This article is part of the supplement: Computational Vaccinology: State-of-the-art Assessments
Research
Concept and application of a computational vaccinology workflow
-
* Corresponding author: Johannes Söllner johannes.soellner@emergentec.com
1 emergentec biodevelopment GmbH, Rathausstrasse 5/3, 1010 Vienna, Austria
2 University of Applied Sciences, Softwarepark 11, 4232 Hagenberg, Austria
3 RT-Europe Research Center, 9200 Mosonmagyarovar, Var 2, Hungary
4 Galenbio Kft., Erdőszél köz 21, 1037 Budapest, Hungary and GalenBio, Inc., 5922 Farnsworth Ct, Carlsbad, CA 92008, USA
5 Institute for Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090 Vienna, Austria
Immunome Research 2010, 6(Suppl 2):S7 doi:10.1186/1745-7580-6-S2-S7
Published: 3 November 2010Abstract
Background
The last years have seen a renaissance of the vaccine area, driven by clinical needs in infectious diseases but also chronic diseases such as cancer and autoimmune disorders. Equally important are technological improvements involving nano-scale delivery platforms as well as third generation adjuvants. In parallel immunoinformatics routines have reached essential maturity for supporting central aspects in vaccinology going beyond prediction of antigenic determinants. On this basis computational vaccinology has emerged as a discipline aimed at ab-initio rational vaccine design.
Here we present a computational workflow for implementing computational vaccinology covering aspects from vaccine target identification to functional characterization and epitope selection supported by a Systems Biology assessment of central aspects in host-pathogen interaction. We exemplify the procedures for Epstein Barr Virus (EBV), a clinically relevant pathogen causing chronic infection and suspected of triggering malignancies and autoimmune disorders.
Results
We introduce pBone/pView as a computational workflow supporting design and execution of immunoinformatics workflow modules, additionally involving aspects of results visualization, knowledge sharing and re-use. Specific elements of the workflow involve identification of vaccine targets in the realm of a Systems Biology assessment of host-pathogen interaction for identifying functionally relevant targets, as well as various methodologies for delineating B- and T-cell epitopes with particular emphasis on broad coverage of viral isolates as well as MHC alleles.
Applying the workflow on EBV specifically proposes sequences from the viral proteins LMP2, EBNA2 and BALF4 as vaccine targets holding specific B- and T-cell epitopes promising broad strain and allele coverage.
Conclusion
Based on advancements in the experimental assessment of genomes, transcriptomes and proteomes for both, pathogen and (human) host, the fundaments for rational design of vaccines have been laid out. In parallel, immunoinformatics modules have been designed and successfully applied for supporting specific aspects in vaccine design. Joining these advancements, further complemented by novel vaccine formulation and delivery aspects, have paved the way for implementing computational vaccinology for rational vaccine design tackling presently unmet vaccine challenges.