domain of gD can be removed; iii. the large portion at the N-terminus of gD (from aa 6 to aa 38) can be removed without loss of key function; iv. R-LM113 and R-LM249 recombinants are ready to be assayed in animal models of mammary and ovary tumour. This finding and the avaibility of a large number of scFv greatly increase the collection of potential receptors to which HSV can be redirected. II. The production and purification of recombinant truncated form of the heterodimer gHgL. We cloned a stable insect cell line expressing a soluble form of gH in complex with gL under the control of a metalloprotein inducible promoter and purified the heterodimer by means of ONE-STrEP-tag system by IBA. With respect to biological function, the purified heterodimer is capable: • of reacting to antibodies that recognize conformation dependent epitopes and neutralize virion infectivity; • of binding a variety cells at cell surface. No doubt, the availability of biological active purified gHgL heterodimer, in sufficient quantities, will speed up the efforts to solve its crystal structure and makes it feasible to identify more clearly whether gHgL has a cellular partner, and what is the role of this interaction on virus entry.

Meccanismi evolutivi dei parapoxvirus: caratterizzazione genomica di pseudocowpoxvirus e messa a punto di sistemi per lo studio delle ricombinazioni

The Poxviruses are a family of double stranded DNA (dsDNA) viruses that cause disease in many species, both vertebrate and invertebrate. Their genomes range in size from 135 to 365 kbp and show conservation in both organization and content. In particular, the central genomic regions of the chordopoxvirus subfamily (those capable of infecting vertebrates) contain 88 genes which are present in all the virus species characterised to date and which mostly occur in the same order and orientation. In contrast, however, the terminal regions of the genomes frequently contain genes that are species or genera-specific and that are not essential for the growth of the virus in vitro but instead often encode factors with important roles in vivo including modulation of the host immune response to infection and determination of the host range of the virus. The Parapoxviruses (PPV), of which Orf virus is the prototypic species, represent a genus within the chordopoxvirus subfamily of Poxviridae and are characterised by their ability to infect ruminants and humans. The genus currently contains four recognised species of virus, bovine papular stomatitis virus (BPSV) and pseudocowpox virus (PCPV) both of which infect cattle, orf virus (OV) that infects sheep and goats, and parapoxvirus of red deer in New Zealand (PVNZ). The ORFV genome has been fully sequenced, as has that of BPSV, and is ~138 kb in length encoding ~132 genes. The vast majority of these genes allow the virus to replicate in the cytoplasm of the infected host cell and therefore encode proteins involved in replication, transcription and metabolism of nucleic acids. These genes are well conserved between all known genera of poxviruses. There is however another class of genes, located at either end of the linear dsDNA genome, that encode proteins which are non-essential for replication and generally dictate host range and virulence of the virus. The non-essential genes are often the most variable within and between species of virus and therefore are potentially useful for diagnostic purposes. Given their role in subverting the host-immune response to infection they are also targets for novel therapeutics. The function of only a relatively small number of these proteins has been elucidated and there are several genes whose function still remains obscure principally because there is little similarity between them and proteins of known function in current sequence databases. It is thought that by selectively removing some of the virulence genes, or at least neutralising the proteins in some way, current vaccines could be improved. The evolution of poxviruses has been proposed to be an adaptive process involving frequent events of gene gain and loss, such that the virus co-evolves with its specific host. Gene capture or horizontal gene transfer from the host to the virus is considered an important source of new viral genes including those likely to be involved in host range and those enabling the virus to interfere with the host immune response to infection. Given the low rate of nucleotide substitution, recombination can be seen as an essential evolutionary driving force although it is likely underestimated. Recombination in poxviruses is intimately linked to DNA replication with both viral and cellular proteins participate in this recombination-dependent replication. It has been shown, in other poxvirus genera, that recombination between isolates and perhaps even between species does occur, thereby providing another mechanism for the acquisition of new genes and for the rapid evolution of viruses. Such events may result in viruses that have a selective advantage over others, for example in re-infections (a characteristic of the PPV), or in viruses that are able to jump the species barrier and infect new hosts. Sequence data related to viral strains isolated from goats suggest that possible recombination events may have occurred between OV and PCPV (Ueda et al. 2003). The recombination events are frequent during poxvirus replication and comparative genomic analysis of several poxvirus species has revealed that recombinations occur frequently on the right terminal region. Intraspecific recombination can occur between strains of the same PPV species, but also interspecific recombination can happen depending on enough sequence similarity to enable recombination between distinct PPV species. The most important pre-requisite for a successful recombination is the coinfection of the individual host by different virus strains or species. Consequently, the following factors affecting the distribution of different viruses to shared target cells need to be considered: dose of inoculated virus, time interval between inoculation of the first and the second virus, distance between the marker mutations, genetic homology. At present there are no available data on the replication dynamics of PPV in permissive and non permissive hosts and reguarding co-infetions there are no information on the interference mechanisms occurring during the simultaneous replication of viruses of different species. This work has been carried out to set up permissive substrates allowing the replication of different PPV species, in particular keratinocytes monolayers and organotypic skin cultures. Furthermore a method to isolate and expand ovine skin stem cells was has been set up to indeep further aspects of viral cellular tropism during natural infection. The study produced important data to elucidate the replication dynamics of OV and PCPV virus in vitro as well as the mechanisms of interference that can arise during co-infection with different viral species. Moreover, the analysis carried on the genomic right terminal region of PCPV 1303/05 contributed to a better knowledge of the viral genes involved in host interaction and pathogenesis as well as to locate recombination breakpoints and genetic homologies between PPV species. Taken together these data filled several crucial gaps for the study of interspecific recombinations of PPVs which are thought to be important for a better understanding of the viral evolution and to improve the biosafety of antiviral therapy and PPV-based vectors.

