APPEALING: An integrated APProach focusEd on defining the moleculAr and biological mechanisms reguLatING viral reactivation and persistence
ProgettoThe knowledge about the persistence capacity of viruses such as Human polyomaviruses (HPyVs), Herpes Simplex virus 1 (HSV-1), Human Cytomegalovirus (CMV), Epstein-Barr virus (EBV), Varicella-Zoster (VZV), Human Immunodeficiency Virus (HIV), Parvovirus B19 (B19V) and Hepatitis B virus (HBV) is well established. Some mechanisms underlying their persistence dynamics in human body are known, yet the systematic characterization of viral and host genetic factors that modulate their persistence, spread and reactivation is still missing. Despite recent advancements in the diagnostic technologies for rapid assessment of these infections, the host cell responses to these life-long infections, their role in controlling viral replication in specific sites (e.g., CNS), or in concurring to long-term damages during immune suppression have yet to be disclosed. More specifically, from an operative point of view, consistent viral genetic data are still missing (regarding the full-length sequencing of viral genomes), as well as the extensive characterization of "omics" human elements which correlate with disease evolution.
APPEALING project proposes to extend the attention not only to single gene level, or even specific mutations, but also to the concept of connections between mutations (and alterations of genetic pathways) with translational and post-translational modulations, epigenetic alterations, and the complex mechanisms of protein interaction. The results potentially represent a new paradigm to address a systematic analysis of causal mechanisms and profiles associated with viral persistence and reactivation in immune-competent and immunosuppressed individuals. Application of next generation sequencing (NGS) techniques allows a thorough description of genetic diversity within viral populations, and offers a unique opportunity for studying large-scale population dynamics, epigenetic control of viral expression, interaction of viral variants with host restriction factors, and the effect of selective pressure exerted by immune or pharmacological actions. This is made possible by the extensive availability of biological samples of reactivated/persistent viruses, together with advanced technologies in the field of viral genetics, immunology and molecular biology
To fill the knowledge gaps, the major goal of the project is the creation of a multidisciplinary, collaborative national network, able to develop an advanced basic research, aimed at the characterization of new viral and host factors predictors of persistence, spread and reactivation events in the setting of immunocompromised patients. The study of viral and host genetic markers (and of their synergistic action) will be essential to set new and proper diagnostic markers of reactivation, as well as effective therapeutic regimens, capable of properly controlling virus replication, and thus limiting the severe manifestations often present at the time of reactivation. The combination of clinical data with advanced molecular expertises in the viral and cellular field will make possible the characterization of the elements favouring the persistence and reactivation of these viruses in human host.
The main specific aims of this project are:
i) Creation and consolidation of a multidisciplinary collaborative network, consisting of vanguard centers for viral sequencing, genomic, proteomic, modeling, together with some of the largest clinical virology reference centers distributed on Italian territory.
ii) Definition of a map of viral and host genetic markers, able to modulate persistence, spread and reactivation of viruses most frequently responsible for public health threatens, such as HBV, HPV, CMV, EBV, VZV, HSV-1, Merkel cell polyomavirus (MCPyV), BKV, HIV and B19V in specific immunocompromised settings.
In particular the project:
1. will provide new insights on the interplay between HBV and host factors in determining HBV reactivation in high-risk settings (Responsible UNIT1);
2. will gain new insights into the role of Interferons (IFN) type I and III, and other mucosal innate response determinants, in persistence and progression of HPV-related lesion in view of a potential therapeutic approach (Responsible UNIT2);
3. will provide new CMV- EBV- and VZV- specific immunological markers that could be predictive of virus-related infectious episodes (Responsible UNIT3);
4. will gain more insights into the viral and host factors that contribute to the persistence of MCPyV and BKPyV infection in their natural setting (Responsible UNIT4);
5. will perform a fine characterization of host responses to HSV-1 infection and their role in long-term damages in the CNS (Responsible UNIT5);
6. will gain insights into the extent and role of genetic diversity and minority variants in latency and reactivation of HIV and B19V, combining quantitative determination of viral genomes and viral transcripts with analysis of viral quasispecies structure (Responsible UNIT6).
APPEALING project proposes to extend the attention not only to single gene level, or even specific mutations, but also to the concept of connections between mutations (and alterations of genetic pathways) with translational and post-translational modulations, epigenetic alterations, and the complex mechanisms of protein interaction. The results potentially represent a new paradigm to address a systematic analysis of causal mechanisms and profiles associated with viral persistence and reactivation in immune-competent and immunosuppressed individuals. Application of next generation sequencing (NGS) techniques allows a thorough description of genetic diversity within viral populations, and offers a unique opportunity for studying large-scale population dynamics, epigenetic control of viral expression, interaction of viral variants with host restriction factors, and the effect of selective pressure exerted by immune or pharmacological actions. This is made possible by the extensive availability of biological samples of reactivated/persistent viruses, together with advanced technologies in the field of viral genetics, immunology and molecular biology
To fill the knowledge gaps, the major goal of the project is the creation of a multidisciplinary, collaborative national network, able to develop an advanced basic research, aimed at the characterization of new viral and host factors predictors of persistence, spread and reactivation events in the setting of immunocompromised patients. The study of viral and host genetic markers (and of their synergistic action) will be essential to set new and proper diagnostic markers of reactivation, as well as effective therapeutic regimens, capable of properly controlling virus replication, and thus limiting the severe manifestations often present at the time of reactivation. The combination of clinical data with advanced molecular expertises in the viral and cellular field will make possible the characterization of the elements favouring the persistence and reactivation of these viruses in human host.
The main specific aims of this project are:
i) Creation and consolidation of a multidisciplinary collaborative network, consisting of vanguard centers for viral sequencing, genomic, proteomic, modeling, together with some of the largest clinical virology reference centers distributed on Italian territory.
ii) Definition of a map of viral and host genetic markers, able to modulate persistence, spread and reactivation of viruses most frequently responsible for public health threatens, such as HBV, HPV, CMV, EBV, VZV, HSV-1, Merkel cell polyomavirus (MCPyV), BKV, HIV and B19V in specific immunocompromised settings.
In particular the project:
1. will provide new insights on the interplay between HBV and host factors in determining HBV reactivation in high-risk settings (Responsible UNIT1);
2. will gain new insights into the role of Interferons (IFN) type I and III, and other mucosal innate response determinants, in persistence and progression of HPV-related lesion in view of a potential therapeutic approach (Responsible UNIT2);
3. will provide new CMV- EBV- and VZV- specific immunological markers that could be predictive of virus-related infectious episodes (Responsible UNIT3);
4. will gain more insights into the viral and host factors that contribute to the persistence of MCPyV and BKPyV infection in their natural setting (Responsible UNIT4);
5. will perform a fine characterization of host responses to HSV-1 infection and their role in long-term damages in the CNS (Responsible UNIT5);
6. will gain insights into the extent and role of genetic diversity and minority variants in latency and reactivation of HIV and B19V, combining quantitative determination of viral genomes and viral transcripts with analysis of viral quasispecies structure (Responsible UNIT6).