DNAVAxDB: DNA Vaccine database

Introduction

A DNA vaccine is a bacterial plasmid constructed to express an encoded protein antigen(s) after in vivo administration and subsequent transfection of cells. The plasmid must encode a promoter that is active in mammalian cells. The first DNA vaccine studies were conducted in 1990s, with the first successful experiment done in 1990 when protein DNA was injected into mice and the protein was successfully synthesized in mice. Once expressed, the protective protein antigen encoded by a gene in a DNA vaccine can be degraded into peptides by an antigen presenting cell. The protective immune peptides (i.e., epitopes) can then be transferred to the cell surface and activate T cells. If the DNA vaccine is taken up by muscle cells, the muscle cells can transfer the expressed protein to the antigen presenting cells to stimulate the T cells. DNA vaccines can also stimulate antibody responses through antigen recognition by B cells. Compared to other types of vaccines (e.g., live attenuated or killed whole organism vaccines, and subunit vaccine), DNA vaccines are safe, easy to prepare and store, cost effective, focused immunity on antigen of interest, and the ability of inducing natural long-lasting and various immune responses in vivo.

Intensive efforts have been taken to study and use DNA vaccines. There have been over 20,000 articles indexed in PubMed or Google Scholar. Four DNA vaccines have been licensed for veterinary uses. Although there has not been a licensed human DNA vaccine on the market, many clinical trials on DNA vaccines are being conducted, and many DNA vaccine research has been conducted to further understand the mechanism of DNA vaccine and how to boost DNA vaccine immunity.

While intensive research has been conducted and resulted in DNA vaccine research, there is no web-based central resource that allows storage, annotation, comparison, and analysis of DNA vaccines. VIOLIN is the first web-based comprehensive vaccine database and analysis system that targets vaccine research. Currently VIOLIN has included more than 3,200 vaccines for over 180 infectious diseases and many non-infectious diseases (e.g., cancers and arthritis). Each of the curated vaccines has been shown to induce significant protection against a disease in a natural host or at least one laboratory animal model. Many of the vaccines in VIOLIN are verified DNA vaccines. However, the general VIOLIN system does not include any specific information about DNA vaccine plasmids. The general VIOLIN vaccine database does not separate and study those protective antigens used in DNA vaccines, which may preserve DNA vaccine-specific patterns. A specific query system for DNA vaccines is not available either in the general system.

The DNA vaccine research has become its own independent research and has its own community (for example, there is an active DNA Vaccines LinkedIn group). To address many needs of the DNA vaccine community, we have developed this DNAVaxDB, a web-based DNA vaccine database and analysis system. As a relatively independent program under the umbrella of the VIOLIN vaccine database and analysis sytem, DNAVaxDB includes many unique features specific for DNA vaccines. For example, it includes new manualy curated databases for over 400 DNA vaccines and over 130 DNA vaccine plasmids, a collection of protective antigens specifically used in DNA vaccine development, and a query system for querying various DNA vaccines, plasmids, and antigens specific for DNA vaccines.

Your suggestions, comments, and collaborations are more than welcome and appreciated!