Abstract
Peptide-based subunit vaccines are coming to the forefront of current vaccine approaches, with safety and cost-effective production among their top advantages. Peptide vaccine formulations consist of multiple synthetic linear epitopes that together trigger desired immune responses that can result in robust immune memory. The advantages of linear compared to conformational epitopes are their simple structure, ease of synthesis, and ability to stimulate immune responses by means that do not require complex 3D conformation. Prediction of linear epitopes through use of computational tools is fast and cost-effective, but typically of low accuracy, necessitating extensive experimentation to verify results. On the other hand, identification of linear epitopes through experimental screening has been an inefficient process that requires thorough characterization of previously identified full-length protein antigens, or laborious techniques involving genetic manipulation of organisms. In this study, we apply a newly developed generalizable screening method that enables efficient identification of B-cell epitopes in the proteomes of pathogenic bacteria. As a test case, we used this method to identify epitopes in the proteome of Francisella tularensis (Ft), a Select Agent with a well-characterized immunoproteome. Our screen identified many peptides that map to known antigens, including verified and predicted outer membrane proteins and extracellular proteins, validating the utility of this approach. We then used the method to identify seroreactive peptides in the less characterized immunoproteome of Select Agent Burkholderia pseudomallei (Bp). This screen revealed known Bp antigens as well as proteins that have not been previously identified as antigens. Although B-cell epitope prediction tools Bepipred 2.0 and iBCE-EL classified many of our seroreactive peptides as epitopes, they did not score them significantly higher than the non-reactive tryptic peptides in our study, nor did they assign higher scores to seroreactive peptides from known Ft or Bp antigens, highlighting the need for experimental data instead of relying on computational epitope predictions alone. The present workflow is easily adaptable to detecting peptide targets relevant to the immune systems of other mammalian species, including humans (depending upon the availability of convalescent sera from patients), and could aid in accelerating the discovery of B-cell epitopes and development of vaccines to counter emerging biological threats.
Highlights
Development of an effective vaccine against a biothreat agent or emerging pathogen is a costly and cumbersome process that can take years to decades to complete
We focused on two intracellular bacterial pathogens, Francisella tularensis (Ft) and Burkholderia pseudomallei (Bp), organisms which pose a high risk for misuse as bioweapons and are considered Tier 1 Select Agents by the US Centers for Disease Control and Prevention
We applied this method to two bacterial Select Agent pathogens: Francisella tularensis and Burkholderia pseudomallei
Summary
Development of an effective vaccine against a biothreat agent or emerging pathogen is a costly and cumbersome process that can take years to decades to complete. Peptide vaccine formulations consist of multiple synthetic linear epitopes that together trigger immune responses resulting in robust immune memory This multi-epitope, multi-target approach has the potential to be broadly protective across divergent strains (e.g., the first universal influenza vaccine to enter phase III clinical trials was a peptide vaccine), and could be effective for pathogens with complex life cycles (e.g., several malaria peptide vaccines are currently in clinical trials) [1,2,3]. It has been reported that conformational (discontinuous) epitopes make up the majority of B-cell epitopes [4], linear epitopes possess several advantages for vaccine design over conformational epitopes Due to their short sequence and lack of complex secondary and tertiary structure, short antigenic peptides can be synthesized, and multiplexed into vaccine formulations, for high-throughput assessment of efficacy. Peptide-based vaccines are potentially powerful medical countermeasures that would seem amenable to rapid development in responding to infectious disease outbreaks
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