Alterazioni dell'immunità umorale nei pazienti con sarcoma di Kaposi classico: caratterizzazione dei linfociti B circolanti e delle loro sottopopolazioni

Objectives: Human Herpesvirus 8 (HHV-8) is the etiological agent of Kaposi’s Sarcoma (KS) and it is also associated with two B cell lymphoproliferative diseases: primary effusion lymphoma (PEL), and the plasmablastic form of multicentric Castelman’s disease (MCD). HHV-8 establishes persistent infection in the host with tropism for multiple cell types. In KS patients, the virus is found in tumor-spindle cells, peripheral blood monocytes, endothelial progenitor circulating cells, T and B lymphocytes. Peripheral B cells represent one of the major virus reservoir, but the consequences of HHV-8 infection of these cells have been poorly characterized. Therefore, in this study the frequency, the immunophenotypic profile and the functional activity of different peripheral B cell subsets in patients with classic KS (cKS) was analysed in order to identify potential alterations of these cells. The classic variant of KS is ideal to perform such studies, as it lacks confounding factors such as HIV or EBV infection and immunosuppression. Methods: Whole-blood samples from patients with the classical form of KS (cKS) (n=62) and healthy age and sex-matched seronegative controls (HSN) (n=43) were analyzed by multiparametric flow-cytometry to determine the frequency of B cells and their subpopulations, as well as their surface expression of immunoglobulins and activation markers. Results: The frequency of circulating B cells was significantly higher in cKS patients than in controls. In particular, the analysis of the B cell subsets revealed a higher frequency of naïve B cells (CD19+CD27-), among which transitional CD19+CD38highCD5+ and pre-naïve (CD27-CD38intCD5+ ) B cells demonstrated an expansion. Memory B cells (CD19+CD27+) did not differ between the two study groups, except from a higher frequency of CD19+CD27+IgM+IgD+ B cells, the typical phenotype of marginal zone (MZ) B cells, in cKS patients. The characterization of membrane surface activation markers showed lower levels of the activation marker HLA-DR only on CD27- B cells, while CD80 and CD86 were less represented in all the the B cells from cKS patients. Moreover, B cells from cKS patients were smaller and with less granules than the ones from controls. Conclusion: Taken together, these results clearly indicate that circulating B cells are altered in patients with cKS, showing an expansion of the immature phenotypes. These B cell alterations may be due to an indirect viral effect rather than to a direct one: the cytokines expressed in the microenvironment typical of cKS may cause a faster release of immature cells from the bone marrow and a lower grade of peripheral differentiation, as already suggested for other chronic viral infections such as HIV and HCV. Further studies will be necessary to understand how these alterations contribute to the pathogenesis of KS and, eventually, to the different clinical evolution of the disease.

Meccanismi replicativi e di regolazione dell'espressione genica di Parvovirus B19

Il Parvovirus B19, virus patogeno umano della famiglia Parvoviridae, mostra uno specifico tropismo per i precursori eritroidi e una limitata replicazione in alcune linee cellulari megacarioblastoidi. Allo scopo di sviluppare sistemi utili allo studio delle caratteristiche biologiche del virus, diversi laboratori si sono occupati della costruzione di cloni genomici di B19 dotati di competenza funzionale e capaci di generare virus infettante. Parte del presente lavoro ha riguardato l’analisi funzionale di diversi cloni genomici di B19 e ha permesso di caratterizzare le regioni terminali del virus e di identificare requisiti essenziali per la loro funzionalità. Nel contesto intracellulare, esistono differenti livelli di restrizione in relazione alla capacità della cellula di supportare la replicazione virale, non ancora del tutto caratterizzati. Inoltre si sono accumulate evidenze circa la capacità del B19 di instaurare persistenza in numerosi tessuti. Non sono ancora note le caratteristiche funzionali del genoma virale in questo stato, è possibile che il virus persista in forma silente e meccanismi epigenetici possano regolare tale silenziamento. In questo studio è stato analizzato lo stato di metilazione del genoma di B19 e il suo possibile effetto sul ciclo replicativo virale ed è stata investigata la possibile associazione del DNA virale agli istoni cellulari nel corso di infezione in vitro. I risultati ottenuti confermano la presenza di questi meccanismi epigenetici, potendo ipotizzare che giochino un importante ruolo nella regolazione della funzionalità virale e nell’interazione B19-cellula e siano un elemento critico per l’adattamento del virus nell’ambiente in cui si trova. Inoltre l’ipotesi che anche i microRNA possano assumere un importante significato nell’interazione B19-cellula è stata proposta da diversi lavori e nel presente studio è stata valutata la produzione di queste piccole molecole durante l'infezione in vitro, ricercando microRNA (cellulari e/o virali) con omologia di sequenza per il genoma di B19 e quindi specifici per il virus.

