UZH-Logo

Maintenance Infos

Functional genomic approaches to study human adenoviruses and frontier research on miRNAs


Trinh, H V. Functional genomic approaches to study human adenoviruses and frontier research on miRNAs. 2011, University of Zurich, Faculty of Science.

Abstract

Viruses are self-organized, symmetrical and rather simple structures, which can cause devastating diseases in humans and animals. They are able to readily react to cellular cues by changing gene expressions and conformations, which in turn enables dynamic interactions with their hosts. A large body of research has shown that the full complexity of viruses is unfolded as soon as they interact with host cells. Although studies of virus-host interactions have emerged as a key driving force in the research of infectious diseases, our understanding of the systems properties of viral infections has remained incomplete. Human adenoviruses (HAdVs) are most commonly associated with respiratory and gastrointestinal tract infections. In addition, HAdVs are the most common viral vectors in clinical gene transfer trials. Although HAdVs have been well characterized, there are many unresolved aspects, such as receptor usage by species B viruses (HAdV-B), dynamic expression profiles of viral and cellular proteins in the infected cells, and how this can be influenced by signal transduction, or virally encoded miRNAs. To address some of these issues, we employed comprehensive functional genomics
and biochemistry approaches to obtain a global picture of the infection dynamics of HAdVs in cultured cells, from entry to gene regulations. In the stage of HAdV entry, we
studied the interaction of HAdV-B3/HAdV-B7 fiber knob (FK) to cellular receptor CD46 by using Biacore and quantitative microscopy. In the progress of dynamic interactions and regulations, we targeted three molecular levels including miRNA, mRNA and proteins by using quantitative transcriptomics and proteomics of both viruses and host
infected human epithelial cells. The transcriptomics analysis was carried out by using the Agilent microarray and deep sequencing while proteomics was performed by using
iTRAQ-8plex labeling of peptides or label-free method, followed by LC-MS/MS analyses at different time points of infection with different HAdV types. Subsequently, the networks were analyzed by using Metacore. For identifying novel miRNAs, we applied both in silico predictions and multi-detection methods including RT-PCR, miRNA microarray, deep sequencing and Northern blot analysis. Our results show that direct binding of HAdV-B3/HAdV-B7-FK to CD46 occurs by an avidity mechanism and resolves the controversy about CD46 being a receptor for HAdV-B. Based on quantitative transcriptomics, proteomics and miRNAs, we defined some common networks of HAdV serotypes of 3, 5, 11p and 35, such as cytoskeleton and cell cycle. We found new components such as galectin-1 (gal-1) and galectin-3 (gal-3), which were triggered to be secreted into the cell culture supernate. Preliminary data suggested that gal-1 and gal-3 interacted with CD46 as well as viral capsids
including hexon and penton. Concerning the miRNAs, we found four small viral miRNAs (vmiRNAs) derived from VA-RNAI and one small vmiRNA derived from a noncoding viral sequence. Based on in silico analyses of potential targets for these
vmiRNAs and transcriptomics analysis we found that there are many potential cellular and viral gene targets. In summary, this study addressed several systems aspects of
HAdV infections, including post-translational modifications, potential anti-viral factors of innate immunity, small vmiRNAs, and it clarified the role of CD46 for HAdV-B infections.

Viruses are self-organized, symmetrical and rather simple structures, which can cause devastating diseases in humans and animals. They are able to readily react to cellular cues by changing gene expressions and conformations, which in turn enables dynamic interactions with their hosts. A large body of research has shown that the full complexity of viruses is unfolded as soon as they interact with host cells. Although studies of virus-host interactions have emerged as a key driving force in the research of infectious diseases, our understanding of the systems properties of viral infections has remained incomplete. Human adenoviruses (HAdVs) are most commonly associated with respiratory and gastrointestinal tract infections. In addition, HAdVs are the most common viral vectors in clinical gene transfer trials. Although HAdVs have been well characterized, there are many unresolved aspects, such as receptor usage by species B viruses (HAdV-B), dynamic expression profiles of viral and cellular proteins in the infected cells, and how this can be influenced by signal transduction, or virally encoded miRNAs. To address some of these issues, we employed comprehensive functional genomics
and biochemistry approaches to obtain a global picture of the infection dynamics of HAdVs in cultured cells, from entry to gene regulations. In the stage of HAdV entry, we
studied the interaction of HAdV-B3/HAdV-B7 fiber knob (FK) to cellular receptor CD46 by using Biacore and quantitative microscopy. In the progress of dynamic interactions and regulations, we targeted three molecular levels including miRNA, mRNA and proteins by using quantitative transcriptomics and proteomics of both viruses and host
infected human epithelial cells. The transcriptomics analysis was carried out by using the Agilent microarray and deep sequencing while proteomics was performed by using
iTRAQ-8plex labeling of peptides or label-free method, followed by LC-MS/MS analyses at different time points of infection with different HAdV types. Subsequently, the networks were analyzed by using Metacore. For identifying novel miRNAs, we applied both in silico predictions and multi-detection methods including RT-PCR, miRNA microarray, deep sequencing and Northern blot analysis. Our results show that direct binding of HAdV-B3/HAdV-B7-FK to CD46 occurs by an avidity mechanism and resolves the controversy about CD46 being a receptor for HAdV-B. Based on quantitative transcriptomics, proteomics and miRNAs, we defined some common networks of HAdV serotypes of 3, 5, 11p and 35, such as cytoskeleton and cell cycle. We found new components such as galectin-1 (gal-1) and galectin-3 (gal-3), which were triggered to be secreted into the cell culture supernate. Preliminary data suggested that gal-1 and gal-3 interacted with CD46 as well as viral capsids
including hexon and penton. Concerning the miRNAs, we found four small viral miRNAs (vmiRNAs) derived from VA-RNAI and one small vmiRNA derived from a noncoding viral sequence. Based on in silico analyses of potential targets for these
vmiRNAs and transcriptomics analysis we found that there are many potential cellular and viral gene targets. In summary, this study addressed several systems aspects of
HAdV infections, including post-translational modifications, potential anti-viral factors of innate immunity, small vmiRNAs, and it clarified the role of CD46 for HAdV-B infections.

Downloads

352 downloads since deposited on 13 Mar 2012
50 downloads since 12 months
Detailed statistics

Additional indexing

Item Type:Dissertation
Referees:Hemmi S, Greber U F
Communities & Collections:07 Faculty of Science > Institute of Molecular Life Sciences
Dewey Decimal Classification:570 Life sciences; biology
Language:German
Date:2011
Deposited On:13 Mar 2012 11:56
Last Modified:05 Apr 2016 15:37
Related URLs:http://opac.nebis.ch/F/?local_base=NEBIS&CON_LNG=GER&func=find-b&find_code=SYS&request=006861466
Permanent URL: https://doi.org/10.5167/uzh-59151

Download

[img]
Preview
Filetype: PDF
Size: 7MB

TrendTerms

TrendTerms displays relevant terms of the abstract of this publication and related documents on a map. The terms and their relations were extracted from ZORA using word statistics. Their timelines are taken from ZORA as well. The bubble size of a term is proportional to the number of documents where the term occurs. Red, orange, yellow and green colors are used for terms that occur in the current document; red indicates high interlinkedness of a term with other terms, orange, yellow and green decreasing interlinkedness. Blue is used for terms that have a relation with the terms in this document, but occur in other documents.
You can navigate and zoom the map. Mouse-hovering a term displays its timeline, clicking it yields the associated documents.

Author Collaborations