Human congenital cytomegalovirus infection: characteristics and pathogenesis of fetal brain damage

Human cytomegalovirus (HCMV) causes congenital neurological lifelong disabilities. The study analyzed 10 HCMV-infected human fetuses at 21 weeks of gestation to evaluate the characteristics and pathogenesis of brain injury related to congenital human CMV (cCMV) infection. Specifically, tissues from cortical and white matter areas, subventricular zone, thalamus, hypothalamus, hippocampus, basal ganglia and cerebellum were analysed by: i) immunohistochemistry (IHC) to detect HCMV-infected cell distribution, ii) hematoxylin-eosin staining to evaluate histological damage and iii) real-time PCR to quantify tissue viral load (HCMV-DNA). Viral tropism was assessed by double IHC to detect HCMV-antigens and neural/neuronal markers: nestin (expressed in early differentiation stage), doublecortin (DCX, identifying neuronal precursor cells) and neuronal nuclei (NeuN, identifying mature neurons). HCMV-positive cells and viral DNA were found in the brain of 8/10 (80%) fetuses. For these cases, brain damage was classified in mild (n=4, 50%), moderate (n=3, 37.5%) and severe (n=1, 12.5%) based on presence of i) diffuse astrocytosis, microglial activation and vascular changes; ii) occasional (in mild) or multiple (in moderate/severe) microglial nodules and iii) necrosis (in severe). The highest median HCMV-DNA level was found in the hippocampus (212 copies/5ng of humanDNA [hDNA], range: 10-7,505) as well as the highest mean HCMV-infected cell value (2.9 cells, range: 0-23), followed by that detected in subventricular zone (1.8 cells, range: 0-19). This suggests a preferential HCMV tropism for immature neuronal cells, residing in these regions, confirmed by the detection of DCX and nestin in 94% and 63.3% of HCMV-positive cells, respectively. NeuN was not found among HCMV-positive cells and was nearly absent in the brain with severe damage, suggesting HCMV does not infect mature neurons and immature HCMV-infected neuronal cells do not differentiate into neurons. HCMV preferential tropism in immature neural/neuronal cells delays/inhibits their differentiation interfering with brain development processes that lead to structural and functional brain defects.

A genome editing approach to the study of Parvovirus B19

Parvovirus B19 (B19V) is a ssDNA virus, with a 5596 nt long genome encapsidated within an icosahedral capsid with a diameter of 22 nm. Viral proteins are subdivided into structural and non-structural: the main non-structural one is the NS1, while the 2 structural proteins VP1 and VP2 assemble originating the capsid shell. B19V tropism is mainly limited to erythroid progenitor cells (EPCs), however, virus can be detected in several districts persisting in tissues possibly lifelong. The virus can induce anemia and erythroid aplasia. Therapeutic strategies are only symptomatic, so the search for antivirals is strongly active, with screenings showing the activity in vitro of different compounds like hydroxyurea, cidofovir and brincidofovir. In the first project, a functional minigenome of B19V was developed, able to express only the NS1 protein. This minigenome proved able to replicate and express the NS1 at levels comparable to unmodified clones. Furthermore, the ability of this minigenome to complement the function of NS1-deficient genomes was demonstrated, thus providing a proof-of-concept of B19V genome editing possibility and, at the same time, a useful tool to study the NS1 protein also as an antiviral target. In the second project I addressed the interplay between B19V and the cellular restriction factor APOBEC3B (A3B), a cytidine deaminase acting on ssDNA, whose footprint on B19V genome was proved by a bioinformatic sequence analysis performed by the hosting lab. To understand whether A3B still exerts activity and a potential antiviral effect on B19V, the UT7/EpoS1 cells were transduced with lentiviral vectors to silence A3B expression, then used as a model to study viral behavior. No significant role of A3B on B19V was demonstrated, in agreement with the hypothesis of viral adaptation to this cellular restriction factor; anyway, virus ability to alter A3B expression would deserve further investigations.